code
stringlengths 2
1.05M
| repo_name
stringlengths 5
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stringlengths 3
922
| language
stringclasses 1
value | license
stringclasses 15
values | size
int64 2
1.05M
|
|---|---|---|---|---|---|
#!/usr/bin/env bash
mvn compile && mvn exec:java -Dexec.args="-i $1 -o $2"
|
essepuntato/rash
|
sources/docx2rash/compile-script.sh
|
Shell
|
isc
| 75 |
export DOTFILES_PATH=~/.dotfiles
export SHELLS_SRC_PATH=${DOTFILES_PATH}/all_shells
source ${SHELLS_SRC_PATH}/.profile
#just dummy values to make the AWS-SDK happy during local tests.
export AWS_ACCESS_KEY_ID=NONE
export AWS_SECRET_KEY=NONE
|
afranken/dotfiles
|
oh-my-zsh/custom/profile.zsh
|
Shell
|
mit
| 243 |
#!/bin/bash
docker run --name nginx \
-d -p 8080:80 \
-v $(PWD)/sites-enabled:/etc/nginx/sites-enabled \
-v $(PWD)/log/nginx:/var/log/nginx \
saltfactory/nginx
|
saltfactory/docker-nginx
|
run-nginx.sh
|
Shell
|
mit
| 161 |
#!/bin/bash
currDir=`pwd`
currTimestamp=`date +%s`
# Cleanup from previous runs
rm -rf /tmp/rs-docs-*/
# Clone the repo
git clone --depth 1 https://github.com/rightscale/docs /tmp/rs-docs-$currTimestamp/
cd "/tmp/rs-docs-$currTimestamp"
echo '[rs-docs-edit-statusPage] Creating new branch'
git checkout -b "edit-statusPage-$currTimestamp"
# Open the account page in the browser
### Find out what OS we are running on so we can launch the browser properly
platform='unknown'
unamestr=`uname`
if [[ "$unamestr" == 'Linux' ]]; then
platform='linux'
elif [[ "$unamestr" == 'FreeBSD' ]]; then
platform='freebsd'
elif [[ "$unamestr" == 'Darwin' ]]; then
platform='osx'
fi
echo "[rs-docs-edit-statusPage] Platform detected: $platform."
### Set the openHandler to handle various OSes and input types (URLs, files, etc..)
if [[ $platform == 'linux' ]]; then
openHandler='xdg-open';
elif [[ $platform == 'osx' ]]; then
openHandler='open';
fi
echo "[rs-docs-edit-statusPage] Opening status.html.md in text editor and web browser (live reload)"
$openHandler "/tmp/rs-docs-$currTimestamp/source/status.html.md" &> /dev/null
$openHandler "http://localhost:4567/status.html" &> /dev/null
echo "[rs-docs-edit-statusPage] Starting MiddleMan Server. Hit CTRL+C when finished."
bundle exec middleman server > /dev/null
while true; do
read -p "[rs-docs-edit-statusPage] Would you like to commit your changes [yes/no]? " yn
case $yn in
[Yy]* ) git commit -a; break;;
[Nn]* ) echo "[rs-docs-edit-statusPage] All done -- exiting script"; exit;;
* ) echo "Please answer yes or no.";;
esac
done
while true; do
read -p "[rs-docs-edit-statusPage] Would you like to push your changes to GitHub [yes/no]? " yn
case $yn in
[Yy]* ) git push --all; echo "[rs-docs-edit-statusPage] Opening Pull Request page GitHub. Create a pull request and merge it to `master` to complete the process."; $openHandler "https://github.com/rightscale/docs/compare/edit-statusPage-$currTimestamp?expand=1"; break;;
[Nn]* ) echo "[rs-docs-edit-statusPage] All done -- exiting script"; exit;;
* ) echo "Please answer yes or no.";;
esac
done
|
bryankaraffa/rightscale_scripts
|
tools/rs-docs-edit-statusPage.sh
|
Shell
|
mit
| 2,175 |
#!/bin/bash
# --------------------------------------
# Watcher
# --------------------------------------
#
# Autonomous bot that detects when new
# domains are acquired and verify for
# duplicates. When unique domains are
# confirmed the watcher send them to the
# domain delegators.
#
# The watcher is not the only script that
# removes duplicates. A divide and conquer
# approach is utilized to increase the
# speed of the removal.
#
# Author: Thiago Moreno
# <[email protected]>
# --------------------------------------
# START | Config
# --------------------------------------
WATCH_REFRESH_INTERVAL=0.5
FOUND_DOMAINS_FILE=`qbot path`"foundDomains.list"
DOMAINS_FILE="domains.list"
OFFLINE_FILE=`qbot path`"offlineDomains.list"
DOMAINS_HISTORY_FILE=`qbot path`"domains.history"
SCRAPED_FILE=`qbot path`"scrapedDomains.list"
OBSERVE_FILE=`qbot path`"qbot.log"
UNIQUE_FILE=`qbot path`"uniqueDomains.list"
OUTPUT_FILE=`qbot path`"output.log"
RAM_DIRECTORY='/mnt/qbot'
DELEGATORS_LIMIT=6
# --------------------------------------
# END | Config
# START | Helpers
# --------------------------------------
# Check if determined script is running on background (coupled, from "_qbot.sh" script's prototype)
is_running()
{
if [ "`ps -A --context | grep -E \"${1}.s[h]\" | wc -l`" -gt "0" ]
then
return 0
else
return 1
fi
}
# --------------------------------------
# END | Helpers
# START | Initialize
# --------------------------------------
qbotPath=`qbot path`
# Ram Allocation
if [ ! -d "${RAM_DIRECTORY}" ]
then
mkdir "${RAM_DIRECTORY}"
mount -t tmpfs -o size=1024m tmpfs "${RAM_DIRECTORY}"
fi
chmod +rw $FOUND_DOMAINS_FILE
chmod +rw $DOMAINS_FILE
chmod +rw $DOMAINS_HISTORY_FILE
chmod +rw $SCRAPED_FILE
chmod +rw $OBSERVE_FILE
chmod +rw $UNIQUE_FILE
echo -n "" > ${RAM_DIRECTORY}/${FOUND_DOMAINS_FILE#${qbotPath}}.temp
echo -n "" > ${RAM_DIRECTORY}/${SCRAPED_FILE#${qbotPath}}.temp
[ ! -d "${RAM_DIRECTORY}/queue" ] && mkdir "${RAM_DIRECTORY}/queue"
oldLines=0
currentLines=0
# Reset delegators
[ "`ls ${RAM_DIRECTORY}/queue | wc -l`" != "0" ] && rm ${RAM_DIRECTORY}/queue/*
echo "N---1"
# Re-initiale spiders if they were running
if [ "`ls \"${RAM_DIRECTORY}\" | grep -E 'spider-.*-queue.list' | wc -l`" -gt "0" ]
then
for spiderQueueFile in "${RAM_DIRECTORY}"/spider-*-queue.list
do
spiderName=${spiderQueueFile/${RAM_DIRECTORY}\/spider-}
spiderName=${spiderName%-queue.list}
echo $spiderName
if [ "`cat \"${spiderQueueFile}\" | wc -l`" -gt "0" ]
then
if [ -f "`qbot path`spider-${spiderName}.sh" ] && ! `is_running spider-${spiderName}`
then
nohup `qbot path`"spider-${spiderName}.sh" > ${OUTPUT_FILE} 2>&1&
fi
else
[ -f "${spiderQueueFile}.lock" ] && rm ${spiderQueueFile}.lock
fi
if [ ! -f "`qbot path`spider-${spiderName}.sh" ]
then
qbot add spider "${spiderName}" &>`qbot path`output.log
fi
done
fi
# --------------------------------------
# END | Initialize
# START | Watcher loop event
# --------------------------------------
echo "The Watcher is waiting for domains"
echo "The Watcher is waiting for domains" >> $OBSERVE_FILE
while :
do
sleep "$WATCH_REFRESH_INTERVAL"
# START | Watcher loop event
# --------------------------------------
# currentLinesRefresh="`sed -n '$=' ${FOUND_DOMAINS_FILE}`"
currentLines="`sed -n '$=' ${FOUND_DOMAINS_FILE}`"
# [ "${currentLinesRefresh}" = "${currentLines}" ] && currentLines="${currentLinesRefresh}"
diffLines=$((currentLines - oldLines))
# Skip if there are no new lines
[[ "${diffLines}" = "0" && "`cat ${DOMAINS_FILE#${qbotPath}}.temp | wc -l`" != "0" ]] && continue
cat <(tail -n +"$((oldLines+1))" "${FOUND_DOMAINS_FILE}") >> ${RAM_DIRECTORY}/${FOUND_DOMAINS_FILE#${qbotPath}}.temp
oldLines=${currentLines}
awk '!a[$0]++' "${FOUND_DOMAINS_FILE#${qbotPath}}" > "${FOUND_DOMAINS_FILE#${qbotPath}}".unduplicated &&\
cp "${FOUND_DOMAINS_FILE#${qbotPath}}".unduplicated "${FOUND_DOMAINS_FILE#${qbotPath}}" &&\
rm "${FOUND_DOMAINS_FILE#${qbotPath}}".unduplicated
s_time_taken=$(date +%s)
echo "The Watcher is handling duplicates..."
echo "The Watcher is handling duplicates..." >> $OBSERVE_FILE
# START | Handling new domains duplicates
cat $SCRAPED_FILE > ${RAM_DIRECTORY}/${SCRAPED_FILE#${qbotPath}}.temp
cat $OFFLINE_FILE > ${RAM_DIRECTORY}/${OFFLINE_FILE#${qbotPath}}.temp
awk '!a[$0]++' ${RAM_DIRECTORY}/${OFFLINE_FILE#${qbotPath}}.temp > ${RAM_DIRECTORY}/${OFFLINE_FILE#${qbotPath}}.temp2
rm ${RAM_DIRECTORY}/${OFFLINE_FILE#${qbotPath}}.temp
mv ${RAM_DIRECTORY}/${OFFLINE_FILE#${qbotPath}}.temp2 ${RAM_DIRECTORY}/${OFFLINE_FILE#${qbotPath}}.temp
awk '!a[$0]++' ${RAM_DIRECTORY}/${SCRAPED_FILE#${qbotPath}}.temp > ${RAM_DIRECTORY}/${SCRAPED_FILE#${qbotPath}}.temp2
rm ${RAM_DIRECTORY}/${SCRAPED_FILE#${qbotPath}}.temp
mv ${RAM_DIRECTORY}/${SCRAPED_FILE#${qbotPath}}.temp2 ${RAM_DIRECTORY}/${SCRAPED_FILE#${qbotPath}}.temp
awk '!a[$0]++' ${RAM_DIRECTORY}/${FOUND_DOMAINS_FILE#${qbotPath}}.temp > ${RAM_DIRECTORY}/${FOUND_DOMAINS_FILE#${qbotPath}}.temp2
rm ${RAM_DIRECTORY}/${FOUND_DOMAINS_FILE#${qbotPath}}.temp
mv ${RAM_DIRECTORY}/${FOUND_DOMAINS_FILE#${qbotPath}}.temp2 ${RAM_DIRECTORY}/${FOUND_DOMAINS_FILE#${qbotPath}}.temp
comm -13 <(sort ${RAM_DIRECTORY}/${SCRAPED_FILE#${qbotPath}}.temp) <(sort ${RAM_DIRECTORY}/${FOUND_DOMAINS_FILE#${qbotPath}}.temp) > ${DOMAINS_FILE#${qbotPath}}.temp2
comm -13 <(sort ${RAM_DIRECTORY}/${OFFLINE_FILE#${qbotPath}}.temp) <(sort ${DOMAINS_FILE#${qbotPath}}.temp2) > ${DOMAINS_FILE#${qbotPath}}.temp
# awk 'NR==FNR{a[$0]="";next}; !($0 in a)' ${RAM_DIRECTORY}/${FOUND_DOMAINS_FILE#${qbotPath}}.temp ${RAM_DIRECTORY}/${SCRAPED_FILE#${qbotPath}}.temp > ${DOMAINS_FILE#${qbotPath}}.temp2
# awk 'NR==FNR{a[$0]="";next}; !($0 in a)' ${DOMAINS_FILE#${qbotPath}}.temp2 ${RAM_DIRECTORY}/${OFFLINE_FILE#${qbotPath}}.temp > ${DOMAINS_FILE#${qbotPath}}.temp
# END | Handling new domains duplicates
uniqueDomainsCount="`cat ${DOMAINS_FILE#${qbotPath}}.temp | wc -l`"
e_time_taken=$(date +%s)
echo "The Watcher is holding ${uniqueDomainsCount} unique domain(s). ("$((e_time_taken - s_time_taken))"s)." >> $OBSERVE_FILE
echo "The watcher is handling duplicates... Done. Holding ${uniqueDomainsCount} unique domain(s). ("$((e_time_taken - s_time_taken))"s)."
# START | Reading domains found phase 2 (enqueue from domains.list)
if [ "${uniqueDomainsCount}" -gt "0" ]
then
C_unduplicateTimer=0
while read -r domainToDelegate
do
# Verify if the domain is already being scraped, then skip
if [ "`ls \"${RAM_DIRECTORY}\" | grep -E 'spider-.*-queue.list' | wc -l`" -gt "0" ]
then
for spiderQueue in "${RAM_DIRECTORY}"/spider-*-queue.list
do
[ "`head -1 \"${spiderQueue}\"`" = "${domainToDelegate}" ] && continue 2
done
fi
[ "`grep \"${domainToDelegate}\" \"${SCRAPED_FILE}\" | wc -l`" -gt "0" ] && continue
while :
do
# Wait
if [ "`ls ${RAM_DIRECTORY}/queue | wc -l`" -lt "${DELEGATORS_LIMIT}" ]
then
# if ! grep -q "[d]omainDelegator.sh ${domainToDelegate}" <(ps -ef S)
if [ "`ps -A --context | grep [d]omainDelegator | wc -l`" -lt "${DELEGATORS_LIMIT}" ]
then
nohup "`qbot path`domainDelegator.sh" "${domainToDelegate}" 2>&1&
fi
break
fi
((C_unduplicateTimer++))
if [ "${C_unduplicateTimer}" = "1200" ]
then
C_unduplicateTimer=0
awk '!a[$0]++' "${FOUND_DOMAINS_FILE#${qbotPath}}" > "${FOUND_DOMAINS_FILE#${qbotPath}}".unduplicated &&\
cp "${FOUND_DOMAINS_FILE#${qbotPath}}".unduplicated "${FOUND_DOMAINS_FILE#${qbotPath}}" &&\
rm "${FOUND_DOMAINS_FILE#${qbotPath}}".unduplicated
fi
sleep 0.5
done
done < <(shuf ${DOMAINS_FILE#${qbotPath}}.temp) # shuf: non-posix (randomizing lines)
fi
# currentLines="`sed -n '$=' ${FOUND_DOMAINS_FILE}`"
cat ${DOMAINS_FILE#${qbotPath}}.temp >> $DOMAINS_HISTORY_FILE
echo -n "" > ${DOMAINS_FILE#${qbotPath}}.temp
# END | Reading domains found phase 2 (enqueue)
done
# --------------------------------------
# END | Watcher loop event
|
Quicktech-Moreno/qbot
|
watcher.sh
|
Shell
|
mit
| 8,333 |
#!/bin/bash
#: Title : install-global
#: Synopsis : none
#: Date : 2014-08-29 15:46:22
#: Author : shulei
#: version : 1.0
#: Description : install global
#: Options : -v set to display message
pushd $PWD
## Script path
script_path="${0%/*}" # remove the script name ,get the path
script_path=${script_path/\./$(pwd)} # if path start with . , replace with $PWD
cd "${script_path}"
## source lib
source ../libbash/bashr.sh
##init parameters
MESSAGE_ENABLED=n
## get parameters
## parse command-line options, -m
while getopts "vb:" var
do
case $var in
v)
MESSAGE_ENABLED=y
;;
esac
done
shift $(( $OPTIND - 1 ))
##content
echoH1 "Start install global"
setup "validation ~/source-install directory exists" \
ls ~/source-install \
"can't find ~/source-install dir ,please create it first" \
;
setup "validation ctags exists" \
ls /usr/local/bin/ctags \
"can't ctags ,please install it first" \
;
setup "create ~/source-install/global workspace" \
mkdir ~/source-install/global \
"can't creat ~/source-install/global dir, please check the reason" \
;
setup "cp global tar file into ~/source-install/global" \
cp -r global-6.3.1.tar.gz ~/source-install/global \
"cp tar file into ~/source-install/global failed" \
;
## change dir
cd ~/source-install/global/
setup "tar the global tar file" \
tar -xf global-6.3.1.tar.gz \
"tar the global tar file failed" \
;
setup "install libncurses5-dev libs" \
sudo apt-get install -y -q libncurses5-dev \
"install libncurses5-dev lib failed" \
;
cd ~/source-install/global/global-6.3.1/
echoH2 "try build global"
setup "run configure" \
./configure --with-exuberant-ctags=/usr/local/bin/ctags \
"global configure failed" \
;
setup "make install" \
sudo make install \
"global make install failed" \
;
popd > /dev/null
|
qinshulei/ubuntu-install
|
source-install/install-global.sh
|
Shell
|
mit
| 2,010 |
#!/bin/sh
set -u
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.7.0_25.jdk/Contents/Home/ gr -i publish
|
ae6rt/httplite
|
publish.sh
|
Shell
|
mit
| 108 |
# Ruby
alias be='bundle exec'
alias sc='script/console'
alias sg='script/generate'
alias sd='script/destroy'
|
ninjabiscuit/dotfiles
|
ruby/aliases.zsh
|
Shell
|
mit
| 109 |
#!/usr/bin/bash
SALT_DIR=/path/to/salt/files
seasalt_start() {
runit master 0 "-v ${SALT_DIR}:/srv/salt"
runit minion 1 "--link salt-master-0 -e SALT_ID=host.id1"
runit minion 2 "--link salt-master-0 -e SALT_ID=host.id1"
runit minion 3 "--link salt-master-0 -e SALT_ID=host.id3"
}
seasalt_stop() {
killit master 0
killit minion 1
killit minion 2
killit minion 3
}
|
mckay-software/seasalt
|
seasalt.example.sh
|
Shell
|
mit
| 399 |
#!/bin/bash
cp /home/dwu/msm/drivers/staging/android/binder.c .
cp /home/dwu/msm/drivers/staging/android/binder_filter.c .
cp /home/dwu/msm/drivers/staging/android/binder_filter.h .
cp /home/dwu/msm/drivers/staging/android/Makefile .
cp /home/dwu/msm/drivers/staging/android/Kconfig .
|
dxwu/BinderFilter
|
src/copyFilesToHere.sh
|
Shell
|
mit
| 286 |
#!/bin/bash
rm -rf test-file*
echo "mysecretext" > test1
openssl aes-256-cbc -e -pass pass:mysecret -in test1 -out test1.enc
openssl aes-256-cbc -e -pass pass:mysecret -in test2 -out test2.enc
openssl aes-256-cbc -e -pass pass:mysecret -in test3 -out test3.enc
|
jonatan-alama/node-decipher-openssl
|
test/createData.sh
|
Shell
|
mit
| 263 |
sh analyse_instruction.sh "jmp .LoooooooooooooooooooooongLabel{loop_id} S .LoooooooooooooooooooooongLabel{loop_id}:" 10000 50000
sh analyse_instruction.sh "jmp .L{loop_id} S .L{loop_id}:" 5000 500000
sh analyse_instruction.sh "jmp .L{loop_id} S .L{loop_id}:" 2500 500000
sh analyse_instruction.sh "jmp .L{loop_id} S .L{loop_id}:" 1000 500000
|
realead/asmeter
|
src/jmp_test.sh
|
Shell
|
mit
| 350 |
rm *.o;make test INCLUDEMAIN=1 DEBUG=1 OBJECTS=xor.o TARGET_NAME=xor
|
frranck/asm2c
|
asmTests/xor/createTest.sh
|
Shell
|
mit
| 69 |
#!/usr/bin/env bash
# (C) Oliver Schoenborn
#
# Publish the disk usage below a certain path on an EC2 instance
# Uses `du ... path` and `aws cloudwatch put-metric-data`
#
# Requires that the ec2 have following policy
# {
# "Version": "2012-10-17",
# "Statement": [
# {
# "Action": [
# "cloudwatch:PutMetricData"
# ],
# "Effect": "Allow",
# "Resource": "*"
# }
# ]
# }
#
# First arg must be the CloudWatch namespace to push metrics to;
# Second arg must be the path to measure from.
#
# Example: $0 MyNamespace /var/log/nginx
set -o errexit
if [[ ! -f ec2-metadata ]]; then
echo "Downloading ec2-metadata"
wget http://s3.amazonaws.com/ec2metadata/ec2-metadata
chmod u+x ec2-metadata
fi
namespace=$1
folder_path=$2
if [[ -z $folder_path ]]; then
echo "Specify folder path"
exit 1
fi
PATH=/usr/local/bin:$PATH
space=$(du --bytes ${folder_path} | cut -f 1)
echo "$(date -Isec) - Disk space used by ${folder_path}: ${space} bytes"
iid=$(./ec2-metadata --instance-id | cut -f 2 -d " ")
if aws cloudwatch put-metric-data --namespace ${namespace} --metric-name DiskSpaceUsed \
--unit Bytes --value ${space} --dimensions Path="${folder_path}",InstanceId=${iid}
then
echo "# Metric pushed to CloudWatch, check https://console.aws.amazon.com/cloudwatch -> ${namespace} -> Path,InstanceId"
echo "# -------"
else
echo "# ERROR could not push to CloudWatch: $?"
fi
|
schollii/sandals
|
send-disk-use-from-path-to-cloudwatch.sh
|
Shell
|
mit
| 1,474 |
#!/bin/zsh
MODEL_SAVE_PATH="/n/sd8/inaguma/result/tensorflow/svc"
# Select GPU
if [ $# -ne 2 ]; then
echo "Error: set GPU number & config path." 1>&2
echo "Usage: ./run_attention.sh path_to_config_file gpu_index" 1>&2
exit 1
fi
# Set path to CUDA
export PATH=$PATH:/usr/local/cuda-8.0/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-8.0/lib64:/usr/local/cuda-8.0/extras/CUPTI/lib64
# Set path to python
PYTHON=/home/lab5/inaguma/.pyenv/versions/anaconda3-4.1.1/bin/python
config_path=$1
gpu_index=$2
filename=$(basename $config_path | awk -F. '{print $1}')
mkdir -p log
# Standard output version
# CUDA_VISIBLE_DEVICES=$gpu_index $PYTHON train_attention.py \
# $config_path $MODEL_SAVE_PATH
# Background job version
CUDA_VISIBLE_DEVICES=$gpu_index nohup $PYTHON train_attention.py \
$config_path $MODEL_SAVE_PATH > log/$filename".log" &
|
hirofumi0810/tensorflow_end2end_speech_recognition
|
examples/svc/training/run_attention.sh
|
Shell
|
mit
| 867 |
#!/bin/bash -x
if [ ! -d $MAGE_ROOT_DIR/.modman ] ; then
cd $MAGE_ROOT_DIR && modman init
fi
cd $MAGE_ROOT_DIR && modman $@
|
ffuenf/docker-modman
|
modman-wrapper.sh
|
Shell
|
mit
| 128 |
if [[ -d "/usr/share/git-core/contrib" ]]; then
export PATH="$PATH:/usr/share/git-core/contrib"
elif [[ -d "/usr/local/share/git-core/contrib/diff-highlight" ]]; then
export PATH="$PATH:/usr/local/share/git-core/contrib/diff-highlight"
fi
|
amarshall/dotfiles
|
lib/shell/plugins/git/env.zsh
|
Shell
|
mit
| 243 |
#!/bin/sh
#
# @sacloud-once
# httpdのインストール
yum install -y httpd || exit 1
# 確認用ページ
hostname >> /var/www/html/index.html || exit1
# サービス起動設定
systemctl enable httpd.service || exit 1
systemctl start httpd.service || exit 1
# ファイアウォール設定
firewall-cmd --add-service=http --zone=public --permanent || exit 1
firewall-cmd --reload || exit 1
exit 0
|
zembutsu/sakura-terraform
|
7-load-balancing/install_httpd.sh
|
Shell
|
mit
| 408 |
#!/bin/sh
# CYBERWATCH SAS - 2017
#
# Security fix for DSA-2715-1
#
# Security announcement date: 2013-06-26 00:00:00 UTC
# Script generation date: 2017-01-01 21:06:36 UTC
#
# Operating System: Debian 7 (Wheezy)
# Architecture: x86_64
#
# Vulnerable packages fix on version:
# - puppet:2.7.18-5
#
# Last versions recommanded by security team:
# - puppet:2.7.23-1~deb7u3
#
# CVE List:
# - CVE-2013-3567
#
# More details:
# - https://www.cyberwatch.fr/vulnerabilites
#
# Licence: Released under The MIT License (MIT), See LICENSE FILE
sudo apt-get install --only-upgrade puppet=2.7.23-1~deb7u3 -y
|
Cyberwatch/cbw-security-fixes
|
Debian_7_(Wheezy)/x86_64/2013/DSA-2715-1.sh
|
Shell
|
mit
| 607 |
#!/usr/bin/env bash
. $(dirname ${0})/common.sh
[[ -f ${_RESTAFARI_HOME}/env.sh ]] && . ${_RESTAFARI_HOME}/env.sh
cd ${_RESTAFARI_HOME}
pip3 install -e .
python3 setup.py install
[[ -z $(which restafari 2>/dev/null) ]] && echo "Restafari is not installed properly" && exit 1
restafari --version
[[ ${?} -gt 0 ]] && echo "Restafari is not installed properly" && exit 1
exit 0
|
manoelhc/restafari
|
ci/install.sh
|
Shell
|
mit
| 383 |
#!/bin/bash
./node_modules/vows/bin/vows
|
demee/text
|
scripts/test.sh
|
Shell
|
mit
| 41 |
#!/bin/bash
# Change working directory to the top-most Finder window location
# Source: https://github.com/mathiasbynens/dotfiles/blob/master/.functions#L8
alias cdf='cd $(osascript -e "tell app \"Finder\" to POSIX path of (insertion location as alias)")'
alias dt="cd ~/Desktop"
co() {
local open_path other_args
open_path="$1"
other_args=("${@:2}")
if [ -z "$open_path" ]; then
code . "${other_args[@]}"
return
fi
if [ -d "$open_path" ] || [ -f "$open_path" ]; then
code "$open_path" "${other_args[@]}"
return
fi
local repository_path
repository_path="$REPOSITORIES_DIRECTORY/$1"
if [ -d "$repository_path" ]; then
code "$repository_path" "${other_args[@]}"
return
fi
code "$open_path" "${other_args[@]}"
}
_rps_autocomplete co
o() {
open -a Finder "$1"
}
rc() {
cd "$HOME/dotfiles"
code "$HOME/dotfiles"
}
mcd() {
mkdir "$1" && cd "$_" || return
}
rn() {
local new_name
new_name="$1"
if [ -z "$new_name" ]; then
echo 'Rename the current directory.\nUsage: rn <new_name>'
return
fi
local old_name
old_name="$(basename $(pwd))"
cd ../ && mv "$old_name" "$new_name" && cd "$new_name"
}
|
kvendrik/dotfiles
|
file-system/miscellaneous.bash
|
Shell
|
mit
| 1,179 |
#!/bin/sh
cd "$( dirname "$0" )/..";
grunt build && grunt exec:test;
|
ChristianGrete/mout-lang-type
|
bin/test.sh
|
Shell
|
mit
| 71 |
#!/bin/bash
apt-get update
apt-get install -y aptitude
aptitude install -y apache2
|
quanah/vagrant-webserver
|
vagrant/bootstrap.sh
|
Shell
|
mit
| 84 |
#network interface on which to limit traffic
IF="eth0"
#limit of the network interface in question
LINKCEIL="1gbit"
#limit outbound Testcoin protocol traffic to this rate
LIMIT="160kbit"
#defines the address space for which you wish to disable rate limiting
LOCALNET="192.168.0.0/16"
#delete existing rules
tc qdisc del dev ${IF} root
#add root class
tc qdisc add dev ${IF} root handle 1: htb default 10
#add parent class
tc class add dev ${IF} parent 1: classid 1:1 htb rate ${LINKCEIL} ceil ${LINKCEIL}
#add our two classes. one unlimited, another limited
tc class add dev ${IF} parent 1:1 classid 1:10 htb rate ${LINKCEIL} ceil ${LINKCEIL} prio 0
tc class add dev ${IF} parent 1:1 classid 1:11 htb rate ${LIMIT} ceil ${LIMIT} prio 1
#add handles to our classes so packets marked with <x> go into the class with "... handle <x> fw ..."
tc filter add dev ${IF} parent 1: protocol ip prio 1 handle 1 fw classid 1:10
tc filter add dev ${IF} parent 1: protocol ip prio 2 handle 2 fw classid 1:11
#delete any existing rules
#disable for now
#ret=0
#while [ $ret -eq 0 ]; do
# iptables -t mangle -D OUTPUT 1
# ret=$?
#done
#limit outgoing traffic to and from port 8333. but not when dealing with a host on the local network
# (defined by $LOCALNET)
# --set-mark marks packages matching these criteria with the number "2"
# these packages are filtered by the tc filter with "handle 2"
# this filter sends the packages into the 1:11 class, and this class is limited to ${LIMIT}
iptables -t mangle -A OUTPUT -p tcp -m tcp --dport 8333 ! -d ${LOCALNET} -j MARK --set-mark 0x2
iptables -t mangle -A OUTPUT -p tcp -m tcp --sport 8333 ! -d ${LOCALNET} -j MARK --set-mark 0x2
|
L5hunter/TestCoin
|
contrib/qos/tc.sh
|
Shell
|
mit
| 1,671 |
#!/usr/bin/env bash
docker build -t plex .
|
stevenbower/docker-plex
|
build.sh
|
Shell
|
mit
| 44 |
#!/usr/bin/env bash
rm graphs/cpu-all.html; bin/example.sh examples.CPU -g html all >> graphs/cpu-all.html
rm graphs/diskio-diskio.html; bin/example.sh examples.DiskIO -g html disk-io >> graphs/diskio-diskio.html
rm graphs/mem-faults.html; bin/example.sh examples.Mem -g html faults >> graphs/mem-faults.html
rm graphs/mem-all.html; bin/example.sh examples.Mem -g html all >> graphs/mem-all.html
|
romario13/bonfire
|
bin/examples-all.sh
|
Shell
|
mit
| 399 |
#!/bin/sh
# CYBERWATCH SAS - 2017
#
# Security fix for DSA-3126-1
#
# Security announcement date: 2015-01-12 00:00:00 UTC
# Script generation date: 2017-02-07 21:05:29 UTC
#
# Operating System: Debian 7 (Wheezy)
# Architecture: x86_64
#
# Vulnerable packages fix on version:
# - php5:5.4.36-0+deb7u3
#
# Last versions recommanded by security team:
# - php5:5.4.45-0+deb7u7
#
# CVE List:
# - CVE-2014-9652
#
# More details:
# - https://www.cyberwatch.fr/vulnerabilites
#
# Licence: Released under The MIT License (MIT), See LICENSE FILE
sudo apt-get install --only-upgrade php5=5.4.45-0+deb7u7 -y
|
Cyberwatch/cbw-security-fixes
|
Debian_7_(Wheezy)/x86_64/2015/DSA-3126-1.sh
|
Shell
|
mit
| 608 |
#!/usr/bin/env bash
function go_to_project_top_directory() {
local -r script_dir=$(dirname "${BASH_SOURCE[0]}")
cd "$script_dir/../../.." || exit 1
}
function prepare_typescript_build_directory() {
rm -rf platforms/typescript/dist
}
function build_typescript() {
pushd platforms/typescript || exit 1
npm run build
popd || exit 1
}
function main() {
go_to_project_top_directory
source ./scripts/shared/shared.sh || exit 1
shared.set_bash_error_handling
prepare_typescript_build_directory
build_typescript
shared.display_success_message "Typescript build completed successfully 🏗️"
}
main
|
walterscarborough/LibSpacey
|
platforms/typescript/scripts/build-typescript.sh
|
Shell
|
mit
| 624 |
gcc -c 02_mixed_headers.c
gcc -o 02_mixed_headers.test 02_mixed_headers.o -L/usr/lib/x86_64-linux-gnu -lcurl
|
rbauduin/mbdetect
|
archives/tests/02_build.sh
|
Shell
|
mit
| 109 |
#!/usr/bin/env bash
for i in rq2 rq3; do
docker-compose -f docker-compose.yml -f docker-compose.scale_rq.yml exec "$i" \
sh -c 'rabbitmqctl stop_app; rabbitmqctl join_cluster rabbit@rq1; rabbitmqctl start_app'
done
docker-compose -f docker-compose.yml -f docker-compose.scale_rq.yml exec rq1 rabbitmqctl cluster_status
|
madeddie/hotjar-task
|
cluster_rq.sh
|
Shell
|
mit
| 327 |
#!/bin/bash
# Convert text to FASTA file
# Assumes no header
# Default parameter
length=74
while getopts f:l:: option
do
case "${option}"
in
f) fasta=${OPTARG};;
l) length=${OPTARG};;
exit;;
esac
done
echo ">${fasta%.*}" > ${fasta%.*}.fa
fold -w $length ${fasta} >> ${fasta%.*}.fa
echo 'Done!'
|
essigmannlab/dcs_scripts
|
scripts/convert_to_fasta.sh
|
Shell
|
mit
| 310 |
#!/bin/bash
echo 'standby 0' | cec-client -s > /dev/null
|
futurice/chilipie-kiosk
|
home/cec-off.sh
|
Shell
|
mit
| 58 |
#!/bin/sh
echo "execute ./run/bin/mruby ${1}"
./run/bin/mruby $1
|
ncq/rumin
|
mtest.sh
|
Shell
|
mit
| 66 |
#!/bin/bash
export HL_TRACE=3
export HL_TRACE_FILE=/dev/stdout
export HL_NUMTHREADS=4
rm -f $1/camera_pipe.avi
$1/process ../images/bayer_small.png 3700 1.8 50 1 $1/out.png |
../../bin/HalideTraceViz -t 1000 -s 1920 1080 \
-f input 0 1024 -1 1 1 10 348 1 0 0 1 \
-f denoised 0 1024 -1 1 1 305 360 1 0 0 1 \
-f deinterleaved 0 1024 -1 1 1 580 120 1 0 0 1 0 220 \
-f r_gr 0 1024 -1 1 1 720 120 1 0 0 1 \
-f g_gr 0 1024 -1 1 1 860 120 1 0 0 1 \
-f b_gr 0 1024 -1 1 1 1000 120 1 0 0 1 \
-f r_r 0 1024 -1 1 1 720 340 1 0 0 1 \
-f g_r 0 1024 -1 1 1 860 340 1 0 0 1 \
-f b_r 0 1024 -1 1 1 1000 340 1 0 0 1 \
-f r_b 0 1024 -1 1 1 720 560 1 0 0 1 \
-f g_b 0 1024 -1 1 1 860 560 1 0 0 1 \
-f b_b 0 1024 -1 1 1 1000 560 1 0 0 1 \
-f r_gb 0 1024 -1 1 1 720 780 1 0 0 1 \
-f g_gb 0 1024 -1 1 1 860 780 1 0 0 1 \
-f b_gb 0 1024 -1 1 1 1000 780 1 0 0 1 \
-f demosaiced 0 1024 2 1 1 1140 360 1 0 0 1 0 0 \
-f corrected 0 1024 2 1 1 1400 360 1 0 0 1 0 0 \
-f processed 0 256 2 1 1 1660 360 1 0 0 1 0 0 | \
avconv -f rawvideo -pix_fmt bgr32 -s 1920x1080 -i /dev/stdin -c:v h264 $1/camera_pipe.avi
#mplayer -demuxer rawvideo -rawvideo w=1920:h=1080:format=rgba:fps=30 -idle -fixed-vo -
|
ronen/Halide
|
apps/camera_pipe/viz.sh
|
Shell
|
mit
| 1,339 |
#!/bin/bash
cd $APPS_BASE
make clean
make
|
raphui/rnk
|
tools/make_apps.sh
|
Shell
|
mit
| 43 |
#!/bin/bash -x
#
# Generated - do not edit!
#
# Macros
TOP=`pwd`
CND_CONF=CanStick
CND_DISTDIR=dist
TMPDIR=build/${CND_CONF}/${IMAGE_TYPE}/tmp-packaging
TMPDIRNAME=tmp-packaging
OUTPUT_PATH=dist/${CND_CONF}/${IMAGE_TYPE}/Source.${IMAGE_TYPE}.${OUTPUT_SUFFIX}
OUTPUT_BASENAME=Source.${IMAGE_TYPE}.${OUTPUT_SUFFIX}
PACKAGE_TOP_DIR=source/
# Functions
function checkReturnCode
{
rc=$?
if [ $rc != 0 ]
then
exit $rc
fi
}
function makeDirectory
# $1 directory path
# $2 permission (optional)
{
mkdir -p "$1"
checkReturnCode
if [ "$2" != "" ]
then
chmod $2 "$1"
checkReturnCode
fi
}
function copyFileToTmpDir
# $1 from-file path
# $2 to-file path
# $3 permission
{
cp "$1" "$2"
checkReturnCode
if [ "$3" != "" ]
then
chmod $3 "$2"
checkReturnCode
fi
}
# Setup
cd "${TOP}"
mkdir -p ${CND_DISTDIR}/${CND_CONF}/package
rm -rf ${TMPDIR}
mkdir -p ${TMPDIR}
# Copy files and create directories and links
cd "${TOP}"
makeDirectory ${TMPDIR}/source/bin
copyFileToTmpDir "${OUTPUT_PATH}" "${TMPDIR}/${PACKAGE_TOP_DIR}bin/${OUTPUT_BASENAME}" 0755
# Generate tar file
cd "${TOP}"
rm -f ${CND_DISTDIR}/${CND_CONF}/package/source.tar
cd ${TMPDIR}
tar -vcf ../../../../${CND_DISTDIR}/${CND_CONF}/package/source.tar *
checkReturnCode
# Cleanup
cd "${TOP}"
rm -rf ${TMPDIR}
|
medo64/CanStick
|
Firmware/Source/nbproject/Package-CanStick.bash
|
Shell
|
mit
| 1,352 |
#!/bin/bash
MPC="/usr/bin/mpc"
ALBUM_TITLE=$1
$MPC clear
#$MPC findadd ALBUM_TITLE ${ALBUM_TITLE}
$MPC search album "$ALBUM_TITLE" | $MPC add
$MPC play
|
ggilestro/majordomo
|
bin/play_cd.sh
|
Shell
|
mit
| 153 |
# use for ultimate plumber instead of up
# which collides w/ sh/scripts/up.sh for traversing
# directories
alias ulp='up'
gocover () {
t="/tmp/go-cover.$$.tmp"
go test -coverprofile=$t $@ && go tool cover -html=$t && unlink $t
}
|
mdzhang/dotfiles
|
golang/.config/sh/golang/aliases.sh
|
Shell
|
mit
| 238 |
#!/usr/bin/env bash
set -o errexit
set -o pipefail
set -o nounset
cd "$(dirname "${BASH_SOURCE[0]}")"
if [[ -d dist ]]; then
echo "Please delete $(pwd)/dist" >&2
exit 1
fi
if ! pandoc -v &> /dev/null; then
echo "Please install pandoc (brew install pandoc)" >&2
exit 1
fi
if ! rst-lint -h &> /dev/null; then
echo "Please install rst-lint (pip install restructuredtext_lint)" >&2
exit 1
fi
if ! twine -h &> /dev/null; then
echo "Please install twine (pip install twine)" >&2
exit 1
fi
echo
echo "### Generating RST from Markdown"
mkdir -p build
pandoc --from=markdown --to=rst --output=build/README.rst README.md
echo
echo "### Checking RST for compatibility with PyPI (this is non-trivial)"
rst-lint build/README.rst
echo
echo "### Preparing distribution"
python setup.py bdist_wheel
echo
echo "### Uploading to PyPI (it may ask for your credentials)"
twine upload dist/*
|
adamcath/ads
|
publish_to_pypi.sh
|
Shell
|
mit
| 912 |
#!/bin/sh
(cd ./mcmatools && ./buildImage.sh)
(cd ./gcclatest && ./buildImage.sh)
(cd ./gccgtestlatest && ./buildImage.sh)
|
Zuehlke/BiZEPS
|
buildTools/buildgccgtestlatest.sh
|
Shell
|
mit
| 124 |
#!/bin/bash
echo "Starting Alvaro's vim setup"
DO_FULL_INSTALL=false; [ "$1" == "--install" ] && DO_FULL_INSTALL=true
# Create the necessary directories
[ -e ~/.config/nvim ] || mkdir -p ~/.config/nvim
[ -e ~/.config/nvim/bundle ] || mkdir -p ~/.config/nvim/bundle
[ -e ~/.config/nvim/ftplugin ] || mkdir -p ~/.config/nvim/ftplugin
[ -e ~/.config/nvim/syntax ] || mkdir -p ~/.config/nvim/syntax
# Install Plug
if [ ! -e ~/.config/nvim/autoload/plug.vim ]; then
curl -fLo ~/.config/nvim/autoload/plug.vim --create-dirs \
https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim
fi
# Copy files
cp ftplugin/*.vim ~/.config/nvim/ftplugin
cp syntax/*.vim ~/.config/nvim/syntax
cp vimrc ~/.config/nvim/init.vim
# Create symbolic links
[ -e ~/.vim ] || ln -s ~/.config/nvim ~/.vim
[ -e ~/.vimrc ] || ln -s ~/.config/nvim/init.vim ~/.vimrc
# Install neovim and dependencies
if [ "$DO_FULL_INSTALL" = true ]; then
OS_T="$OSTYPE"
if [[ $OS_T == "linux-gnu" ]]; then
# Linux (Ubuntu)
sudo apt-get install git python-pip neovim -y
elif [[ $OS_T == "darwin"* ]]; then
# Mac OS X
brew install git neovim/neovim/neovim fzf
fi
# Setup virtualenv for neovim
source `which virtualenvwrapper.sh`
mkvirtualenv nvim
pip install --upgrade pip autopep8 neovim pep8 flake8
deactivate
mkvirtualenv --python=`which python3` nvim-python3
pip install --upgrade pip autopep8 neovim pep8 flake8
deactivate
# TODO: change PYTHONPATH to nvim virtualenv instead of installing system-wide
if ! $(python -c "import autopep8" &> /dev/null); then sudo pip install autopep8; fi;
if ! $(python -c "import neovim" &> /dev/null); then sudo pip install neovim; fi;
if ! $(python -c "import pep8" &> /dev/null); then sudo pip install pep8; fi;
if ! $(python -c "import flake8" &> /dev/null); then sudo pip install flake8; fi;
# Install npm packages
# TODO: ensure npm is installed
sudo npm i -g eslint eslint-plugin-standard eslint-plugin-skip-nolint-lines
fi
# Install plugins
nvim +PlugInstall +qall
echo "Done setting up vim"
|
alvaromorales/dotfiles
|
vim/vimify.sh
|
Shell
|
mit
| 2,072 |
#!/bin/sh
# GCVIEWER_JAR=/path/to/gcviewer.jar
if [ -z $GCVIEWER_JAR ]; then
GCVIEWER_JAR=$1
fi
if [ -z $GCVIEWER_JAR ]; then
echo "Generate GC log summary using gcviewer. Please specify gcviewer.jar path in the first parameter."
echo "https://github.com/chewiebug/GCViewer"
echo ""
echo "Usage: $0 <gcviewer.jar>"
exit 1
fi
for f in `find . -name '*.log'`; do
if [ ! -f "$f-summary.txt" ]; then
java -jar $GCVIEWER_JAR $f $f-summary.txt
fi
done
|
nekop/gclogs
|
summary.sh
|
Shell
|
mit
| 490 |
#!/usr/bin/env bash
# Use single quotes instead of double quotes to make it work with special-character passwords
PASSWORD='12345678'
HOMEDIRFOLDER='www'
PROJECTFOLDER='projects'
# create project folder
sudo mkdir "/var/www/html/${HOMEDIRFOLDER}"
sudo mkdir "/var/www/html/${PROJECTFOLDER}"
echo "<?php phpinfo(); ?>" > /var/www/html/${HOMEDIRFOLDER}/index.php
# update / upgrade
sudo apt -y update
sudo apt -y upgrade
# install apache and php 7
sudo apt install -y apache2
sudo apt install -y php libapache2-mod-php
# install cURL and Mcrypt
sudo apt install -y php-curl
sudo apt install -y php-mcrypt
# install mysql and give password to installer
sudo debconf-set-selections <<< "mysql-server mysql-server/root_password password $PASSWORD"
sudo debconf-set-selections <<< "mysql-server mysql-server/root_password_again password $PASSWORD"
sudo apt install -y mysql-server
sudo apt install -y php-mysql
# install phpmyadmin and give password(s) to installer
# for simplicity I'm using the same password for mysql and phpmyadmin
sudo debconf-set-selections <<< "phpmyadmin phpmyadmin/dbconfig-install boolean true"
sudo debconf-set-selections <<< "phpmyadmin phpmyadmin/app-password-confirm password $PASSWORD"
sudo debconf-set-selections <<< "phpmyadmin phpmyadmin/mysql/admin-pass password $PASSWORD"
sudo debconf-set-selections <<< "phpmyadmin phpmyadmin/mysql/app-pass password $PASSWORD"
sudo debconf-set-selections <<< "phpmyadmin phpmyadmin/reconfigure-webserver multiselect apache2"
sudo apt install -y phpmyadmin
# setup hosts file
VHOST=$(cat <<EOF
<VirtualHost *:80>
DocumentRoot "/var/www/html/${HOMEDIRFOLDER}"
<Directory "/var/www/html/${HOMEDIRFOLDER}">
AllowOverride All
Require all granted
</Directory>
</VirtualHost>
EOF
)
echo "${VHOST}" > /etc/apache2/sites-available/000-default.conf
# enable mod_rewrite
sudo a2enmod rewrite
# restart apache
sudo service apache2 restart
# restart mysql
sudo service mysql restart
# install git
sudo apt install -y git
# install Composer
sudo apt install -y composer
|
muhammadtaqi/learning-tools
|
vagrant/xenial-lamp/bootstrap.sh
|
Shell
|
mit
| 2,062 |
#!/usr/bin/env bash
#
# Copyright (c) 2019-2020 The Fujicoin Core developers
# Distributed under the MIT software license, see the accompanying
# file COPYING or http://www.opensource.org/licenses/mit-license.php.
export LC_ALL=C.UTF-8
export CONTAINER_NAME=ci_macos_cross
export DOCKER_NAME_TAG=ubuntu:20.04 # Check that Focal can cross-compile to macos (Focal is used in the gitian build as well)
export HOST=x86_64-apple-darwin18
export PACKAGES="cmake imagemagick librsvg2-bin libz-dev libtiff-tools libtinfo5 python3-setuptools xorriso"
export XCODE_VERSION=12.1
export XCODE_BUILD_ID=12A7403
export RUN_UNIT_TESTS=false
export RUN_FUNCTIONAL_TESTS=false
export GOAL="deploy"
export FUJICOIN_CONFIG="--with-gui --enable-reduce-exports"
|
fujicoin/fujicoin
|
ci/test/00_setup_env_mac.sh
|
Shell
|
mit
| 744 |
#!/usr/bin/env bash
apt-add-repository ppa:brightbox/ruby-ng
apt-get update -y && apt-get upgrade -y
apt-get build-dep ruby2.0-dev -y
apt-get install libsqlite3-dev sqlite3 ruby2.2-dev ruby2.2 -y
mv /usr/bin/ruby /usr/bin/ruby-old
mv /usr/bin/gem /usr/bin/gem-old
ln -s /usr/bin/ruby2.2 /usr/bin/ruby
ln -s /usr/bin/gem2.2 /usr/bin/gem
ln -s /vagrant /home/vagrant/gamesbot
gem install bundler rake rspec
cd /vagrant
echo "Installing gems.."
sudo -u vagrant bundle install --without extradrivers
echo "Running tests.."
sudo -u vagrant bundle exec rspec
echo "Complete!"
|
Zarthus/irc-games-bot
|
.vagrant_bootstrap.sh
|
Shell
|
mit
| 578 |
source "$(dirname $BASH_SOURCE)/system.sh"
source "$(dirname $BASH_SOURCE)/utils.sh"
source "$(dirname $BASH_SOURCE)/deb.sh"
readonly MAME_DEB_URL="file://$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/../deb/mame_0.153_amd64.deb"
readonly MAME_FILES_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/../files/mame"
readonly MAME_SRC_URL="http://mame.mirrors.zippykid.com/releases/mame0153s.zip"
readonly MAME_VERSION="0.153"
readonly MAME_SRC_PATH="/usr/local/src/mame_${MAME_VERSION}"
readonly MAME_BUILD_PATH="/tmp/mame_build"
readonly MAME_BUILD_DEPENDENCIES="build-essential libsdl1.2-dev libsdl-ttf2.0-dev \
libqt4-dev libfontconfig1-dev libxinerama-dev"
readonly MAME_DEB_DEPENDENCIES="libasound2 libqtgui4 libsdl1.2debian \
libsdl-ttf2.0-0 libxinerama1"
mame_install_build_dependencies() {
install_packages $MAME_BUILD_DEPENDENCIES
}
mame_download_sources() {
download_and_extract_archive $MAME_SRC_URL /tmp/mame
mkdir --parents $MAME_SRC_PATH
unzip -q /tmp/mame/mame.zip -d $MAME_SRC_PATH
rm --force /tmp/mame/mame.zip
}
mame_compile() {
cd $MAME_SRC_PATH
make
rm --recursive --force $MAME_BUILD_PATH
mkdir --parents $MAME_BUILD_PATH/bin
cp mame64 $MAME_BUILD_PATH/bin/mame
}
mame_build_package() {
local dst_dir=$1
declare_debian_package_dependencies mame $MAME_DEB_DEPENDENCIES
build_debian_package $MAME_BUILD_PATH mame $MAME_VERSION bin/
mv mame_${MAME_VERSION}_amd64.deb $dst_dir/
}
mame_install_package() {
install_packages $MAME_DEB_DEPENDENCIES
install_package_from_url $MAME_DEB_URL mame
}
# Generate a default `mame.ini` file and display it to stdout
# Changes in the default mame configuration:
# * update core output directory path
# * update rom path
# * enable opengl
# * enable multithreading
mame_generate_config() {
local rom_path=$1
cd /tmp
mame -createconfig &> /dev/null
replace_config_line "multithreading" "multithreading 1" "/tmp/mame.ini"
replace_config_line "video" "video opengl" "/tmp/mame.ini"
replace_config_line "cfg_directory" 'cfg_directory $HOME/.mame/cfg' "/tmp/mame.ini"
replace_config_line "nvram_directory" 'nvram_directory $HOME/.mame/nvram' "/tmp/mame.ini"
replace_config_line "memcard_directory" 'memcard_directory $HOME/.mame/memcard' "/tmp/mame.ini"
replace_config_line "input_directory" 'input_directory $HOME/.mame/inp' "/tmp/mame.ini"
replace_config_line "state_directory" 'state_directory $HOME/.mame/sta' "/tmp/mame.ini"
replace_config_line "snapshot_directory" 'snapshot_directory $HOME/.mame/snap' "/tmp/mame.ini"
replace_config_line "diff_directory" 'diff_directory $HOME/.mame/diff' "/tmp/mame.ini"
replace_config_line "comment_directory" 'comment_directory $HOME/.mame/comments' "/tmp/mame.ini"
replace_config_line "ctrlrpath" 'ctrlrpath $HOME/.mame/ctrlr' "/tmp/mame.ini"
replace_config_line "rompath" "rompath $rom_path" "/tmp/mame.ini"
cat mame.ini
}
mame_generate_controls_config() {
cat $MAME_FILES_DIR/default.cfg
}
|
garnieretienne/arcade
|
lib/mame.sh
|
Shell
|
mit
| 2,966 |
#!/usr/bin/env bash
chown -R www-data var/
chown -R www-data web/mediafile
chmod -R 777 var/
bower install --allow-root
if [ "$APPLICATION_LIVE" = 1 ]; then
app/console assetic:dump --env=prod
else
app/console assetic:dump --env=dev
fi
/usr/local/sbin/php-fpm --nodaemonize
|
weburnit/sample-lumen-docker
|
images/php/slaver.sh
|
Shell
|
mit
| 278 |
#!/bin/bash
source ~/scripts/common.sh
$HADOOP_INSTALL/bin/hadoop jar kmeans.jar KMeans
|
viveksjain/repro_rdd
|
ec2/run_hadoopkmeans.sh
|
Shell
|
mit
| 88 |
#!/bin/bash
sudo -u www-data php app/console cache:clear --env=dev
sudo rm -r app/cache/dev/*
sudo -u www-data php app/console cache:warmup --env=dev
|
alexmazinho/foment.alexmazinho
|
cache_script.sh
|
Shell
|
mit
| 150 |
#!/bin/bash
set -e
if [ -z "`ls /usr/local/etc/php/conf.d`" ]
then
cp -R /etc-start/php/conf.d/* /usr/local/etc/php/conf.d
# Set environments
TIMEZONE1=${TIMEZONE:-Asia/Ho_Chi_Minh}
PHP_MEMORY_LIMIT1=${PHP_MEMORY_LIMIT:-512M}
MAX_UPLOAD1=${MAX_UPLOAD:-520M}
PHP_MAX_FILE_UPLOAD1=${PHP_MAX_FILE_UPLOAD:-200}
PHP_MAX_POST1=${PHP_MAX_POST:-520M}
MAX_INPUT_TIME1=${MAX_INPUT_TIME:-3600}
MAX_EXECUTION_TIME1=${MAX_EXECUTION_TIME:-3600}
sed -i -E \
-e "s|;*date.timezone =.*|date.timezone = ${TIMEZONE1}|i" \
-e "s|;*memory_limit =.*|memory_limit = ${MAX_UPLOAD1}|i" \
-e "s|;*upload_max_filesize =.*|upload_max_filesize = ${MAX_UPLOAD1}|i" \
-e "s|;*max_file_uploads =.*|max_file_uploads = ${PHP_MAX_FILE_UPLOAD1}|i" \
-e "s|;*post_max_size =.*|post_max_size = ${PHP_MAX_POST1}|i" \
-e "s/max_input_time = 60/max_input_time = ${MAX_INPUT_TIME1}/" \
-e "s/max_execution_time = 30/max_execution_time = ${MAX_EXECUTION_TIME1}/" \
-e "s/error_reporting = .*/error_reporting = E_ALL/" \
-e "s/display_errors = .*/display_errors = On/" \
/usr/local/etc/php/conf.d/babim.ini
fi
# set ID docker run
agid=${agid:-$auid}
auser=${auser:-www-data}
if [[ -z "${auid}" ]]; then
echo "start"
elif [[ "$auid" = "0" ]] || [[ "$aguid" == "0" ]]; then
echo "run in user root"
export auser=root
export APACHE_RUN_USER=$auser
export APACHE_RUN_GROUP=$auser
#sed -i -e "/^user = .*/cuser = $auser" /usr/local/etc/php-fpm.conf
#sed -i -e "/^group = .*/cgroup = $auser" /usr/local/etc/php-fpm.conf
else
if id $auser >/dev/null 2>&1; then
echo "user exists"
#sed -i -e "/^user = .*/cuser = $auser" /usr/local/etc/php-fpm.conf
#sed -i -e "/^group = .*/cgroup = $auser" /usr/local/etc/php-fpm.conf
export APACHE_RUN_USER=$auser
export APACHE_RUN_GROUP=$auser
# usermod alpine
#deluser $auser && delgroup $auser
#addgroup -g $agid $auser && adduser -D -H -G $auser -s /bin/false -u $auid $auser
# usermod ubuntu/debian
usermod -u $auid $auser
groupmod -g $agid $auser
else
echo "user does not exist"
export APACHE_RUN_USER=$auser
export APACHE_RUN_GROUP=$auser
# create user alpine
#addgroup -g $agid $auser && adduser -D -H -G $auser -s /bin/false -u $auid $auser
# create user ubuntu/debian
groupadd -g $agid $auser && useradd --system --uid $auid --shell /usr/sbin/nologin -g $auser $auser
#sed -i -e "/^user = .*/cuser = $auser" /usr/local/etc/php-fpm.conf
#sed -i -e "/^group = .*/cgroup = $auser" /usr/local/etc/php-fpm.conf
fi
fi
# option with entrypoint
if [ -f "/option.sh" ]; then /option.sh; fi
exec "$@"
|
babim/docker-phpbase
|
docker-entrypoint.sh
|
Shell
|
mit
| 2,594 |
elasticsearch --config=/usr/local/opt/elasticsearch/config/elasticsearch.yml
|
bootinge/bootinge
|
python/run_elasticsearch.sh
|
Shell
|
mit
| 77 |
#!/bin/bash
cat > /etc/hosts << "EOF"
# Begin /etc/hosts (network card version)
127.0.0.1 localhost
<192.168.1.1> <HOSTNAME.example.org> [alias1] [alias2 ...]
# End /etc/hosts (network card version)
EOF
|
taoyilee/tyLFS
|
SetUpBootScripts/createHosts.sh
|
Shell
|
mit
| 204 |
#!/bin/sh
. "$(pwd)/test/helper.sh"
test_do "bundlizer install https://bitbucket.org/naotos/sample.git"
test_do "bundlizer update sample"
test_do "bundlizer which sample"
|
Tomohiro/bundlizer
|
test/bitbucket_install_test.sh
|
Shell
|
mit
| 173 |
#!/bin/bash
CURDIR=$PWD
./edockerinstall.sh --alias
cd tests
/opt/bats/bin/bats edocker_tests.bats
/opt/bats/bin/bats edocker_platforms.bats
cd $CURDIR
|
pamtrak06/edocker
|
run_tests.sh
|
Shell
|
mit
| 152 |
#!/usr/bin/env bash
set -eu
PATTERN="-e ."
if [ $# -gt 0 ]
then
PATTERN="$1"
fi
exec find src \
-path src/examples/attitude_estimator_ekf -prune -o \
-path src/examples/ekf_att_pos_estimator -prune -o \
-path src/lib/DriverFramework -prune -o \
-path src/lib/ecl -prune -o \
-path src/lib/external_lgpl -prune -o \
-path src/lib/mathlib -prune -o \
-path src/lib/matrix -prune -o \
-path src/modules/attitude_estimator_ekf -prune -o \
-path src/modules/commander -prune -o \
-path src/modules/mavlink -prune -o \
-path src/modules/navigator -prune -o \
-path src/modules/sdlog2 -prune -o \
-path src/modules/systemlib/uthash -prune -o \
-path src/modules/uavcan -prune -o \
-path src/modules/uavcan/libuavcan -prune -o \
-type f \( -name "*.c" -o -name "*.h" -o -name "*.cpp" -o -name "*.hpp" \) | grep $PATTERN
|
darknight-007/Firmware
|
Tools/files_to_check_code_style.sh
|
Shell
|
mit
| 884 |
sort > generated/expected-output <<EOF
config: line 2: string ".hidden 2" matches ".hidden 2"
config: line 7: regex "^.hidden" matches ".hidden 2"
nb: ambiguous rules for path: "$PROJECT_PATH/test/data/test directory/.hidden 2"
EOF
|
AlxHnr/nano-backup
|
test/full program tests/mismatched path warnings/ambiguous rules/1/post-init.sh
|
Shell
|
mit
| 232 |
# Bundle a full git repo for sneakernet
function bundle() {
repo=$1
git clone --mirror [email protected]:dsanara/${repo}.git
cd ${repo}.git
git bundle create ../${repo}.bundle --all
cd ..
}
bundle the-repo
|
jpittard/jpittard.github.io
|
posts/git_bundle.sh
|
Shell
|
mit
| 219 |
#!/bin/sh
GODIR=$GOPATH/src/gitlab.com/tmaczukin/goliscan
mkdir -p "$(dirname $GODIR)"
ln -sfv "$(pwd -P)" "$GODIR"
cd "$GODIR"
|
chespinoza/goliscan
|
ci/prepare.sh
|
Shell
|
mit
| 129 |
#!/bin/sh
test -f /data/.shadow/.etc/wpa_supplicant.enabled
|
rdm-dev/meta-jens
|
recipes-core/init-ifupdown/init-ifupdown/wifi/pre_up.sh
|
Shell
|
mit
| 61 |
#!/bin/bash
#### Recreates mints for sample-data server assets.
server_id="r1fUoHwJOWCuK3WBAAySjmKYqsG6G2TYIxdqY6YNuuG"
server_user_id="voeqDVAJwDwROywFtg5mEyYpcu2dcPJRLFHYh7tyhqk"
##### game tokens
asset_id="7f8nlUn795x8931JParRnmKAyw8cegRyBMcFg9FccaF"
createmint ${server_id} ${server_user_id} ${asset_id}
##### US Dollars
asset_id="EYGad9FjZWgGKeVbgh2FbA0Hf8oP0XlnRyYCsvSIYKL"
createmint ${server_id} ${server_user_id} ${asset_id}
##### silver grams
asset_id="JY7kEFnm2c50CGNphdpgnlVo2hOZuLrBua5cFqWWR9Q"
createmint ${server_id} ${server_user_id} ${asset_id}
#### Bitcoins
asset_id="XU1Gu6sjcLxg260FmRgrSvRz9L0OohXRSEhlkeSd9j2"
createmint ${server_id} ${server_user_id} ${asset_id}
|
murrekatt/opentxs-sample-data
|
createmint-sample.sh
|
Shell
|
mit
| 691 |
#!/bin/bash
URL='http://google.com'; for ((;;)); do URL=$(curl -s --data-urlencode 'longurl='$URL xbryn.com/short/shorten.php); echo $URL; done
|
thedicearecubed/script-kiddies
|
shorten_bryn.sh
|
Shell
|
mit
| 145 |
#!/bin/sh
set -e
if [ "$BACKUP_MODE" != "none" ]; then
if [ ! -f /root/.rclone.conf ]; then
cat << EOF > /root/.rclone.conf
[s3]
type = s3
env_auth = false
access_key_id = $AWS_ACCESS_KEY_ID
secret_access_key = $AWS_SECRET_ACCESS_KEY
region = $AWS_S3_REGION
endpoint =
location_constraint =
acl =
server_side_encryption =
EOF
fi
fi
exec "$@"
|
kivy/kivy-server
|
downloads/cont/script/entry.sh
|
Shell
|
mit
| 352 |
# Ensure that the jumped-to folder is echoed
export _ZO_ECHO=1
eval "$(zoxide init --cmd j zsh)"
|
kaihowl/dotfiles
|
zoxide/load.zsh
|
Shell
|
mit
| 98 |
#!/usr/bin/env osascript
tell application "System Events"
tell process "Sublime Text 2"
return name of every menu item of menu 1 of menu bar item "Window" of menu bar 1
end tell
end tell
|
deborasetton/Sublime-Switch-Window
|
get_windows.sh
|
Shell
|
mit
| 196 |
dockutil --add "/System/Applications/App Store.app" --no-restart
dockutil --add "/Applications/Safari.app" --no-restart
dockutil --add "/Applications/Google Chrome.app" --no-restart
dockutil --add "/System/Applications/Mail.app" --no-restart
dockutil --add "/System/Applications/Messages.app" --no-restart
dockutil --add "/Applications/WhatsApp.app" --no-restart
dockutil --add "/Applications/LINE.app" --no-restart
dockutil --add "/Applications/Threema.app" --no-restart
dockutil --add "/Applications/Messenger.app" --no-restart
dockutil --add "/System/Applications/FaceTime.app" --no-restart
dockutil --add "/System/Applications/Contacts.app" --no-restart
dockutil --add "/Applications/Fantastical.app" --no-restart
dockutil --add "/System/Applications/Reminders.app" --no-restart
dockutil --add "/Applications/Trello.app" --no-restart
dockutil --add "/System/Applications/Notes.app" --no-restart
dockutil --add "/Applications/Bear.app" --no-restart
dockutil --add "/Applications/Dropbox Paper.app" --no-restart
dockutil --add "/Applications/Day One.app" --no-restart
dockutil --add "/Applications/Numbers.app" --no-restart
dockutil --add "/System/Applications/Photos.app" --no-restart
dockutil --add "/Applications/Adobe Lightroom Classic/Adobe Lightroom Classic.app" --no-restart
dockutil --add "/Applications/DaVinci Resolve/DaVinci Resolve.app" --no-restart
dockutil --add "/Applications/Spotify.app" --no-restart
dockutil --add "/System/Applications/Music.app" --no-restart
dockutil --add "/System/Applications/TV.app" --no-restart
dockutil --add "/System/Applications/FindMy.app" --no-restart
dockutil --add "/System/Applications/System Preferences.app" --no-restart
dockutil --add "/Applications/Parallels Desktop.app" --no-restart
dockutil --add "/Applications/Slack.app" --no-restart
dockutil --add "/Applications/iTerm.app" --no-restart
dockutil --add "/System/Applications/Utilities/Activity Monitor.app" --no-restart
dockutil --add "/Applications/WebStorm.app" --no-restart
dockutil --add "/Applications/Xcode.app" --no-restart
dockutil --add "/Applications/AppCode.app" --no-restart
dockutil --add "/Applications/Visual Studio Code.app" --no-restart
dockutil --add "/Applications/Postman.app" --no-restart
dockutil --add "/Applications/Outbank.app" --no-restart
dockutil --add "/Users/michaelkuck/Documents/Akten" --view fan --display stack --no-restart
dockutil --add "/Users/michaelkuck/Desktop" --view fan --display stack --no-restart
dockutil --add "/Users/michaelkuck/Documents" --view fan --display stack --no-restart
dockutil --add "/Users/michaelkuck/Downloads" --view fan --display stack --no-restart
|
mikumi/dotfiles
|
configure-dock.sh
|
Shell
|
mit
| 2,662 |
#!/bin/bash
# pull in any upstream changes from master
git checkout master
git fetch upstream
git merge upstream/master
git push origin master
# EOF
|
mamund/hal-forms
|
merge-upstream.sh
|
Shell
|
mit
| 152 |
#! /bin/bash
# Program: bwa (alignment via Burrows-Wheeler transformation)
# Version: 0.7.5a-r405
#
# Program: samtools (Tools for alignments in the SAM format)
# Version: 1.1 (using htslib 1.1)
#
# Program: bam2fastq - extract sequences from a BAM file
# Version: v1.1.0
#
# Program: bedtools genomecov (aka genomeCoverageBed)
# Version: v2.16.2
# Summary: Compute the coverage of a feature file among a genome.
#
# Program: fastq_to_fasta - Part of FASTX Toolkit
# Version: 0.0.13.2
#
# Program: convert - convert SVG to PNG (ImageMagick)
# Version: 6.6.9-7 2014-03-06 Q16
#
# Program: blastn
# Version: 2.2.30+
#
set -x # Echo all commands
genomes=(anthracis cereus)
declare -A samples
samples["SRR1748707"]="P00134"
samples["SRR1748708"]="P00134"
samples["SRR1749083"]="P00497"
declare -A reference
reference["anthracis"]="references/index/CP009541-anthracis"
reference["cereus"]="references/index/NC_003909-cereus"
# BLASTN parameters
OUTFMT="6 stitle sseqid qseqid qstart qend sstart send evalue bitscore score length pident nident mismatch positive means gapopen ppos qcovs qcovhsp"
NT="/data1/home/groups/readgp/nt/nt"
for s in ${!samples[@]}; do
for p in ${genomes[@]}; do
wd="results/mapping/bacilli-nyc/${s}/${p}"
mkdir -p ${wd}/coverage
mkdir -p ${wd}/aligned-reads
fq1="sra-pathogens/anthracis/${samples[$s]}/${s}_1.fastq.gz"
fq2="sra-pathogens/anthracis/${samples[$s]}/${s}_2.fastq.gz"
sam="${wd}/${s}.sam"
bam="${wd}/${s}.bam"
cov="${wd}/coverage/${s}.coverage.gz"
# Align using BWA, sort sam to bam and index bam
bin/bwa mem -t 20 ${reference[$p]} ${fq1} ${fq2} > ${sam}
samtools view -@ 10 -bS ${sam} | samtools sort -@ 10 - ${wd}/${s}
samtools index -b ${bam}
rm ${sam}
# Use genomeCoverageBed to get the coverage for each position and plot
# the coverage for differening sliding windows with 0.5 overlap
genomeCoverageBed -d -ibam ${bam} | gzip --best - > ${cov}
scripts/mapping/plot-coverage.R ${cov} 0.5 ${p}
# Extract aligned reads using bam2fastq and convert to fasta
ofq="${wd}/aligned-reads/${samples[$s]}_${s}#.fastq"
bin/bam2fastq -o ${ofq} --no-unaligned ${bam}
cat ${wd}/aligned-reads/*.fastq | fastq_to_fasta -Q33 -n | gzip --best - > ${wd}/aligned-reads/${samples[$s]}_${s}.fasta.gz
gzip --best "${wd}/aligned-reads/${samples[$s]}_${s}_1.fastq"
gzip --best "${wd}/aligned-reads/${samples[$s]}_${s}_2.fastq"
done
done
|
Read-Lab-Confederation/nyc-subway-anthrax-study
|
data/02-mapping/map-bacilli-nyc.sh
|
Shell
|
mit
| 2,548 |
export STEAM_FRAME_FORCE_CLOSE=1
|
marcinrogacki/dotfiles
|
repository/games/.slash/etc/bashrc.d/500-steam.sh
|
Shell
|
mit
| 33 |
#!/bin/bash
file="$1"
if [$file -eq ""] || [[ $file != *.ipa ]] ; then
echo "Please pass in an ipa file"
exit 2
fi
HTML=0
JS=0
CSS=0
EXE=0
mkdir "testScratch"
cp "$file" "testScratch/testScratch.zip"
cd "testScratch"
unzip "testScratch.zip" >/dev/null
#find . -name '*.png' -exec fun \;
#Check for HTML Files
for i in $(find . -name '*.html');
do HTML=$((HTML+1));
done;
#Check for JS Files
for i in $(find . -name '*.js');
do JS=$((JS+1));
done;
#Check for CSS Files
for i in $(find . -name '*.css');
do CSS=$((CSS+1));
done;
#Check for EXE Files
for i in $(find . -name '*.exe');
do EXE=$((EXE+1));
done;
if [ $HTML -eq 0 ] && [ $JS -eq 0 ] && [ $CSS -eq 0 ] && [ $EXE -eq 0 ] ; then
echo "native"
else
echo "not Native"
fi
cd ..
rm -rf "testScratch"
|
QueueSoftwareInc/isItNative
|
isItNative.sh
|
Shell
|
mit
| 793 |
#!/bin/bash
# Shortcut so that other files don't have to use such a long path when loading the spinner
. .gp/bash/third-party/bash-spinner/spinner.sh
|
concrete5/concrete5
|
.gp/bash/spinner.sh
|
Shell
|
mit
| 149 |
#!/bin/bash
WORKSPACE=/psikon/.jenkins/jobs/psistatsrd/workspace
PYTHONPATH=$WORKSPACE:$PYTHONPATH pylint $1 $2 $3 $4 $5 $6 $7
|
alex-dow/psistatsrd
|
build-sonar.sh
|
Shell
|
mit
| 129 |
#!/bin/sh
VERSION=`python setup.py --version`
echo "# Releasing pydocs v$VERSION..."
echo "# doing git..."
git tag -a v$VERSION -m v$VERSION
git push --tags
echo "# doing pypi..."
python setup.py sdist upload
echo "# Done!"
|
Fizzadar/pydocs
|
release.sh
|
Shell
|
mit
| 229 |
source "${HOME}/.bashrc.d/dependencies/liquidprompt/liquidprompt"
# fix a bug showing the temperature in any case
LP_ENABLE_TEMP=0
|
ydubreuil/dotfiles
|
homedir/.bashrc.d/liquidprompt.sh
|
Shell
|
mit
| 131 |
apt-get -qqy update
apt-get -qqy install python-flask
apt-get -qqy install python-sqlalchemy
apt-get -qqy install python-pip
pip install bleach
pip install oauth2client
pip install requests
pip install httplib2
pip install redis
pip install Flask-SQLAlchemy
pip install --upgrade google-api-python-client
pip install dicttoxml
pip install Flask-WTF
vagrantTip="[35m[1mThe shared directory is located at /vagrant\nTo access your shared files: cd /vagrant(B[m"
echo -e $vagrantTip > /etc/motd
wget http://download.redis.io/redis-stable.tar.gz
tar xvzf redis-stable.tar.gz
cd redis-stable
make
make install
|
brianquach/udacity-nano-fullstack-catalog
|
vagrant/pg_config.sh
|
Shell
|
mit
| 610 |
#!/bin/bash
# arguments
#
# 1 - N_divs for wall mounted brick
# 2 - lattice type [ 'D3Q15' | 'D3Q19' | 'D3Q27' ]
# 3 - dynamics [ 1 = LBGK | 2 = RBGK | 3 = MRT]
# 4 - partition methodology [ '1D' | '3D' | 'metis' ]
# 5 - number of partitions
# 6 - number of omp threads
# 7 - pre-process
# saves mat file named ChanCavityTest.mat
MAT_FILE=ChanCavityTest.mat
Num_ts=300001
ts_rep_freq=1000
Warmup_ts=0
plot_freq=10000
Re=3000
dt=0.0002
Cs=0
Restart_flag=0
# must re-process if you change:
# N_divs, partition methodology, or the number of partitions.
# if the lattice type changes, you do not have to re-do pre-processing,
# but the resulting partitions may not be the same as what would have
# been picked with new lattice type
if [ "$7" = "1" ]; then
aprun -n 1 ./channel_cavity_geom.py $1
if [ "$4" = "metis" ]; then
module swap PrgEnv-gnu PrgEnv-intel
fi
aprun -n 1 ./pyNFC_partition.py $MAT_FILE $2 $4 $5
if [ "$4" = "metis" ]; then
module swap PrgEnv-intel PrgEnv-gnu
fi
else
echo "pre-processing skipped, commencing time steps"
fi
# basically, pyNFC_preprocess.py just writes params.lbm now.
aprun -n 1 ./pyNFC_preprocess.py $MAT_FILE $2 $3 $4 $5 \
$Num_ts $ts_rep_freq $Warmup_ts $plot_freq $Re $dt $Cs $Restart_flag
export OMP_NUM_THREADS=$6
aprun -n $5 -d $6 ./pyNFC_run.py
#python ./processNFC.py
aprun -n 1 ./processNFC_serial
|
stu314159/pyNFC
|
run_chanCav.sh
|
Shell
|
mit
| 1,360 |
#!/usr/bin/env bash
# http://genometools.org/
URL="http://genometools.org/pub/genometools-1.5.7.tar.gz"
tarball=$(basename "$URL")
dir=$(echo $tarball | sed 's/\.tar\.gz//')
if [ ! -e "$tarball" ]
then
wget "$URL"
fi
if [ ! -e "$dir" ]
then
tar xzf "$tarball"
fi
cd "$dir"
# Needs pango-devel and cairo-devel installed
make errorcheck=no
# On 1.5.7 a number of test categories fail, but the application seems OK
# at a first glance. Maybe just spurious?
make test
make prefix="/ad/eng/support/software/linux/opt/64/$dir/" install
# Then symlink as usual
|
eng-it/linux-builds
|
genometools/build.sh
|
Shell
|
cc0-1.0
| 557 |
#!/bin/bash
# Snips out only the quality string lines from a FASTQ file
for file in $@
do
awk ' NR % 4 ==0 { print;}' $file > $file.qual
done
|
yunwilliamyu/snippets
|
fastq_qual_snip.sh
|
Shell
|
cc0-1.0
| 143 |
#!/bin/sh
test_description='git fsck random collection of tests'
. ./test-lib.sh
test_expect_success setup '
test_commit A fileA one &&
git checkout HEAD^0 &&
test_commit B fileB two &&
git tag -d A B &&
git reflog expire --expire=now --all
'
test_expect_success 'HEAD is part of refs' '
test 0 = $(git fsck | wc -l)
'
test_expect_success 'loose objects borrowed from alternate are not missing' '
mkdir another &&
(
cd another &&
git init &&
echo ../../../.git/objects >.git/objects/info/alternates &&
test_commit C fileC one &&
git fsck >out &&
! grep "missing blob" out
)
'
# Corruption tests follow. Make sure to remove all traces of the
# specific corruption you test afterwards, lest a later test trip over
# it.
test_expect_success 'object with bad sha1' '
sha=$(echo blob | git hash-object -w --stdin) &&
echo $sha &&
old=$(echo $sha | sed "s+^..+&/+") &&
new=$(dirname $old)/ffffffffffffffffffffffffffffffffffffff &&
sha="$(dirname $new)$(basename $new)"
mv .git/objects/$old .git/objects/$new &&
git update-index --add --cacheinfo 100644 $sha foo &&
tree=$(git write-tree) &&
cmt=$(echo bogus | git commit-tree $tree) &&
git update-ref refs/heads/bogus $cmt &&
(git fsck 2>out; true) &&
grep "$sha.*corrupt" out &&
rm -f .git/objects/$new &&
git update-ref -d refs/heads/bogus &&
git read-tree -u --reset HEAD
'
test_expect_success 'branch pointing to non-commit' '
git rev-parse HEAD^{tree} > .git/refs/heads/invalid &&
git fsck 2>out &&
grep "not a commit" out &&
git update-ref -d refs/heads/invalid
'
cat > invalid-tag <<EOF
object ffffffffffffffffffffffffffffffffffffffff
type commit
tag invalid
tagger T A Gger <[email protected]> 1234567890 -0000
This is an invalid tag.
EOF
test_expect_success 'tag pointing to nonexistent' '
tag=$(git hash-object -t tag -w --stdin < invalid-tag) &&
echo $tag > .git/refs/tags/invalid &&
test_must_fail git fsck --tags >out &&
cat out &&
grep "broken link" out &&
rm .git/refs/tags/invalid
'
cat > wrong-tag <<EOF
object $(echo blob | git hash-object -w --stdin)
type commit
tag wrong
tagger T A Gger <[email protected]> 1234567890 -0000
This is an invalid tag.
EOF
test_expect_success 'tag pointing to something else than its type' '
tag=$(git hash-object -t tag -w --stdin < wrong-tag) &&
echo $tag > .git/refs/tags/wrong &&
test_must_fail git fsck --tags 2>out &&
cat out &&
grep "error in tag.*broken links" out &&
rm .git/refs/tags/wrong
'
test_done
|
byang/line
|
t/t1450-fsck.sh
|
Shell
|
gpl-2.0
| 2,478 |
#!/usr/bin/env bash
# ____ _________ ____ _________
# / __ \/ ___/ __ \/ __ \/ ___/ __ \
# / /_/ / / / /_/ / /_/ / / / /_/ /
# / .___/_/ \____/ .___/_/ \____/
# /_/ /_/
#
# Built from: vagrant.propro
unset UCF_FORCE_CONFFOLD
export UCF_FORCE_CONFFNEW="YES"
export DEBIAN_FRONTEND="noninteractive"
# Propro package: lib/propro.sh
#!/usr/bin/env bash
set -e
set -u
PROPRO_LOG_FILE="/root/provision.log"
PROPRO_FULL_LOG_FILE="/root/full_provision.log"
PROPRO_LOG_USE_COLOR="yes"
PROPRO_DISABLE_LOG="no"
>$PROPRO_FULL_LOG_FILE
exec > >(tee $PROPRO_FULL_LOG_FILE)
exec 2>&1
function log {
echo -e "$1"
if is-yes $PROPRO_DISABLE_LOG; then
return 0
fi
if [ $PROPRO_LOG_FILE ]; then
touch $PROPRO_LOG_FILE
echo -e "$1" >> $PROPRO_LOG_FILE
fi
}
# $1 text
function section {
local msg="#### $1"
log ""
if is-yes $PROPRO_LOG_USE_COLOR; then
log "\e[32m\e[1m$msg\e[0m"
else
log "$msg"
fi
}
# $1 text
function announce {
if is-yes $PROPRO_LOG_USE_COLOR; then
log "\e[34m\e[1m--->\e[0m $1"
else
log "---> $1"
fi
}
# $1 text
function announce-item {
if is-yes $PROPRO_LOG_USE_COLOR; then
log " - \e[36m$1\e[0m"
else
log " - $1"
fi
}
function finished {
if is-yes $PROPRO_LOG_USE_COLOR; then
log "\e[35m\e[1m Fin.\e[0m"
else
log " Fin."
fi
log ""
}
function get-tmp-dir {
mktemp -d
}
# $1 "yes" or "no"
function is-yes {
if [ $1 == "yes" ]; then
return 0
else
return 1
fi
}
# $1 "yes" or "no"
function is-no {
if [ $1 == "no" ]; then
return 0
else
return 1
fi
}
# $1 comma separated list
#
# example:
# > $ csl-to-wsl "item1,item2,item3"
# > item1 item2 item3
function csl-to-wsl {
echo "$1" | sed 's/,/ /g'
}
# $1 path or relative uri
#
# example:
# > $ path-to-id example.com/neat/stuff
# > example_com_neat_stuff
function path-to-id {
echo "$1" | sed -r 's/[-\.:\/\]/_/g'
}
# Propro package: lib/ubuntu.sh
#!/usr/bin/env bash
function get-processor-count {
nproc
}
function release-codename {
lsb_release -c -s
}
# $@ package names
function install-packages {
announce "Installing packages:"
for package in $@; do
announce-item "$package"
done
aptitude -q -y -o Dpkg::Options::="--force-confnew" install $@
}
function get-archtype {
if [ $(getconf LONG_BIT) == 32 ]; then
echo 'x86'
else
echo 'x64'
fi
}
function update-sources {
sed -i "/^# deb.*multiverse/ s/^# //" /etc/apt/sources.list
apt-get -qq -y update
}
function add-repository {
add-apt-repository -y $1
}
# $1 unix user
# $2 service name
# $3 service args
function add-sudoers-entries {
for event in start status stop reload restart; do
if [ $3 ]; then
tee -a /etc/sudoers.d/$2-entries <<EOT
$1 ALL=NOPASSWD: /sbin/$event $2 $3
EOT
else
tee -a /etc/sudoers.d/$2-entries <<EOT
$1 ALL=NOPASSWD: /sbin/$event $2
EOT
fi
chmod 0440 /etc/sudoers.d/$2-entries
done
}
function reboot-system {
shutdown -r now
}
# $1 package name
function reconfigure-package {
dpkg-reconfigure -f noninteractive $1
}
# $1 key URL
function add-source-key {
wget --quiet -O - $1 | apt-key add -
}
# $@ files to extract
function extract {
tar xzf $@
}
# $1 URL to download
function download {
wget -nv $1
}
function get-ram-bytes {
free -m -b | awk '/^Mem:/{print $2}'
}
function get-page-size {
getconf PAGE_SIZE
}
function get-ram-pages {
echo "$(get-ram-bytes) / $(get-page-size)" | bc
}
# $1 shmall percent
function get-kernel-shmall {
echo "($(get-ram-pages) * $1) / 1" | bc
}
# $1 shmmax percent
function get-kernel-shmmax {
echo "($(get-ram-bytes) * $1) / 1" | bc
}
# $1 unix user
# $2 path
function as-user-mkdir {
mkdir -p $2
chown $1:$1 $2
}
function upgrade-system {
update-sources
apt-get -qq -y install aptitude
aptitude -q -y -o Dpkg::Options::="--force-confnew" full-upgrade
}
# $1 timezone
function set-timezone {
echo $1 > /etc/timezone
reconfigure-package tzdata
}
# $1 locale eg: en_US.UTF-8
function set-locale {
export LANGUAGE=$1
export LANG=$1
export LC_ALL=$1
locale-gen $1
reconfigure-package locales
update-locale
}
# $1 hostname
function set-hostname {
echo $1 > /etc/hostname
hostname -F /etc/hostname
}
# $1 unix user
# $2 unix group
# $3 password
function add-user {
if [ $2 ]; then
announce "Adding $1 user to group $2"
useradd -m -s /bin/bash -g $2 $1
else
announce "Adding $1 user"
useradd -m -s /bin/bash $1
fi
if [ $3 ]; then
announce "Setting password for $1 user"
echo "$1:$3" | chpasswd
fi
}
# $1 unix user
# $2 github usernames for public keys
function add-pubkeys-from-github {
announce "Installing public keys for $1 from GitHub users:"
local ssh_dir="/home/$1/.ssh"
local keys_file="$ssh_dir/authorized_keys"
mkdir -p $ssh_dir
touch $keys_file
for user in $2; do
announce-item "$user"
local url="https://github.com/$user.keys"
tee -a $keys_file <<EOT
# $url
$(wget -qO- $url)
EOT
done
chmod 700 $ssh_dir
chmod 600 $keys_file
chown -R $1 $ssh_dir
}
# Propro package: lib/system.sh
#!/usr/bin/env bash
SYSTEM_SHMALL_PERCENT="0.75" # @specify
SYSTEM_SHMMAX_PERCENT="0.5" # @specify
SYSTEM_BASE_PACKAGES="curl vim-nox less htop build-essential openssl git tree python-software-properties"
SYSTEM_TIMEZONE="Etc/UTC" # @specify
SYSTEM_LOCALE="en_US.UTF-8" # @specify
SYSTEM_SOURCES_PG_KEY_URL="http://apt.postgresql.org/pub/repos/apt/ACCC4CF8.asc"
function system-configure-shared-memory {
announce "Configuring shared memory"
install-packages bc
local shmall=$(get-kernel-shmall $SYSTEM_SHMALL_PERCENT)
local shmmax=$(get-kernel-shmmax $SYSTEM_SHMMAX_PERCENT)
sysctl -w kernel.shmall=$shmall
sysctl -w kernel.shmmax=$shmmax
tee -a /etc/sysctl.conf <<EOT
kernel.shmall = $shmall
kernel.shmmax = $shmmax
EOT
}
function system-install-packages {
install-packages $SYSTEM_BASE_PACKAGES
}
function system-configure-timezone {
announce "Set timezone to $SYSTEM_TIMEZONE"
set-timezone $SYSTEM_TIMEZONE
}
function system-configure-locale {
announce "Set locale to $SYSTEM_LOCALE"
set-locale $SYSTEM_LOCALE
}
function system-upgrade {
announce "Update and upgrade system packages"
upgrade-system
}
function system-add-pg-source {
announce "Add PostgreSQL sources:"
tee /etc/apt/sources.list.d/pgdg.list <<EOT
deb http://apt.postgresql.org/pub/repos/apt/ $(release-codename)-pgdg main
EOT
announce-item "apt.postgresql.org"
add-source-key $SYSTEM_SOURCES_PG_KEY_URL
update-sources
}
function system-install-sources {
system-add-pg-source
}
# Propro package: lib/pg.sh
#!/usr/bin/env bash
PG_VERSION="9.3" # @specify
PG_EXTENSIONS="btree_gin btree_gist fuzzystrmatch hstore intarray ltree pg_trgm tsearch2 unaccent" # @specify see: http://www.postgresql.org/docs/9.3/static/contrib.html
PG_CONFIG_FILE="/etc/postgresql/$PG_VERSION/main/postgresql.conf"
PG_HBA_FILE="/etc/postgresql/$PG_VERSION/main/pg_hba.conf"
PG_TUNE_VERSION="0.9.3"
PG_USER="postgres"
function get-pg-tune-url {
echo "http://pgfoundry.org/frs/download.php/2449/pgtune-$PG_TUNE_VERSION.tar.gz"
}
function pg-install-packages {
install-packages postgresql-$PG_VERSION libpq-dev postgresql-contrib-$PG_VERSION
}
function pg-tune {
local tmpdir=$(get-tmp-dir)
cd "$tmpdir"
announce "Tune PostgreSQL $PG_VERSION"
download $(get-pg-tune-url)
extract pgtune-$PG_TUNE_VERSION.tar.gz
./pgtune-$PG_TUNE_VERSION/pgtune -i $PG_CONFIG_FILE -o $PG_CONFIG_FILE.pgtune
mv $PG_CONFIG_FILE $PG_CONFIG_FILE.original
mv $PG_CONFIG_FILE.pgtune $PG_CONFIG_FILE
chown $PG_USER:$PG_USER $PG_CONFIG_FILE
cd ~/
rm -rf "$tmpdir"
}
# $1 db user name
# $2 db name
function pg-createdb {
announce "Create database: $2"
su - $PG_USER -c "createdb -O $1 $2"
if [ $PG_EXTENSIONS ]; then
announce "Add extensions:"
for extension in $PG_EXTENSIONS; do
announce-item "$extension"
su - $PG_USER -c "psql -d $2 -c \"CREATE EXTENSION IF NOT EXISTS $extension;\""
done
fi
}
# Propro package: lib/rvm.sh
#!/usr/bin/env bash
# requires app.sh
RVM_CHANNEL="stable"
RVM_REQUIRED_PACKAGES="curl gawk g++ gcc make libc6-dev libreadline6-dev zlib1g-dev libssl-dev libyaml-dev libsqlite3-dev sqlite3 autoconf libgdbm-dev libncurses5-dev automake libtool bison pkg-config libffi-dev"
RVM_DEFAULT_GEMS="bundler" #@specify
# $1 unix user
# $2 ruby version
function rvm-install-for-user {
section "RVM"
install-packages $RVM_REQUIRED_PACKAGES
announce "Install RVM for user $1"
su - $1 -c "curl -L https://get.rvm.io | bash -s $RVM_CHANNEL"
su - $1 -c "rvm autolibs read-fail"
announce "Install Ruby $2 for user $1"
su - $1 -c "rvm install $2"
announce "Set Ruby $2 as default for user $1"
su - $1 -c "rvm --default use $2"
announce "Install default gems"
su - $1 -c "gem install $RVM_DEFAULT_GEMS"
}
# Propro package: lib/nginx.sh
#!/usr/bin/env bash
NGINX_VERSION="1.6.0" # @specify
NGINX_USER="nginx"
NGINX_CONFIGURE_OPTS="--with-http_ssl_module --with-http_gzip_static_module" # @specify
NGINX_CONF_FILE="/etc/nginx.conf"
NGINX_ETC_DIR="/etc/nginx"
NGINX_LOG_DIR="/var/log/nginx"
NGINX_ACCESS_LOG_FILE_NAME="access.log"
NGINX_ERROR_LOG_FILE_NAME="error.log"
NGINX_DEPENDENCIES="libpcre3-dev libssl-dev"
NGINX_WORKER_COUNT=$(get-processor-count)
NGINX_SERVER_NAMES_HASH_BUCKET_SIZE="64"
NGINX_PID_FILE="/var/run/nginx.pid"
NGINX_CLIENT_MAX_BODY_SIZE="5m" # @specify
NGINX_WORKER_CONNECTIONS="2000" # @specify
NGINX_SITES_DIR="$NGINX_ETC_DIR/sites"
NGINX_CONF_DIR="$NGINX_ETC_DIR/conf"
function get-nginx-url {
echo "http://nginx.org/download/nginx-$NGINX_VERSION.tar.gz"
}
function nginx-install {
local tmpdir=$(get-tmp-dir)
cd "$tmpdir"
install-packages $NGINX_DEPENDENCIES
announce "Download $NGINX_VERSION"
download $(get-nginx-url)
announce "Extract"
extract nginx-$NGINX_VERSION.tar.gz
announce "Configure"
cd nginx-$NGINX_VERSION
./configure $NGINX_CONFIGURE_OPTS
announce "Compile"
make
announce "Install $NGINX_VERSION"
make install
cd ~/
rm -rf "$tmpdir"
}
function nginx-configure {
announce "Creating Nginx user"
useradd -r $NGINX_USER
announce "Adding Nginx directories"
as-user-mkdir $NGINX_USER $NGINX_LOG_DIR
mkdir -p $NGINX_ETC_DIR
mkdir -p $NGINX_SITES_DIR
mkdir -p $NGINX_CONF_DIR
announce "Creating base Nginx config: $NGINX_CONF_FILE"
tee $NGINX_CONF_FILE <<EOT
user $NGINX_USER;
pid $NGINX_PID_FILE;
ssl_engine dynamic;
worker_processes $NGINX_WORKER_COUNT;
events {
multi_accept on;
worker_connections $NGINX_WORKER_CONNECTIONS;
use epoll;
}
http {
sendfile on;
tcp_nopush on;
tcp_nodelay off;
client_max_body_size $NGINX_CLIENT_MAX_BODY_SIZE;
client_body_temp_path /var/spool/nginx-client-body 1 2;
server_names_hash_bucket_size $NGINX_SERVER_NAMES_HASH_BUCKET_SIZE;
default_type application/octet-stream;
include /etc/nginx/conf/*.conf;
include /etc/nginx/sites/*.conf;
}
EOT
announce "Writing Nginx upstart /etc/init/nginx.conf"
tee /etc/init/nginx.conf <<EOT
description "Nginx HTTP Daemon"
author "George Shammas <[email protected]>"
start on (filesystem and net-device-up IFACE=lo)
stop on runlevel [!2345]
env DAEMON="/usr/local/nginx/sbin/nginx -c $NGINX_CONF_FILE"
env PID="$NGINX_PID_FILE"
expect fork
respawn
respawn limit 10 5
pre-start script
\$DAEMON -t
if [ \$? -ne 0 ]
then exit \$?
fi
end script
exec \$DAEMON
EOT
}
function nginx-conf-add-mimetypes {
announce "Adding mimetypes config"
tee "$NGINX_CONF_DIR/mimetypes.conf" <<EOT
types_hash_max_size 2048;
types {
application/atom+xml atom;
application/java-archive jar war ear;
application/javascript js;
application/json json;
application/msword doc;
application/pdf pdf;
application/postscript ps eps ai;
application/rtf rtf;
application/vnd.ms-excel xls;
application/vnd.ms-fontobject eot;
application/vnd.ms-powerpoint ppt;
application/vnd.wap.wmlc wmlc;
application/x-7z-compressed 7z;
application/x-bittorrent torrent;
application/x-cocoa cco;
application/x-font-ttf ttf ttc;
application/x-httpd-php-source phps;
application/x-java-archive-diff jardiff;
application/x-java-jnlp-file jnlp;
application/x-makeself run;
application/x-perl pl pm;
application/x-pilot prc pdb;
application/x-rar-compressed rar;
application/x-redhat-package-manager rpm;
application/x-sea sea;
application/x-shockwave-flash swf;
application/x-stuffit sit;
application/x-tcl tcl tk;
application/x-x509-ca-cert der pem crt;
application/x-xpinstall xpi;
application/xhtml+xml xhtml;
application/xml xml;
application/zip zip;
audio/midi mid midi kar;
audio/mpeg mp3;
audio/ogg oga ogg;
audio/x-m4a m4a;
audio/x-realaudio ra;
audio/x-wav wav;
font/opentype otf;
font/woff woff;
image/gif gif;
image/jpeg jpeg jpg;
image/png png;
image/svg+xml svg svgz;
image/tiff tif tiff;
image/vnd.wap.wbmp wbmp;
image/webp webp;
image/x-icon ico;
image/x-ms-bmp bmp;
text/cache-manifest manifest appcache;
text/css css;
text/html html htm shtml;
text/mathml mml;
text/plain txt md;
text/vnd.sun.j2me.app-descriptor jad;
text/vnd.wap.wml wml;
text/x-component htc;
text/xml rss;
video/3gpp 3gpp 3gp;
video/mp4 m4v mp4;
video/mpeg mpeg mpg;
video/ogg ogv;
video/quicktime mov;
video/webm webm;
video/x-flv flv;
video/x-mng mng;
video/x-ms-asf asx asf;
video/x-ms-wmv wmv;
video/x-msvideo avi;
}
EOT
}
function nginx-conf-add-gzip {
announce "Adding gzip config"
tee $NGINX_CONF_DIR/gzip.conf <<EOT
gzip on;
gzip_buffers 32 4k;
gzip_comp_level 2;
gzip_disable "msie6";
gzip_http_version 1.1;
gzip_min_length 1100;
gzip_proxied any;
gzip_static on;
gzip_vary on;
gzip_types
text/css
text/plain
application/javascript
application/json
application/rss+xml
application/xml
application/vnd.ms-fontobject
font/truetype
font/opentype
image/x-icon
image/svg+xml;
EOT
}
function nginx-create-logrotate {
announce "Create logrotate for Nginx"
tee /etc/logrotate.d/nginx <<EOT
$NGINX_LOG_DIR/*.log {
daily
missingok
rotate 90
compress
delaycompress
notifempty
dateext
create 640 nginx adm
sharedscripts
postrotate
[ -f $NGINX_PID_FILE ] && kill -USR1 `cat $NGINX_PID_FILE`
endscript
}
EOT
}
# Propro package: lib/node.sh
#!/usr/bin/env bash
NODE_VERSION="0.10.26" # @specify
function get-node-pkg-name {
echo "node-v$NODE_VERSION-linux-$(get-archtype)"
}
function get-node-url {
echo "http://nodejs.org/dist/v$NODE_VERSION/$(get-node-pkg-name).tar.gz"
}
function node-install {
local tmpdir=$(get-tmp-dir)
cd "$tmpdir"
announce "Download Node $NODE_VERSION"
download $(get-node-url)
announce "Extract Node $NODE_VERSION"
extract "$(get-node-pkg-name).tar.gz"
announce "Install Node"
cd "./$(get-node-pkg-name)"
cp -r -t /usr/local bin include share lib
cd ~/
rm -r "$tmpdir"
}
# Propro package: lib/redis.sh
#!/usr/bin/env bash
REDIS_VERSION="2.8.9" # @specify
REDIS_USER="redis"
REDIS_CONF_FILE="/etc/redis.conf"
REDIS_DATA_DIR="/var/lib/redis"
REDIS_FORCE_64BIT="no" # @specify Force 64bit build even if available memory is lte 4GiB
function get-redis-url {
echo "http://download.redis.io/releases/redis-$REDIS_VERSION.tar.gz"
}
function redis-install {
local tmpdir=$(get-tmp-dir)
cd "$tmpdir"
announce "Download $REDIS_VERSION"
download $(get-redis-url)
announce "Extract"
extract redis-$REDIS_VERSION.tar.gz
cd redis-$REDIS_VERSION
if [ $(get-ram-bytes) -gt 4294967296 ] || is-yes $REDIS_FORCE_64BIT; then
announce "Compile"
make
else
announce "Compile (32bit, available memory <= 4GiB)"
install-packages libc6-dev-i386
make 32bit
fi
announce "Install $REDIS_VERSION"
make install
announce "Add Redis user: $REDIS_USER"
useradd -r $REDIS_USER
announce "Create Redis directories"
as-user-mkdir $REDIS_USER $REDIS_DATA_DIR
announce "Copy Redis config to $REDIS_CONF_FILE"
cp ./redis.conf $REDIS_CONF_FILE
cd ~/
rm -rf "$tmpdir"
announce "Update Redis config"
tee -a $REDIS_CONF_FILE <<EOT
syslog-enabled yes
syslog-ident redis
dir $REDIS_DATA_DIR
EOT
announce "Create upstart for Redis"
tee /etc/init/redis.conf <<EOT
description "Redis"
start on runlevel [23]
stop on shutdown
exec sudo -u $REDIS_USER /usr/local/bin/redis-server $REDIS_CONF_FILE
respawn
EOT
}
# Propro package: lib/ffmpeg.sh
#!/usr/bin/env bash
# http://askubuntu.com/a/148567
# https://trac.ffmpeg.org/wiki/UbuntuCompilationGuide
# http://juliensimon.blogspot.ca/2013/08/howto-compiling-ffmpeg-x264-mp3-aac.html
FFMPEG_VERSION="git" # @specify (or a version to download: "2.1.4")
FFMPEG_YASM_VERSION="1.2.0"
FFMPEG_XVID_VERSION="1.3.2"
function get-ffmpeg-url {
echo "http://ffmpeg.org/releases/ffmpeg-$FFMPEG_VERSION.tar.gz"
}
function get-ffmpeg-yasm-url {
echo "http://www.tortall.net/projects/yasm/releases/yasm-$FFMPEG_YASM_VERSION.tar.gz"
}
function get-ffmpeg-xvid-url {
echo "http://downloads.xvid.org/downloads/xvidcore-$FFMPEG_XVID_VERSION.tar.gz"
}
function ffmpeg-install {
local tmpdir=$(get-tmp-dir)
cd "$tmpdir"
announce "Install Dependencies"
install-packages build-essential git libfaac-dev libgpac-dev \
libjack-jackd2-dev libmp3lame-dev libopencore-amrnb-dev \
libopencore-amrwb-dev libsdl1.2-dev libtheora-dev libva-dev libvdpau-dev \
libvorbis-dev libxfixes-dev zlib1g-dev libgsm1-dev
announce-item "Yasm"
announce-item "> Download"
download $(get-ffmpeg-yasm-url)
announce-item "> Extract"
extract yasm-$FFMPEG_YASM_VERSION.tar.gz
cd yasm-$FFMPEG_YASM_VERSION
announce-item "> Configure"
./configure
announce-item "> Compile"
make
announce-item "> Install"
make install
make distclean
cd ..
announce-item "X264"
announce-item "> Download"
git clone --depth 1 git://git.videolan.org/x264
announce-item "> Configure"
cd x264
./configure --prefix=/usr/local --enable-shared
announce-item "> Compile"
make
announce-item "> Install"
make install
make distclean
cd ..
announce-item "Xvid"
announce-item "> Download"
download $(get-ffmpeg-xvid-url)
announce-item "> Extract"
extract xvidcore-$FFMPEG_XVID_VERSION.tar.gz
cd xvidcore/build/generic
announce-item "> Configure"
./configure --prefix=/usr/local
announce-item "> Compile"
make
announce-item "> Install"
make install
cd ../../..
announce "Download $FFMPEG_VERSION"
if [ $FFMPEG_VERSION == "git" ]; then
git clone --depth 1 git://source.ffmpeg.org/ffmpeg.git
cd ffmpeg
else
download $(get-ffmpeg-url)
announce "Extract"
extract ffmpeg-$FFMPEG_VERSION.tar.gz
cd ffmpeg-$FFMPEG_VERSION
fi
announce "Configure"
./configure --prefix=/usr/local --enable-gpl --enable-version3 \
--enable-nonfree --enable-shared --enable-libopencore-amrnb \
--enable-libopencore-amrwb --enable-libfaac --enable-libgsm \
--enable-libmp3lame --enable-libtheora --enable-libvorbis \
--enable-libx264 --enable-libxvid
announce "Compile"
make
announce "Install"
make install
make distclean
ldconfig -v
cd ~/
rm -rf "$tmpdir"
}
# Propro package: lib/extras.sh
#!/usr/bin/env bash
EXTRA_PACKAGES="" # @specify
function provision-extras {
if [ -z "$EXTRA_PACKAGES" ]; then
return 0
fi
section "Extras"
install-packages $EXTRA_PACKAGES
}
# Propro package: vagrant.sh
#!/usr/bin/env bash
VAGRANT_USER="vagrant"
VAGRANT_DATA_DIR="/vagrant"
# Propro package: vagrant/system.sh
#!/usr/bin/env bash
function vagrant-system-install-user-aliases {
announce "Installing helper aliases for user: $VAGRANT_USER"
tee -a /home/$VAGRANT_USER/.profile <<EOT
alias be="bundle exec"
alias r="bin/rails"
alias v="cd $VAGRANT_DATA_DIR"
cd $VAGRANT_DATA_DIR
EOT
}
function vagrant-system-purge-grub-menu-config {
ucf --purge /boot/grub/menu.lst
}
function provision-vagrant-system {
section "Vagrant System"
vagrant-system-purge-grub-menu-config
system-upgrade
system-configure-timezone
system-configure-locale
system-install-packages
system-configure-shared-memory
system-install-sources
vagrant-system-install-user-aliases
}
# Propro package: vagrant/pg.sh
#!/usr/bin/env bash
function vagrant-pg-create-user {
announce "Create database user: $VAGRANT_USER"
su - $PG_USER -c "createuser -s $VAGRANT_USER"
}
function provision-vagrant-pg {
section "PostgreSQL Server"
pg-install-packages
pg-tune
vagrant-pg-create-user
}
# Propro package: vagrant/redis.sh
#!/usr/bin/env bash
function provision-vagrant-redis {
section "Redis"
redis-install
}
# Propro package: vagrant/rvm.sh
#!/usr/bin/env bash
VAGRANT_RVM_RUBY_VERSION="2.0.0" # @specify
function provision-vagrant-rvm {
rvm-install-for-user $VAGRANT_USER $VAGRANT_RVM_RUBY_VERSION
}
# Propro package: vagrant/node.sh
#!/usr/bin/env bash
function provision-vagrant-node {
section "Node.js"
node-install
}
# Propro package: vagrant/nginx.sh
#!/usr/bin/env bash
function provision-vagrant-nginx {
section "Nginx"
nginx-install
nginx-configure
nginx-conf-add-gzip
nginx-conf-add-mimetypes
announce "Adding Nginx config for Vagrant"
tee "$NGINX_SITES_DIR/vagrant.conf" <<EOT
upstream rack_app {
server 127.0.0.1:3000 fail_timeout=0;
}
server {
root $VAGRANT_DATA_DIR/public;
access_log /dev/null;
error_log /dev/null;
try_files \$uri/index.html \$uri.html \$uri @upstream_app;
location @upstream_app {
proxy_set_header X-Forwarded-For \$proxy_add_x_forwarded_for;
proxy_set_header Host \$http_host;
proxy_redirect off;
proxy_pass http://rack_app;
}
}
EOT
}
# Propro package: vagrant/ffmpeg.sh
#!/usr/bin/env bash
function provision-vagrant-ffmpeg {
section "FFmpeg"
ffmpeg-install
}
# Options from: vagrant.propro
SYSTEM_SHMALL_PERCENT="0.65"
SYSTEM_SHMMAX_PERCENT="0.35"
PG_VERSION="9.3"
REDIS_VERSION="2.8.9"
VAGRANT_RVM_RUBY_VERSION="2.1.2"
NODE_VERSION="0.10.28"
NGINX_VERSION="1.6.0"
NGINX_WORKER_CONNECTIONS="100"
EXTRA_PACKAGES="man git-core libxslt-dev libxml2-dev"
function main {
provision-vagrant-system
provision-vagrant-pg
provision-vagrant-redis
provision-vagrant-rvm
provision-vagrant-node
provision-vagrant-nginx
provision-extras
finished
reboot-system
}
main
|
unspace/un-uploader-demo
|
server/propro/dist/vagrant.sh
|
Shell
|
gpl-2.0
| 23,787 |
#!/bin/sh
module="cdata"
device="cdata"
module2="cdata_plat_dev"
device2="cdata_plat_dev"
# invoke rmmod with all arguments we got
/sbin/rmmod $module $* || exit 1
/sbin/rmmod $module2 $* || exit 1
# Remove stale nodes
rm -f /dev/${device} /dev/${device}
|
hugh712/my_driver_study
|
009_kobject_2/unload.sh
|
Shell
|
gpl-2.0
| 261 |
#! /bin/sh
#
# Copyright (C) 2011 Texas Instruments Incorporated - http://www.ti.com/
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation version 2.
#
# This program is distributed "as is" WITHOUT ANY WARRANTY of any
# kind, whether express or implied; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# Search for HID event number
source "common.sh"
source "st_log.sh"
############################# Functions #######################################
############################### CLI Params ###################################
############################ DEFAULT Params #######################
############# Do the work ###########################################
HID_Get_Event()
{
device=$1
events=`ls -d $device/input/input*`
for event in $events
do
inputevent=`basename "$event" | cut -c6-7`
echo INPUT event is $hidevent
done
events=`ls -d $device/input/input$inputevent/event*`
for event in $events
do
hidevent=`basename "$event" | cut -c6-7`
echo HID event is $hidevent
done
}
|
rogerq/ltp-ddt
|
testcases/ddt/scripts/usb/usb_HID_get_event.sh
|
Shell
|
gpl-2.0
| 1,228 |
#!/bin/bash
# this is the entry point to the docker container, and is only used there
set -e
export PATH=$PATH:/usr/local/bin/:/usr/local/sbin/
if [ $# -eq 0 ]; then
echo "No arguments provided: specify either 'pktvisor-cli', 'pktvisor-pcap' or 'pktvisord'. Try:"
echo "docker run ns1labs/pktvisor pktvisor-cli -h"
echo "docker run ns1labs/pktvisor pktvisor-pcap --help"
echo "docker run ns1labs/pktvisor pktvisord --help"
exit 1
fi
# backwards compatibility
BINARY="$1"
if [ "$BINARY" = 'pktvisor' ]; then
BINARY='pktvisor-cli'
fi
# Add sleep to allow tty to be ready for Docker when using -it
if [ "$BINARY" = 'pktvisor-cli' ]; then
sleep 1
fi
shift
exec "$BINARY" "$@"
|
nsone/pktvisor
|
docker/entry.sh
|
Shell
|
gpl-2.0
| 691 |
#!/bin/sh
# default variables
fname=rec
# set file name
if [ $# -ge 1 ] ; then
fname=$1
fi
# create fifo
rm -f /tmp/$fname.fifo
mkfifo /tmp/$fname.fifo
# spwan raw
sox -t raw -r 22050 -s -w - -t raw /tmp/$fname.raw </tmp/$fname.fifo 3>/tmp/$fname.fifo &
# remember process id for killing
pid=$!
# trap exit signal
trap 'kill $pid ; rm -f /tmp/$fname.fifo ; exit' TERM INT
# waiting to signal
while true; do
sleep 1
done
|
tiv-source/qtpcr
|
examples/raw.sh
|
Shell
|
gpl-2.0
| 432 |
#!/bin/bash
# run with command line argument:
# $1 <- host, e.g., 127.0.0.1
# $2 <- keyspace, e.g., demo
# $3 <- file, e.g., 2012_medicare_thousand_data.csv
javac -cp ".:./jars/*" Transform.java
java -cp ".:./jars/*" Transform $1 $2 $3
|
ZheyuJin/CS8674.FALL2015.NEUSeattle
|
cassandra/cass_tabulate.sh
|
Shell
|
gpl-2.0
| 237 |
chmod 777 wpa_supplicant
interface=`ifconfig -a | grep "00:23:A7" | cut -f1 -d ' '`
if [ "$1" == "" ]; then
./wpa_supplicant -i$interface -Drsi -c wifi_settings.cfg
else
./wpa_supplicant -i$interface -Drsi -c $1 -dd
fi
|
ptdropper/linux-2.6.34.12
|
drivers/net/wireless/ganges/RS.GENR.LNX.SD_GPL/OSD/LINUX/release/supp.sh
|
Shell
|
gpl-2.0
| 221 |
#!/sbin/sh
#
# /system/addon.d/70-gapps.sh
#
. /tmp/backuptool.functions
list_files() {
cat <<EOF
app/YouTube.apk
EOF
}
case "$1" in
backup)
list_files | while read FILE DUMMY; do
backup_file $S/$FILE
done
;;
restore)
list_files | while read FILE REPLACEMENT; do
R=""
[ -n "$REPLACEMENT" ] && R="$S/$REPLACEMENT"
[ -f "$C/$S/$FILE" ] && restore_file $S/$FILE $R
done
;;
pre-backup)
# Stub
;;
post-backup)
# Stub
;;
pre-restore)
# Stub
;;
post-restore)
# Stub
;;
esac
|
dotmaniac/famigo_gapps
|
gapps/Other/YouTube/addon.d/70-youtube.sh
|
Shell
|
gpl-2.0
| 544 |
#!/bin/bash
# Add modules to an LZMA compressed initramfs
# Copyright (C) 2007-2010 Daniel Collins <[email protected]>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
tmp="addmod.tmp"
initramfs=""
abort() {
if [ $# -eq "1" ]
then
echo "$1" 1>&2
fi
rm -rf "$tmp"
exit 1
}
cprog() {
if which "$1" > /dev/null; then
return 0
fi
abort "No executable '$1' program found in \$PATH"
}
if [ $# -lt 2 ]; then
abort "Usage: $0 <initramfs> <module> [<module> ...]"
fi
cprog tar
cprog lzcat
cprog find
cprog cpio
cprog lzma
rm -rf "$tmp"
mkdir -p "$tmp/modules/"
for mod in "$@"
do
if [ -z "$initramfs" ]
then
initramfs="$mod"
else
is_ko=`echo "$mod" | grep -E '\.ko$'`
is_tar=`echo "$mod" | grep -E '\.(tar(\.(gz|bz2))?|tgz)$'`
is_tlz=`echo "$mod" | grep -E '\.(tar\.lzma|tlz)$'`
if [ -n "$is_ko" ]
then
cp "$mod" "$tmp/modules/" || abort
fi
if [ -n "$is_tar" ]
then
tar -xf "$mod" -C "$tmp/modules/" || abort
fi
if [ -n "$is_tlz" ]
then
# TAR is really stupid
tar --lzma -xf "$mod" -C "$tmp/modules/" || abort
fi
if [ -z "$is_ko" -a -z "$is_tar" -a -z "$is_tlz" ]
then
abort "Unknown file extension: $mod"
fi
fi
done
lzcat -S "" "$initramfs" > "$tmp/initramfs.cpio" || abort
for f in `cpio -it --quiet < "$tmp/initramfs.cpio" | egrep '^modules\/.+'`
do
rm -f "$tmp/$f"
done
bash -c "cd \"$tmp\" && find modules -iname '*.ko' | cpio -o --format=newc --quiet --append -F initramfs.cpio" || abort
lzma -9 "$tmp/initramfs.cpio" -c > "$initramfs" || abort
rm -rf "$tmp"
|
solemnwarning/kexec-loader
|
addmod.sh
|
Shell
|
gpl-2.0
| 2,219 |
export PATH=/bin:/sbin:/usr/bin:/usr/sbin;
sleep 600
logger 'SCIFI - Starting Snmpd'
/etc/init.d/snmpd start
|
Sci-Fi/el-scifi
|
modules/SCIFIAPI/12/init_snmpd.sh
|
Shell
|
gpl-2.0
| 109 |
#!/bin/bash
echo BB-ADC > /sys/devices/bone_capemgr.*/slots
|
beaverb1ll/SeniorDesign_MPPTC
|
systemd/enable-BBB-ADC.sh
|
Shell
|
gpl-2.0
| 59 |
#!/bin/bash
memTotal_b=`free -b |grep Mem |awk '{print $2}'`
memFree_b=`free -b |grep Mem |awk '{print $4}'`
memBuffer_b=`free -b |grep Mem |awk '{print $6}'`
memCache_b=`free -b |grep Mem |awk '{print $7}'`
memTotal_m=`free -m |grep Mem |awk '{print $2}'`
memFree_m=`free -m |grep Mem |awk '{print $4}'`
memBuffer_m=`free -m |grep Mem |awk '{print $6}'`
memCache_m=`free -m |grep Mem |awk '{print $7}'`
CPUPer=`top -b -n1 | grep "Cpu(s)" | awk '{print $2 + $4}'`
hdd=`df -lh | awk '{if ($6 == "/") { print $5 }}' | head -1 | cut -d'%' -f1`
uptime=`uptime`
ProcessCnt=`ps -A | wc -l`
memUsed_b=$(($memTotal_b-$memFree_b-$memBuffer_b-$memCache_b))
memUsed_m=$(($memTotal_m-$memFree_m-$memBuffer_m-$memCache_m))
memUsedPrc=$((($memUsed_b*100)/$memTotal_b))
echo "✅Memory : $memTotal_m MB"
echo "➖➖➖➖➖🎗"
echo "✅Used : $memUsed_m MB - $memUsedPrc% used!"
echo "➖➖➖➖➖🎗"
echo "✅Total : $memTotal_b"
echo "➖➖➖➖➖🎗"
echo '✅CPU Usage : '"$CPUPer"'%'
echo "➖➖➖➖➖🎗"
echo '✅Hdd : '"$hdd"'%'
echo "➖➖➖➖➖🎗"
echo '✅Processes : '"$ProcessCnt"
echo "➖➖➖➖➖🎗"
echo '✅Uptime : '"$uptime"
echo "➖➖➖➖➖🎗"
echo "🌐 BOOM🎗BOOM 🌐"
|
cracker1375/Boom
|
data/cmd.sh
|
Shell
|
gpl-2.0
| 1,221 |
cd ~/Paparazzi/conf
svn status | grep ^\! | cut -c8- | xargs svn rm
svn status | grep ^\? | cut -c8- | xargs svn add
cd ~/Paparazzi/sw
svn status | grep ^\! | cut -c8- | xargs svn rm
svn status | grep ^\? | cut -c8- | xargs svn add
cd ~/Paparazzi/data/maps
svn status | grep ^\! | cut -c8- | xargs svn rm
svn status | grep ^\? | cut -c8- | xargs svn add
cd ~/Paparazzi/var/logs
svn status | grep ^\! | cut -c8- | xargs svn rm
svn status | grep ^\? | cut -c8- | xargs svn add
svn ci
|
bstark2/AggieAir_MESA
|
Commit.sh
|
Shell
|
gpl-2.0
| 483 |
#!/bin/sh
chmod 755 src/main/resources/insecureCmd.sh
mvn clean package cargo:run -Pdeploy -Drunenv=remote
|
h3xstream/Benchmark
|
runRemoteAccessibleBenchmark.sh
|
Shell
|
gpl-2.0
| 107 |
#!/bin/bash
############################################################################################
#
# Per_sample_raw_reads.sh
#
# Script for creating raw Read 1 and Read 2 files for each individual sample of a 16S
# This script take a users QIIME mapping file, the demultiplexed sequences file and the two raw read files as arguments.
# A time-stamped log file of all steps that are conducted is created.
# This file also shows input file MD5 checksums as well as MD5 checksums for all output files.
#
# TODO: Figure out a better way to filter in parallel, prob best done w/in the fastq_filter.py script to remove gnu parallel dependency.
# Incorporate command line arguments using getopt flags instead of placement.
# Allow for optional output directory to be specified instead of CWD.
#
# Created by Michael C. Nelson on 2014-09-09.
# Last revised: 2015-06-23
# Revision #: 7
# Copyright 2014 Michael C. Nelson and the University of Connecticut. All rights reserved.
#
# This script is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
############################################################################################
# Define intitial variables
DATE=`date +%Y-%m-%d`
TIME=`date +%H:%M`
TM=`date +%Y%m%d-%H%M`
LOG=Log_$TM.txt
MAP2=MAP_$TM.txt
#Create log file
echo "Script executed on $DATE at $TIME using the command call: Per_sample_raw_reads.sh $*" | tee $LOG
echo ''
# Initiail sanity checking for script operation
# Are the correct number of arguments given?
if [ "$1" = "" ]; then
echo '' | tee -a $LOG
echo 'ERROR: No arguments were passed to script.' | tee -a $LOG
echo 'USAGE: Per_sample_raw_reads.sh Map.txt seqs.fna Undetermined_R1.fastq.gz Undetermined_R2.fastq.gz' | tee -a $LOG
echo '' | tee -a $LOG
exit 1
elif [ "$(($# % 4))" != 0 ]; then
echo '' | tee -a $LOG
echo 'ERROR: Invalid number of arguments given.' | tee -a $LOG
echo 'USAGE: Per_sample_raw_reads.sh Map.txt seqs.fna Undetermined_R1.fastq.gz Undetermined_R2.fastq.gz' | tee -a $LOG
echo '' | tee -a $LOG
exit 1
fi
# Can the required input files be found?
if [ ! -f $MAP ] && [ ! -f $seqsfna ] && [ ! -f $READ1 ] && [ ! -f $READ2 ]; then
echo '' | tee -a $LOG
echo 'ERROR: Required input files could not be found.' | tee -a $LOG
echo 'Script must be executed in the directory containing the Undertermined Read 1, Read 2, and Index files.' | tee -a $LOG
echo 'USAGE: Per_sample_raw_reads.sh Map.txt seqs.fna Undetermined_R1.fastq.gz Undetermined_R2.fastq.gz' | tee -a $LOG
echo '' | tee -a $LOG
exit 1
else
MAP=$1
MD5MAP=`md5sum $1`
seqsfna=$2
MD5SEQS=`md5sum $2`
READ1=$3
MD5READ1=`md5sum $3`
READ2=$4
MD5READ2=`md5sum $4`
echo '' | tee -a $LOG
echo "Using $MAP as the input mapping file." | tee -a $LOG
echo $MD5MAP| tee -a $LOG
# Changing any carriage returns to newlines in the mapping file... so above is a slight lie
tr '\r' '\n' <$MAP>$MAP2
echo "Using $seqsfna as the input seqs.fna file." | tee -a $LOG
echo $MD5SEQS | tee -a $LOG
echo "Using $READ1 as the raw Read 1 file." | tee -a $LOG
echo $MD5READ1 | tee -a $LOG
echo "Using $READ2 as the raw Read 2 file." | tee -a $LOG
echo $MD5READ2 | tee -a $LOG
fi
# Check to see if GNU parallel is installed.
if hash parallel 2>/dev/null; then
SMP=TRUE
fi
# Step 1: Parse out the raw read files for each sample
line=1 # We start with line 1
total=`grep -c '^' $MAP2` # Determine how many lines are actually in the file (safer than wc -l if map doesn't have a final newline character)
(( samples = $total - 1 )) # Total number of samples should be num lines minus header line
echo '' | tee -a $LOG
echo "There are $samples samples in your mapfile." | tee -a $LOG
echo '' | tee -a $LOG
DATE=`date +%Y-%m-%d`
TIME=`date +%H:%M`
echo "$DATE $TIME: Proceeding to demultiplex the raw reads into per-sample R1 and R2 files." | tee -a $LOG
while [ $line -lt $total ] # While the current line number is less than the total number of sample lines,
do # Do the following actions
DATE=`date +%Y-%m-%d` # Reset Date
TIME=`date +%H:%M` # Reset Time
printf "$DATE $TIME " | tee -a $LOG # Print time stamp so user can track progress rate
printf "Sample: $line " | tee -a $LOG # First we'll print the current sample number
(( line++ )) # Now we need to increase the line count to dissociate from the header line
sampleID=`sed -n "$line{p;q;}" $MAP2 | cut -f1,1` # Now we find out what the sample ID is
names=$sampleID.txt # Set an output file for the read names based on the sample ID
names2=$sampleID'2.txt' # Create name of second names file in case we're running in parallel mode
searchID=$sampleID\_ # Set the search pattern, which is the sample ID
printf "$sampleID " | tee -a $LOG # Print what the name of the names file is for each sample
touch $names # Create the output file as empty
count=`grep -c $searchID $seqsfna` # Check to see how many reads are in seqs.fna
echo "$count seqs" | tee -a $LOG # Print out how many sequences are present for the sample
grep $searchID $seqsfna | tr -d '>' | cut -d\ -f2,2 > $names # Compile the list of SeqIDs for dual_fastq_filter command
RAW1=$sampleID"_R1.fastq.gz" # Define the Read1 output file
RAW2=$sampleID"_R2.fastq.gz" # Define the Read2 output file
dual_fastq_filter.py -f $READ1 -r $READ2 -o $RAW1 -p $RAW2 -n $names # Filter out the raw read1/read2 to gzipped files
rm $names # We no longer need the names file so let's get rid of it
done
# Cleanup phase: step 1, re-zip the input files to again save file space and delete the "cleaned" map file.
DATE=`date +%Y-%m-%d`
TIME=`date +%H:%M`
echo '' | tee -a $LOG
echo "$DATE $TIME: Finished parsing out the raw Read1/Read2 files for each sample."
rm $MAP2
# Step 2, calculate md5 checksums for all of the raw read files. These are needed for SRA submissions and also just nice to have.
echo '' | tee -a $LOG
DATE=`date +%Y-%m-%d`
TIME=`date +%H:%M`
echo "$DATE $TIME: Calculating md5 checksum values for all sample files." | tee -a $LOG
md5sum *_R1.fastq.gz | tee -a $LOG | tee md5sums.txt # This could be done in parallel, but, eh.
md5sum *_R2.fastq.gz | tee -a $LOG | tee -a md5sums.txt # Note that if the files are decompressed and then recompressed using a different method
# (e.g. pigz) then the MD5 values will change.
DATE=`date +%Y-%m-%d`
TIME=`date +%H:%M`
echo '' | tee -a $LOG
echo '' | tee -a $LOG
echo "$DATE $TIME: Script is now finished." | tee -a $LOG
echo "Each sample should have a gzip compressed R1 and R2 read file that you will need to upload to the SRA." | tee -a $LOG
echo "md5 checksum values have been calculated for these files and can be found in the md5sums.txt file." | tee -a $LOG
|
mcnelsonphd/misc_scripts
|
Per_Sample_Raw_Reads.sh
|
Shell
|
gpl-2.0
| 8,512 |
#!/bin/sh
test_description='git rev-list --pretty=format test'
. ./test-lib.sh
test_tick
test_expect_success 'setup' '
touch foo && git add foo && git-commit -m "added foo" &&
echo changed >foo && git-commit -a -m "changed foo"
'
# usage: test_format name format_string <expected_output
test_format() {
cat >expect.$1
test_expect_success "format $1" "
git rev-list --pretty=format:$2 master >output.$1 &&
git diff expect.$1 output.$1
"
}
test_format hash %H%n%h <<'EOF'
commit 131a310eb913d107dd3c09a65d1651175898735d
131a310eb913d107dd3c09a65d1651175898735d
131a310
commit 86c75cfd708a0e5868dc876ed5b8bb66c80b4873
86c75cfd708a0e5868dc876ed5b8bb66c80b4873
86c75cf
EOF
test_format tree %T%n%t <<'EOF'
commit 131a310eb913d107dd3c09a65d1651175898735d
fe722612f26da5064c32ca3843aa154bdb0b08a0
fe72261
commit 86c75cfd708a0e5868dc876ed5b8bb66c80b4873
4d5fcadc293a348e88f777dc0920f11e7d71441c
4d5fcad
EOF
test_format parents %P%n%p <<'EOF'
commit 131a310eb913d107dd3c09a65d1651175898735d
86c75cfd708a0e5868dc876ed5b8bb66c80b4873
86c75cf
commit 86c75cfd708a0e5868dc876ed5b8bb66c80b4873
EOF
# we don't test relative here
test_format author %an%n%ae%n%ad%n%aD%n%at <<'EOF'
commit 131a310eb913d107dd3c09a65d1651175898735d
A U Thor
[email protected]
Thu Apr 7 15:13:13 2005 -0700
Thu, 7 Apr 2005 15:13:13 -0700
1112911993
commit 86c75cfd708a0e5868dc876ed5b8bb66c80b4873
A U Thor
[email protected]
Thu Apr 7 15:13:13 2005 -0700
Thu, 7 Apr 2005 15:13:13 -0700
1112911993
EOF
test_format committer %cn%n%ce%n%cd%n%cD%n%ct <<'EOF'
commit 131a310eb913d107dd3c09a65d1651175898735d
C O Mitter
[email protected]
Thu Apr 7 15:13:13 2005 -0700
Thu, 7 Apr 2005 15:13:13 -0700
1112911993
commit 86c75cfd708a0e5868dc876ed5b8bb66c80b4873
C O Mitter
[email protected]
Thu Apr 7 15:13:13 2005 -0700
Thu, 7 Apr 2005 15:13:13 -0700
1112911993
EOF
test_format encoding %e <<'EOF'
commit 131a310eb913d107dd3c09a65d1651175898735d
commit 86c75cfd708a0e5868dc876ed5b8bb66c80b4873
EOF
test_format subject %s <<'EOF'
commit 131a310eb913d107dd3c09a65d1651175898735d
changed foo
commit 86c75cfd708a0e5868dc876ed5b8bb66c80b4873
added foo
EOF
test_format body %b <<'EOF'
commit 131a310eb913d107dd3c09a65d1651175898735d
commit 86c75cfd708a0e5868dc876ed5b8bb66c80b4873
EOF
test_format colors %Credfoo%Cgreenbar%Cbluebaz%Cresetxyzzy <<'EOF'
commit 131a310eb913d107dd3c09a65d1651175898735d
[31mfoo[32mbar[34mbaz[mxyzzy
commit 86c75cfd708a0e5868dc876ed5b8bb66c80b4873
[31mfoo[32mbar[34mbaz[mxyzzy
EOF
cat >commit-msg <<'EOF'
Test printing of complex bodies
This commit message is much longer than the others,
and it will be encoded in iso8859-1. We should therefore
include an iso8859 character: ¡bueno!
EOF
test_expect_success 'setup complex body' '
git config i18n.commitencoding iso8859-1 &&
echo change2 >foo && git-commit -a -F commit-msg
'
test_format complex-encoding %e <<'EOF'
commit f58db70b055c5718631e5c61528b28b12090cdea
iso8859-1
commit 131a310eb913d107dd3c09a65d1651175898735d
commit 86c75cfd708a0e5868dc876ed5b8bb66c80b4873
EOF
test_format complex-subject %s <<'EOF'
commit f58db70b055c5718631e5c61528b28b12090cdea
Test printing of complex bodies
commit 131a310eb913d107dd3c09a65d1651175898735d
changed foo
commit 86c75cfd708a0e5868dc876ed5b8bb66c80b4873
added foo
EOF
test_format complex-body %b <<'EOF'
commit f58db70b055c5718631e5c61528b28b12090cdea
This commit message is much longer than the others,
and it will be encoded in iso8859-1. We should therefore
include an iso8859 character: ¡bueno!
commit 131a310eb913d107dd3c09a65d1651175898735d
commit 86c75cfd708a0e5868dc876ed5b8bb66c80b4873
EOF
test_expect_success 'empty email' '
test_tick &&
C=$(GIT_AUTHOR_EMAIL= git commit-tree HEAD^{tree} </dev/null) &&
A=$(git show --pretty=format:%an,%ae,%ad%n -s $C) &&
test "$A" = "A U Thor,,Thu Apr 7 15:14:13 2005 -0700" || {
echo "Eh? $A" >failure
false
}
'
test_done
|
xlymian/git
|
t/t6006-rev-list-format.sh
|
Shell
|
gpl-2.0
| 3,897 |
rsync -r doc/html/ [email protected]:public_html/bsp/
(cd ..; rsync -r doc/html/ [email protected]:public_html/quake2/)
ssh [email protected] 'cd public_html/bsp/; ./installdox -l Q2DOXYTAGS@../quake2'
|
lambda/wxQuake2
|
bsptools/upload.sh
|
Shell
|
gpl-2.0
| 220 |
#!/bin/sh
KEYFILE=/home/root/privatekey.pem
PUBKEY=/home/root/pubkey.pem
OPENSSL=/usr/bin/openssl
CERGEN=/usr/bin/Certificate_gen
PUBKEYGEN=/usr/bin/Gen_publickey
echo -e "\nGenerating Public Key from ${KEYFILE}"
if [ ! -r $KEYFILE ]
then
echo "Private Key does not exist. Generate certificate before generating a public key"
$CERGEN
fi
$PUBKEYGEN
echo -e "\nPublic Key written to ${PUBKEY}\n"
|
houlixin/BBB-TISDK
|
example-applications/ti-crypto-examples-git/Gen_public_key/openssl_gen_pubkey.sh
|
Shell
|
gpl-2.0
| 407 |
#!/bin/bash
yum install -y gcc gcc-c++ tcl perl readline-devel pcre-devel openssl-devel
groupadd nginx
useradd -g nginx nignx
wget http://openresty.org/download/ngx_openresty-1.5.11.1.tar.gz
tar xzf ngx_openresty-1.5.11.1.tar.gz
cd ngx_openresty-1.5.11.1
./configure --prefix=/opt/openresty-1.5.11.1 --with-luajit --with-http_iconv_module --pid-path=/var/run/nginx.pid --lock-path=/var/run/nginx.lock --user=nginx --group=nginx --conf-path=/home/nginx/conf/nginx.conf --error-log-path=/home/nginx/logs/error.log --http-log-path=/home/nginx/logs/access.log
gmake && gmake install
|
JianfuLi/shell_scripts
|
centos_openresty_install.sh
|
Shell
|
gpl-2.0
| 581 |
#!/bin/sh
old_tty_settings=$(stty -g)
stty -icanon
trap 'stty "$old_tty_settings"; exit 0' INT
echo "Press (CTRL-C) to interrupt..."
while true; do
nc -u localhost 6789
done
|
acerion/cwdaemon
|
examples/example.sh
|
Shell
|
gpl-2.0
| 180 |
#!/bin/sh
set -o errexit
pmount /dev/sdb1
cp uboot_update_tool/iptvubootupdate.bin /media/sdb1
pumount /dev/sdb1
|
dlintw/twpda-uboot
|
to_usb.sh
|
Shell
|
gpl-2.0
| 113 |
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