code stringlengths 1 1.96M | language stringclasses 1
value |
|---|---|
#!/bin/sh
#
# Detects OS we're compiling on and outputs a file specified by the first
# argument, which in turn gets read while processing Makefile.
#
# The output will set the following variables:
# CC C Compiler path
# CXX C++ Compiler path
# PLATFORM_LDFLAGS ... | Shell |
rm -rf build dist
py2applet --make-setup Zyne.py Resources/*
python setup.py py2app --plist=scripts/Info.plist
rm -f setup.py
rm -rf build
mv dist zyne_0.1.2
if cd zyne_0.1.2;
then
find . -name .svn -depth -exec rm -rf {} \;
find . -name *.pyc -depth -exec rm -f {} \;
find . -name .* -depth -exec rm -f {} \... | Shell |
#!/bin/sh
path=`pwd`
sdir=$(cd "$(dirname "$0")"; pwd)
php ${sdir}/../commands/cli/chili.php $path $*
| Shell |
#!/bin/sh
path=`pwd`
sdir=$(cd "$(dirname "$0")"; pwd)
php ${sdir}/../commands/cli/chili.php $path $*
| Shell |
#!/sbin/runscript
#//************************************//
#//** Developed by ZX Team **//
#//** Web: http://www.zxteam.net **//
#//** E-Mail: dev@zxteam.net **//
#//************************************//
#//** Developer Maxim Anurin **//
#//** Web: http://www.anurin.name **//
#//** E-... | Shell |
#!/bin/bash
SCRIPT_NAME=$(basename $(readlink -f $0))
SCRIPT_DIR=$(dirname $(readlink -f $0))
function cleanup() {
echo "Cleanup..."
[ -n "$PID" ] && kill $PID 2> /dev/null
echo "Kill all children of PID: $$"
pkill -TERM -P $$
exit 1
}
trap cleanup EXIT
function usage {
echo "This script moves snapshot f... | Shell |
#!/bin/bash
SCRIPT_NAME=$(basename $(readlink -f $0))
SCRIPT_DIR=$(dirname $(readlink -f $0))
function cleanup() {
echo "Cleanup..."
[ -n "$PID" ] && kill $PID 2> /dev/null
echo "Kill all children of PID: $$"
pkill -TERM -P $$
exit 1
}
trap cleanup EXIT
function usage {
echo "This script moves snapshot f... | Shell |
#!/bin/bash
# /* zxbackup-create-local-snapshot */
# /* zxbackup-manager-create-remote-snapshot */
# /* zxbackup-manager-download-remote-snapshots */
# /* zxbackup-manager-update-delta */
# /* */
# /* */
# /* */
# /* */
# /* */
# /* */
SCRIPT_NAME=$(basename $(readlink -f $0))
SCRIPT_ACTION=$(basename $0)
SCRIPT_DIR=... | Shell |
#!/bin/bash
# /* zxbackup-create-local-snapshot */
# /* zxbackup-manager-create-remote-snapshot */
# /* zxbackup-manager-download-remote-snapshots */
# /* zxbackup-manager-update-delta */
# /* */
# /* */
# /* */
# /* */
# /* */
# /* */
SCRIPT_NAME=$(basename $(readlink -f $0))
SCRIPT_ACTION=$(basename $0)
SCRIPT_DIR=... | Shell |
#!/sbin/runscript
# Copyright (c) 2014 Max Anurin <theanurin@gmail.com>
#
INSTANCE=${SVCNAME#*.}
if [ -n "${INSTANCE}" ] && [ ${INSTANCE} != "imagemount" ]; then
RUNDIR=/var/run/imagemount.$INSTANCE
else
RUNDIR=/var/run/imagemount
fi
USEDLOOPFILE=${RUNDIR}/loop
USEDVGFILE=${RUNDIR}/vg
USEDMOUNTFILE=${RUNDIR}/mount... | Shell |
#!/sbin/runscript
# Copyright (c) 2014 Max Anurin <theanurin@gmail.com>
#
INSTANCE=${SVCNAME#*.}
if [ -n "${INSTANCE}" ] && [ ${INSTANCE} != "imagemount" ]; then
RUNDIR=/var/run/imagemount.$INSTANCE
else
RUNDIR=/var/run/imagemount
fi
USEDLOOPFILE=${RUNDIR}/loop
USEDVGFILE=${RUNDIR}/vg
USEDMOUNTFILE=${RUNDIR}/mount... | Shell |
#!/sbin/runscript
# Copyright (c) 2012 Max Anurin <theanurin@gmail.com>
#
# Not sure why but gentoo forgot to add /opt/bin to the path.
VBOXPATH="/usr/bin:/opt/bin"
VBOXNAME="${SVCNAME#*.}"
depend() {
need net
if [ "${SVCNAME}" != "virtualbox" ] ; then
need virtualbox
fi
}
c... | Shell |
cp ./third_party/bin/protoc ./tools/protobuf
cp ./third_party/lib/*.a ./lib
| Shell |
#!/bin/bash
LOG_MYSQL_USER="yw"
LOG_MYSQL_PWD="yw"
LOG_SERVER_USER="zybzhao"
LOG_SERVER_PWD="rWgCT#7Y"
LOCALSVR="zybzhao@172.25.42.74"
LOCALPASSMY="zyb"
HOSTFILE='host.xml'
EXEC_EXPECT_SSH_COMMON="set timeout 60000; expect \"*assword:*\" { send \"${LOG_SERVER_PWD}\\r\" } \"yes/no\" { send \"yes\\r\"; expect \"*assw... | Shell |
#!/bin/bash
LOG_MYSQL_USER="yw"
LOG_MYSQL_PWD="yw"
LOG_SERVER_USER="zybzhao"
LOG_SERVER_PWD="rWgCT#7Y"
LOCALSVR="zybzhao@172.25.42.74"
LOCALPASSMY="zyb"
HOSTFILE='host.xml'
EXEC_EXPECT_SSH_COMMON="set timeout 60000; expect \"*assword:*\" { send \"${LOG_SERVER_PWD}\\r\" } \"yes/no\" { send \"yes\\r\"; expect \"*assw... | Shell |
gdb
echo 100
| Shell |
#!/bin/sh
# After initial checkout from svn, you'll want to run this as your first step.
android update project --path . --target "android-11"
| Shell |
#!/bin/sh
scp -q res/values/strings.xml linode:ath/incoming/en.xml
wget --quiet -O /dev/null --ignore-length --post-data="" http://ath.darshancomputing.com/bi/load_new_en
if [ "$?" -ne "0" ]; then
echo "Sorry, something didn't work!"
exit 1
fi
| Shell |
#!/bin/bash
#ruby generate_images.rb
#for i in res/drawable/b[0-9]*.png; do mogrify -resize 25x25 $i; done
#gimp res/drawable/b100.png
#for i in res/drawable/*.png; do mogrify -sharpen 25x25 $i; done
# shift ("roll") images 1px to the right
# for i in numbers/*.png; do convert $i -roll +1+0 $i; done
d=`dirname $(rea... | Shell |
#!/bin/bash
#
# This script checks the java version and bails if it's less
# than Java6 (because we use @Override annotations on interface
# overriding methods. It then proceeds to do a maven build that
# first cleans, then builds the normal lifecycle through compilation
# unit testing (if available) up to packaging. ... | Shell |
#!/bin/bash
#
# Copyright 2010 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | Shell |
#!/bin/bash
# 打开apache.http调试信息
adb shell setprop log.tag.org.apache.http VERBOSE
adb shell setprop log.tag.org.apache.http.wire VERBOSE
adb shell setprop log.tag.org.apache.http.headers VERBOSE
echo "Enable Debug"
| Shell |
source ../testsupport.sh
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f test.txt.hello ] && err "Failed to find expected output test.txt"
[ ! -f test.txt.hello.world ] && err "Failed to find e... | Shell |
rm -f test.txt.* null
| Shell |
source ../testsupport.sh
rm -f test.txt.*
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f test.txt.hello ] && err "Failed to find expected output test.txt"
[ ! -f test.txt.hello.world ] && err... | Shell |
source ../testsupport.sh
run test*.txt
[ `grep -c "Stage hello" test.out` == 3 ] || err "Failed to find expected stage hello 3 times"
[ ! -f test.chr1.hello.csv ] && err "Failed to find expected output test.chr1.hello.csv"
[ ! -f test.chr2.hello.csv ] && err "Failed to find expected output test.chr2.hello.csv"
[ ! ... | Shell |
rm -rf *.csv
| Shell |
source ../testsupport.sh
. ./cleanup.sh
run childdir/s_*.txt
grep -q "Stage dedupe" test.out || err "Failed to find expected stage dedupe"
grep -q "Stage align" test.out || err "Failed to find expected stage align"
[ ! -f s_1_1.align.csv ] && err "Failed to find expected output s_1_1.align.csv"
[ ! -f s_2_1.align.... | Shell |
rm -f *align* *.csv
| Shell |
source ../testsupport.sh
run *.bam
[ `grep -c "Using bam file test.chr1.bam" test.out` == 2 ] || err "Incorrect number of references to test.chr1.bam"
true
| Shell |
rm -f *.vcf *.txt
| Shell |
source ../testsupport.sh
rm -f test.txt.* *.xml hello.*
# Without an input should get a good message back
run
grep -q "Input expected but not provided" test.out || err "Expected error message asking for input"
# Now run with multiple inputs
run test.csv test.txt
grep -q "Stage hello" test.out || err "Failed to fin... | Shell |
source ../testsupport.sh
rm -f test.world.txt test.txt
run
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
grep -q "1 2 3 4" test.out || err "Failed to find expeced output '1 1 cow'"
true
| Shell |
source ../testsupport.sh
run test.txt
exists test.txt.hello
true
| Shell |
rm -f test.txt.*
| Shell |
source ../testsupport.sh
run test.fastq
exists test.align.bai
exists test.align.bam
exists test.align.filter_bam.bam
bpipe cleanup -y >> test.out
exists test.align.filter_bam.bam
# Should be cleaned up because it is an internal node
notexists test.align.bam
# Should be cleaned up because it accompanies an interna... | Shell |
rm -f .bpipe *.bai *.bam
| Shell |
source ../testsupport.sh
run
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
true
| Shell |
source ../testsupport.sh
rm foo.txt bar.txt foo.csv foo.txt.world
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f foo.txt.world ] && err "Failed to find expected output foo.txt.world"
sort ... | Shell |
rm -f foo.txt bar.txt foo.csv foo.txt.world null
| Shell |
source ../testsupport.sh
run test1.txt test2.txt
exists test1.merge.csv
true
| Shell |
rm -f *.merge.*
| Shell |
#!/bin/bash
# A very minimal test script
if [ "$1" == "start" ];
then
#echo "Starting $*"
echo "$COMMAND" >> dummy2.log.txt
bash -c "if $COMMAND ; then echo 0 > $$.txt ; else echo 1 > $$.txt; fi" &
PROCID=$!
echo $PROCID
echo $$ > $PROCID.id.txt
elif [ "$1" == "status" ];
then
SHELL_PROC_ID=`cat $2.id.tx... | Shell |
#!/bin/bash
# A very minimal test script
if [ "$1" == "start" ];
then
#echo "Starting $*"
echo "$COMMAND" >> dummy1.log.txt
bash -c "if $COMMAND ; then echo 0 > $$.txt ; else echo 1 > $$.txt; fi" &
PROCID=$!
echo $PROCID
echo $$ > $PROCID.id.txt
elif [ "$1" == "status" ];
then
SHELL_PROC_ID=`cat $2.id.tx... | Shell |
#!/bin/bash
# A very minimal test script
if [ "$1" == "start" ];
then
#echo "Starting $*"
echo "$COMMAND" >> dummy3.log.txt
bash -c "if $COMMAND ; then echo 0 > $$.txt ; else echo 1 > $$.txt; fi" &
PROCID=$!
echo $PROCID
echo $$ > $PROCID.id.txt
elif [ "$1" == "status" ];
then
SHELL_PROC_ID=`cat $2.id.tx... | Shell |
source ../testsupport.sh
./cleanup.sh
run
grep -q "Stage init" test.out || err "Failed to find expected stage init"
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage there" test.out || err "Failed to find expected stage there"
grep -q "Stage world" test.out || err "Failed to ... | Shell |
ls | grep '[0-9].*.txt' | xargs rm -f
rm -f dummy*.log.txt
| Shell |
source ../testsupport.sh
run s_*.txt
grep -q "INPUTS: s_2_ignore_b_1.txt s_2_ignore_b_2.txt" test.out || err "Failed to find correct split group 2.b"
grep -q "INPUTS: s_1_ignore_b_1.txt s_1_ignore_b_2.txt" test.out || err "Failed to find correct split group 1.b"
grep -q "INPUTS: s_2_ignore_a_1.txt s_2_ignore_a_2.txt"... | Shell |
#!/bin/bash
# Clean up standard unwanted files
for i in .bpipe test.out commandlog.txt doc ;
do
find . -name "$i" | xargs rm -rf
done
# Run individual cleanup scripts
for i in `find . -name cleanup.sh`; do cd `dirname $i`; chmod uga+rx ./cleanup.sh; ./cleanup.sh; cd - > /dev/null 2>&1 ; done
| Shell |
source ../testsupport.sh
rm -f test.txt.*
rm -rf output
bpipe run -d output test.groovy test.txt > test.out 2>&1
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f output/test.txt.hello ] && err "Failed to ... | Shell |
source ../testsupport.sh
. ./cleanup.sh
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
[ ! -f test.hello.txt ] && err "Failed to find expected output test.hello.txt"
[ ! -f .bpipe/outputs/hello.test.hello.txt.properties ] && err "Failed to find expected output meta data fi... | Shell |
rm -f test.*.txt
| Shell |
source ../testsupport.sh
run test1.txt test1.csv test2.txt
exists test2.hello.xml
[ `cat test2.hello.xml | groovy -e 'print(System.in.readLines()[0..1] == ["2","3"])'` == true ] || err "Contents of output file test2.hello.xml didn't match expected"
true
| Shell |
rm -f *.xml
| Shell |
source ../testsupport.sh
run
grep -q "Stage child_stage" test.out || err "Failed to find expected stage child_stage"
true
| Shell |
source ../testsupport.sh
rm -rf doc
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage bar" test.out || err "Failed to find expected stage world"
grep -q "Stage fail" test.out || err "Failed to find expected stage world"
[ -e doc/index.html ] || err "Unable to fi... | Shell |
source ../testsupport.sh
run test.txt
[ ! -f test.chr1.csv ] && err "Failed to find expected output test.chr1.csv"
[ ! -f test.chr20.csv ] && err "Failed to find expected output test.chr20.csv"
[ ! -f test.chrX.csv ] && err "Failed to find expected output test.chrX.csv"
[ ! -f test.chr1.txt ] && err "Failed to find... | Shell |
rm -f test.*.csv test.*.txt *.hello.* test.txt.*;
| Shell |
source ../testsupport.sh
run
grep -q "foo = cat" test.out || err "Failed to find expected output foo = cat"
grep -q "foo = tree" test.out || err "Failed to find expected output foo = tree"
grep -q "foo = fubar" test.out || err "Failed to find expected output foo = fubar"
true
| Shell |
source ../testsupport.sh
rm -f test.world.txt test.txt
run
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f test.txt ] && err "Failed to find expected output test.txt"
[ ! -f test.world.txt ] && err "Failed... | Shell |
source ../testsupport.sh
rm -f *align* *foo*
run s_*.txt
grep -q "Stage dedupe" test.out || err "Failed to find expected stage dedupe"
grep -q "Stage align" test.out || err "Failed to find expected stage align"
[ ! -f s_2_1.txt.foo.align ] && err "Failed to find expected output s_2_1.txt.foo.align"
[ ! -f s_3_1.tx... | Shell |
source ../testsupport.sh
run input*.txt
#grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
#grep -q "Stage world" test.out || err "Failed to find expected stage world"
#grep -q "Stage world2" test.out || err "Failed to find expected stage world2"
#grep -q "Stage end" test.out || err "Failed ... | Shell |
rm -f *.hello *.hello.*
| Shell |
source ../testsupport.sh
run *.bed *.peak
exists s2_macs_sort.macs.intersect.bed s1_macs_sort.macs.intersect.bed
true
| Shell |
rm -f *.intersect.*
| Shell |
source ../testsupport.sh
. ./cleanup.sh
run s_1_1.txt s_1_2.txt s_2_1.txt s_2_2.txt
grep -q "Stage align" test.out || err "Failed to find expected stage align"
[ ! -f s_1_1.chr1.bam ] && err "Failed to find expected output s_1_1.align.txt"
true
| Shell |
rm -f *align* *.bam
| Shell |
source ../testsupport.sh
export BPIPE_LIB=./bpipelib
rm -f test.*.txt
run
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
grep -q "Stage jupiter" test.out || err "Failed to find expected stage jupiter"
grep -q "S... | Shell |
rm -f test.*.txt
| Shell |
source ../testsupport.sh
run test_*.txt test.csv
grep -q "inputs.txt: cat test_1.txt test_2.txt > test_1.txt.hello" test.out || err "Failed to find expected output 'inputs.txt: cat test_1.txt test_2.txt > test_1.txt.hello'"
grep -q "input.txt: cat test_1.txt > test_1.txt.hello" test.out || err "Failed to find expect... | Shell |
rm -f test_1.txt.hello
| Shell |
source ../testsupport.sh
rm -f test.world.txt test.txt
run
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f test.txt ] && err "Failed to find expected output test.txt"
[ ! -f test.world.txt ] && err "Failed... | Shell |
source ../testsupport.sh
run test.txt test2.txt test.csv
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "inputs: test.txt test2.txt test.csv" test.out || err "Failed to find expected output: inputs: test.txt test2.txt test.csv"
true
| Shell |
source ../testsupport.sh
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f mars.txt ] && err "Failed to find expected output mars.txt"
[ ! -f world.txt ] && err "Failed to find expected output wo... | Shell |
rm -f mars.txt world.txt foo.txt query.out
| Shell |
source ../testsupport.sh
bpipe run -n 10 test.groovy > test.out
exists hello hello2 hello3 hello4
# each one should have gotten 3 threads (10/3)
[ `cat hello` == 3 ] || echo "Wrong number of threads assigned to thread variable in multi statement"
[ `cat hello2` == 3 ] || echo "Wrong number of threads assigned to t... | Shell |
rm -f hello*
| Shell |
source ../testsupport.sh
run
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "world" test.out || err "Failed to find expected output world"
true
| Shell |
source ../testsupport.sh
# Should fail!
run test.txt
# Should clean up this file
notexists test.hello.csv
true
| Shell |
rm -f *.csv
| Shell |
source ../testsupport.sh
run test1.txt test2.txt
exists test1.foo.txt test2.foo.txt
true
| Shell |
rm -f *.foo.txt
| Shell |
source ../testsupport.sh
source ./cleanup.sh
run test.txt test2.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f test.hello.txt ] && err "Failed to find expected output test.hello.txt"
[ ! -f test.hello... | Shell |
rm -f test.hell*.txt
| Shell |
source ../testsupport.sh
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
grep -q "Stage world2" test.out || err "Failed to find expected stage world2"
grep -q "Stage end" test.out || err "Failed to fin... | Shell |
rm -f test.txt.*
| Shell |
source ../testsupport.sh
run test.txt
exists test.txt.hello test.txt.hello.there test.txt.hello.world
# The stage "there" shouldn't produce this output meta data because
# meta data for the same output was already produced by the previous stage
notexists .bpipe/outputs/there.test.txt.hello.properties
true
| Shell |
rm -rf .bpipe test.txt.*;
| Shell |
. ../testsupport.sh
. ./cleanup.sh
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q Skipping test.out && err "Found unexpected phrase Skipping steps"
# Running a second time should skip the stages
run test.txt
grep -q "Skipping steps" test.out || err "Failed to f... | Shell |
rm -f *.html *.xls *.csv *.xml
rm -f query.test.out
rm -rf .bpipe/outputs
| Shell |
source ../testsupport.sh
. ./cleanup.sh
../../bin/bpipe run -p foo=foooo -p bar=baaaar test.groovy > test.out
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
grep -q "Stage there" test.out || err "Failed to find e... | Shell |
rm -f test.world.txt test.there.txt test.txt
| Shell |
source ../testsupport.sh
run
grep -q "Command failed" test.out && err "Failed to execute bash command terminated with ampersands"
true
| Shell |
source ../testsupport.sh
BPIPE_LIB_OLD="$BPIPE_LIB"
export BPIPE_LIB=`pwd`/bpipes
uname -a | grep -i -q cygwin && {
export BPIPE_LIB=`cygpath -ma $BPIPE_LIB`
}
echo "Using BPIPE_LIB=$BPIPE_LIB"
rm -f test.world.txt test.txt
run
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -... | Shell |
rm -f test.f*
| Shell |
source ../testsupport.sh
. ./clean.sh
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f test.f1 ] && err "Failed to find expected output test.f1"
[ ! -f test.f2 ] && err "Failed to find expected... | Shell |
rm -f *align*
| Shell |
source ../testsupport.sh
rm -f *align*
run s_*.txt
grep -q "Stage dedupe" test.out || err "Failed to find expected stage dedupe"
grep -q "Stage align" test.out || err "Failed to find expected stage align"
grep -q "Stage compute_statistics" test.out || err "Failed to find expected stage compute_statistics"
[ ! -f s... | Shell |
source ../testsupport.sh
run test.txt test2.txt
# the world stage should create an output file from the CSV files created in hello stage
exists test.hello.world.txt
# Check that it really used BOTH CSV files created by the earlier nested stage
grep -q 'test.hello.csv test2.hello.csv' commandlog.txt || err "Failed to... | Shell |
rm -f *.xml *.csv test.*.txt
| Shell |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.