code stringlengths 1 1.96M | language stringclasses 1
value |
|---|---|
source ../testsupport.sh
. ./cleanup.sh
run
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
cat test.out | grep -o "Stage hello_." | sort | uniq -c > counts.txt
for c in a b c d e ;
do
grep -q "1 Stage hello_$c" counts.txt || err "Wrong counts for stage $c"
done
true
| Shell |
rm -f hello_*.txt
rm -f counts.txt
| Shell |
source ../testsupport.sh
run foo.txt bar.csv
exists bar.hello.xml
true
| Shell |
rm -f *.xml
| Shell |
source ../testsupport.sh
. cleanup.sh
export BPIPE_LIB=./lib
run
grep -q "Stage there" test.out || err "Failed to find expected stage there"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
grep -q "Stage buddy" test.out || err "Failed to find expected stage buddy"
grep -q "Stage foo" te... | Shell |
rm -f test.world.txt test.there.txt test.buddy.txt
| Shell |
source ../testsupport.sh
run s_1.txt
grep -q "foo = cat" test.out || err "Failed to find expected output foo = cat"
grep -q "foo = bar" test.out || err "Failed to find expected output foo = bar"
true
| Shell |
source ../testsupport.sh
run test.txt
exists test.txt.hello
[ `cat test.txt.hello` == foo ] || err "Incorrect contents in output file test.txt.hello"
true
| Shell |
rm -f hello
| Shell |
source ../testsupport.sh
source ./cleanup.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 end" test.out || err "Failed to find expected stage end"
[ ! -f test.txt.hello ] && err "Fa... | Shell |
rm -f test.txt.*
| Shell |
source ../testsupport.sh
run test.vcf test.bam
exists test.ma.bam
true
| Shell |
rm -f *.ma.*
| Shell |
source ../testsupport.sh
run test.txt
grep -q "Stage world" test.out || err "Failed to execute stage world"
exists test.txt.hello test1.world.xml test*.world.tsv
true
| Shell |
rm -rf test.txt.hello test1.csv test1.world.*
| Shell |
source ../testsupport.sh
run test.txt
exists test.hello.csv
exists test.hello.world.csv
true
| Shell |
rm -f *.csv *.hello
| Shell |
source ../testsupport.sh
run test.txt
exists test.txt.hello test.txt.csv
| Shell |
rm -f *.csv test.txt.*
| 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
rm -f *align*
run
grep -q "An input pattern was specified '.*' but no inputs were given when Bpipe was run" test.out || err "Failed to find expected error message"
true
| Shell |
source ../testsupport.sh
. ./cleanup.sh
run
grep -q "Stage there" test.out || err "Failed to find expected stage there"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
grep -q "Stage buddy" test.out || err "Failed to find expected stage buddy"
grep -q "Stage foo" test.out && err "Observe... | Shell |
rm -f test.world.txt test.there.txt test.buddy.txt
| Shell |
#!/bin/bash
TESTS=`find . -maxdepth 1 -type d | grep "[A-Za-z]"`
source testsupport.sh
succ=0
fail=0
failures=""
for t in $TESTS;
do
echo "============== $t ================"
cd "$BASE"/"$t"
rm -rf .bpipe
if ./run.sh;
then
echo
echo "SUCCEEDED"
echo
let 'succ=succ+1'
else
echo
echo "FAILED"
ec... | Shell |
source ../testsupport.sh
rm -f test.txt.* test.hello.* test.bar
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
run test.txt
grep -q "Skipping command" test.out || err "Failed to find stage being sk... | Shell |
rm -rf *.out *.csv *.xml test.*.txt doc
| Shell |
# Add BPipe from the project root to the path
if [ -z "$BASE" ];
then
BASE=`pwd`
if [ ! -e $BASE/../bin/bpipe ] && [ -e $BASE/../../bin/bpipe ] ;
then
BASE=`pwd`/..
fi
fi
PATH="$BASE/../bin:$PATH"
#which bpipe
if [ $? -ne 0 ]; then
echo Cannot find the 'bpipe' launch script on the path. Please make sure that... | Shell |
source ../testsupport.sh
run
exists foo.txt bar.txt
grep -q "Stage async_stuff" test.out || err "Failed to find expected stage async_stuff in output"
grep -q "Command.*failed" test.out || err "Failed to find expected failed command in output"
grep -q "Exit status = 1" test.out || err "Failed to find expected exit s... | Shell |
rm -f foo.txt bar.txt
| Shell |
source ../testsupport.sh
source ./cleanup.sh
run *.chr*.*vcf *.chr*bam
grep -c chr14 test.out | grep -q 1 || err "Unexpected number of references to chr14 - should be only 1"
grep -c chr15 test.out | grep -q 1 || err "Unexpected number of references to chr15 - should be only 1"
true
| Shell |
rm -f hello.txt
| Shell |
source ../testsupport.sh
. cleanup.sh
run test.txt
grep -q "Stage folder" test.out || err "Failed to find expected stage hello"
grep -q "Stage after" test.out || err "Failed to find expected stage world"
grep -q "Skipping" test.out && err "Skipped steps incorrectly on first run"
[ ! -f thefolder/output.csv ] && er... | Shell |
rm -rf thefolder *.after.xml .bpipe/outputs
| Shell |
source ../testsupport.sh
rm -f test.*vcf
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage filter_with_ext" test.out || err "Failed to find expected stage filter_with_ext"
[ ! -f test.vcf ] && err "Failed to find expected output test.vcf"
[ ! -f test.fix.vcf ] &... | Shell |
source ../testsupport.sh
rm -f test.xml test.csv
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.csv ] && err "Failed to find expected output test.csv"
[ ! -f test.xml ] && err "Failed to... | Shell |
source ../testsupport.sh
rm -f *.csv *.xml
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 "Inputs are test.csv test[0-9].xml test[0-9].xml test[0-9].xml" test.out || err "Failed to find expec... | Shell |
source ../testsupport.sh
run test1.fastq test2.fastq ref.fa
exists test1.paired.bam
grep -q "cat test1.fastq test2.fastq ref.fa" commandlog.txt || err "Failed to find correct command in commandlog.txt"
true
| Shell |
rm -f *.bam
| Shell |
source ../testsupport.sh
rm -f test.txt.hello test.csv.world *.hello *.world
run test.txt test.csv
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 te... | Shell |
source ../testsupport.sh
rm -f test.foo.txt test.foo.bar.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.foo.txt ] && err "Failed to find expected output test.foo.txt"
[ ! -f test.foo... | Shell |
source ../testsupport.sh
run
exists test2.csv
| Shell |
rm -rf *.csv .bpipe
| Shell |
source ../testsupport.sh
run *.chr14.*vcf *.chr14.*bam
grep -q "MUW09_C0R8HACXX_ATCACG_L001_R1.fastq.merge.dedupe.merge.reorder.rg.recal.chr14.realign.bam => MUW09_C0R8HACXX_ATCACG_L001_R1.fastq.merge.dedupe.merge.reorder.rg.recal.chr14.realign.test.bam" test.out || err "Expected MUW09_C0R8HACXX_ATCACG_L001_R1.fast... | Shell |
source ../testsupport.sh
rm -f test.world.txt test.txt
run *.fastq
grep -q "SureSelect_Capture_11MG2107_AD0AN0ACXX_GATCAG_L002_R1.fastq SureSelect_Capture_11MG2107_AD0AN0ACXX_GATCAG_L002_R2.fastq" test.out || err "Failed to find expected GATCAG files R1 and R2"
grep -q "SureSelect_Capture_11MG2108_AD0AN0ACXX_TAGCTT_... | 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"
grep -q "Stage world2" test.out || err "Failed to find expected stage world2"
grep -q "Stage end" test.out || ... | Shell |
source ../testsupport.sh
run test*.txt
grep -q "inputs are.*test1.txt.*test2.txt" test.out || err "Failed to find references to split files in output"
true
| Shell |
source ../testsupport.sh
run foo.txt bar.txt
exists foo.txt.hello
| Shell |
rm -f foo.txt.hello
| Shell |
source ../testsupport.sh
. ./cleanup.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 "... | Shell |
rm -f test.txt.*
| Shell |
source ../testsupport.sh
run test.vcf test.bam
exists test.extract.bam
true
| Shell |
rm -f *.extract.* test.bed
| Shell |
source ../testsupport.sh
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.foo.txt ] && err "Failed to find expected output s_2_1.foo.txt"
[ ! -f s_3_1.foo.txt ] && err "Failed to find ex... | Shell |
rm -f *align* *foo*
| Shell |
source ../testsupport.sh
rm check.txt
run
grep -q "Stage check" test.out || err "Failed to find expected stage check"
[ ! -f check.txt ] && err "Failed to find expected output check.txt"
true
| Shell |
source ../testsupport.sh
# Remove files produced by previous run (if any)
rm -f test.out_1 test.out_2
# Run the test
run test.txt
# Check for valid result
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 te... | Shell |
rm 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.txt ] && err "Failed to find expected output test.f1.txt"
[ ! -f test.f1.f2.txt ] && err "Failed t... | Shell |
source ../testsupport.sh
run test.txt
exists test.hello.world.xml
exists test.hello.world_with_filter.xml
exists test.hello.world_with_mismatch_filter.xml
exists test.hello.csv
bpipe cleanup -y >> test.out
notexists test.hello.world.xml
notexists test.hello.csv
notexists test.hello.world_with_filter.xml
# Because ... | Shell |
rm -rf .bpipe *.xml *.csv
| Shell |
source ../testsupport.sh
run *.txt *.csv
exists "result.out"
exists test1.csv.there.xls test2.csv.there.xls
exists test1.txt.me.xml test2.txt.me.xml
wc result.out | grep -q "4[^0-9]*4" || err "Failed to find correct number of files in result.out"
for i in test1.csv.there.xls test2.csv.there.xls test1.txt.me.xml te... | Shell |
rm -rf *.hello* *.help* *world *.xml *.xls commandlog.txt
| Shell |
source ../testsupport.sh
run test.txt test.csv
exists test.over.csv
true
| Shell |
rm -f *.over.*
| Shell |
source ../testsupport.sh
run test.bam test.vcf
exists test.clean.vcf
true
| Shell |
rm -f *.hello.* *.clean.*
| Shell |
source ../testsupport.sh
source ./cleanup.sh
# note option -n 1 is important for this test
bpipe run -n 1 test.groovy s_1.txt > test.out 2>&1
grep -q "Stage how_are_you" test.out || err "Failed to find expected stage how_are_you"
grep -q "Stage take_me_to_your_leader" test.out || err "Failed to find expected stage ... | Shell |
rm -f s_1.txt.*
| Shell |
#!/usr/bin/env bash
# Copyright (c) 2003-2011, CKSource - Frederico Knabben. All rights reserved.
# For licensing, see LICENSE.html or http://ckeditor.com/license
# Use this file to quickly run the sample under Linux.
adl application.xml ../../
| Shell |
#!/usr/bin/env bash
# Copyright (c) 2003-2011, CKSource - Frederico Knabben. All rights reserved.
# For licensing, see LICENSE.html or http://ckeditor.com/license
# Use this file to quickly run the sample under Linux.
adl application.xml ../../
| Shell |
#!/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 |
#!/bin/bash
#
# Copyright (C) 2007 The Android Open Source Project
#
# 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 ap... | Shell |
#!/bin/bash
#
# Copyright (C) 2007 The Android Open Source Project
#
# 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 ap... | Shell |
spawn-fcgi -u www-data -g www-data -d /var/www/simplecd/ -f /var/www/simplecd/code.py -a 127.0.0.1 -p 9001 -F 2
| Shell |
#!/bin/sh
adb shell cat /data/data/com.google.android.apps.iosched/shared_prefs/com.google.android.apps.iosched_preferences.xml | xmllint --format - | Shell |
#!/bin/sh
#
# Copyright 2013 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/sh
adb shell pm clear com.google.android.apps.iosched | Shell |
#!/bin/sh
if [[ -z $ADB ]]; then ADB=adb; fi
MAC_UNAME="Darwin"
if [[ "`uname`" == ${MAC_UNAME} ]]; then
DATE_FORMAT="%Y-%m-%dT%H:%M:%S"
else
DATE_FORMAT="%Y-%m-%d %H:%M:%S"
fi
if [ -z "$1" ]; then
NOW_DATE=$(date "+${DATE_FORMAT}")
echo Please provide a mock time in the format \"${NOW_DATE}\" or \"d\" to del... | Shell |
#!/bin/sh
# Remember VERBOSE only works on debug builds of the app
adb shell setprop log.tag.iosched_SyncHelper VERBOSE
adb shell setprop log.tag.iosched_SessionsHandler VERBOSE
adb shell setprop log.tag.iosched_BitmapCache VERBOSE
| Shell |
#!/bin/sh
if [[ -z $ADB ]]; then ADB=adb; fi
$ADB shell "echo '$*' | sqlite3 -header -column /data/data/com.google.android.apps.iosched/databases/schedule.db" | Shell |
#!/bin/sh
# Sessions list
#adb shell am start -a android.intent.action.VIEW -d content://com.google.android.apps.iosched/tracks/android/sessions
# Vendors list
#adb shell am start -a android.intent.action.VIEW -d content://com.google.android.apps.iosched/tracks/android/vendors
# Session detail
#adb shell am start -a... | Shell |
#!/usr/bin/env bash
##############################################################################
##
## Gradle start up script for UN*X
##
##############################################################################
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to ... | 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 |
#!/bin/sh
SCRIPTDIR=`dirname $0`
cd $SCRIPTDIR/..
RED="0.5 0.5 0.5 0 0 0 0 0 0"
GREEN="0 0 0 0.5 0.5 0.5 0 0 0"
for x in btn_zoom_down_disabled.9 btn_zoom_down_disabled_focused.9 btn_zoom_down_normal.9 btn_zoom_up_disabled.9 btn_zoom_up_disabled_focused.9 btn_zoom_up_normal.9 btn_zoom_width_normal ; do
conv... | Shell |
#!/bin/sh
# make sure ndk-build is in path
SCRIPTDIR=`dirname $0`
MUPDF=mupdf-0.8.165
FREETYPE=freetype-2.4.6
OPENJPEG=openjpeg_v1_4_sources_r697
JBIG2DEC=jbig2dec-0.11
JPEGSRC=jpegsrc.v8a.tar.gz
JPEGDIR=jpeg-8a
cd $SCRIPTDIR/../deps
tar xvf $FREETYPE.tar.bz2
tar xvf $JPEGSRC
tar xvf $MUPDF-source.tar.gz
tar xvf $OPE... | Shell |
#!/bin/sh
SCRIPTDIR=`dirname $0`
cd $SCRIPTDIR/..
for x in upfolder folder home recent1 recent2 recent3 recent4 recent5 ; do
convert res/drawable-hdpi/$x.png -resize 66.7% res/drawable-mdpi/$x.png
convert res/drawable-hdpi/$x.png -resize 50% res/drawable-ldpi/$x.png
done
| Shell |
#!/bin/bash
set -e # fail early
VERS="$1"
[ -n "$VERS" ] && VERS="${VERS}_"
function die() {
echo "Error: " $*
echo
echo "USage: $0 <version>"
echo "Automatically sign [A-Z].apk"
exit 1
}
[ -z "$1" ] && die
shopt -s extglob # extended glob pattern
function process() {
SRC="$1"
BASE="${SRC/.apk/}"
... | Shell |
#!/bin/sh
adb shell cat /data/data/com.google.android.apps.iosched/shared_prefs/com.google.android.apps.iosched_preferences.xml | xmllint --format - | Shell |
#!/bin/sh
#
# Copyright 2013 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/sh
adb shell pm clear com.google.android.apps.iosched | Shell |
#!/bin/sh
if [[ -z $ADB ]]; then ADB=adb; fi
MAC_UNAME="Darwin"
if [[ "`uname`" == ${MAC_UNAME} ]]; then
DATE_FORMAT="%Y-%m-%dT%H:%M:%S"
else
DATE_FORMAT="%Y-%m-%d %H:%M:%S"
fi
if [ -z "$1" ]; then
NOW_DATE=$(date "+${DATE_FORMAT}")
echo Please provide a mock time in the format \"${NOW_DATE}\" or \"d\" to del... | Shell |
#!/bin/sh
# Remember VERBOSE only works on debug builds of the app
adb shell setprop log.tag.iosched_SyncHelper VERBOSE
adb shell setprop log.tag.iosched_SessionsHandler VERBOSE
adb shell setprop log.tag.iosched_BitmapCache VERBOSE
| Shell |
#!/bin/sh
if [[ -z $ADB ]]; then ADB=adb; fi
$ADB shell "echo '$*' | sqlite3 -header -column /data/data/com.google.android.apps.iosched/databases/schedule.db" | Shell |
#!/bin/sh
# Sessions list
#adb shell am start -a android.intent.action.VIEW -d content://com.google.android.apps.iosched/tracks/android/sessions
# Vendors list
#adb shell am start -a android.intent.action.VIEW -d content://com.google.android.apps.iosched/tracks/android/vendors
# Session detail
#adb shell am start -a... | Shell |
#!/usr/bin/env bash
##############################################################################
##
## Gradle start up script for UN*X
##
##############################################################################
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to ... | Shell |
#!/bin/bash
# Tetris Game
# 10.21.2003 xhchen<xhchen@winbond.com.tw>
#颜色定义
cRed=1
cGreen=2
cYellow=3
cBlue=4
cFuchsia=5
cCyan=6
cWhite=7
colorTable=( $cRed $cGreen $cYellow $cBlue $cFuchsia $cCyan $cWhite )
#位置和大小
iLeft=3
iTop=2
((iTrayLeft = iLeft + 2))
((iTrayTop = iTop + 1))
((iTrayWidth = 10))
((iTrayHe... | Shell |
#!/bin/sh
DISTANCES="25 50 75 100 125 145 147 150 152 155 157 160 162 165 167 170 172 175 177 180"
TRIALS="1 2 3 4 5"
echo WiFi Experiment Example
pCheck=`which sqlite3`
if [ -z "$pCheck" ]
then
echo "ERROR: This script requires sqlite3 (wifi-example-sim does not)."
exit 255
fi
pCheck=`which gnuplot`
if [ -z "$... | Shell |
#!/bin/sh
brctl addbr br-left
brctl addbr br-right
tunctl -t tap-left
tunctl -t tap-right
ifconfig tap-left 0.0.0.0 promisc up
ifconfig tap-right 0.0.0.0 promisc up
brctl addif br-left tap-left
ifconfig br-left up
brctl addif br-right tap-right
ifconfig br-right up
pushd /proc/sys/net/bridge
for f in bridge-nf-*; do ec... | Shell |
#!/bin/sh
lxc-destroy -n left
lxc-destroy -n right
ifconfig br-left down
ifconfig br-right down
brctl delif br-left tap-left
brctl delif br-right tap-right
brctl delbr br-left
brctl delbr br-right
ifconfig tap-left down
ifconfig tap-right down
tunctl -d tap-left
tunctl -d tap-right
| Shell |
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