code stringlengths 1 2.01M | repo_name stringlengths 3 62 | path stringlengths 1 267 | language stringclasses 231
values | license stringclasses 13
values | size int64 1 2.01M |
|---|---|---|---|---|---|
rm -f hello.txt
| zxd06407-bpipe | tests/parallel_input_ext_original_inputs/cleanup.sh | Shell | bsd | 16 |
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... | zxd06407-bpipe | tests/folderasoutput/run.sh | Shell | bsd | 1,008 |
folder = {
produce("thefolder/*") {
exec "mkdir thefolder; cp $input thefolder/output.csv"
}
}
after = {
exec "cp $input.csv $output.xml"
}
run { folder + after }
| zxd06407-bpipe | tests/folderasoutput/test.groovy | Groovy | bsd | 175 |
rm -rf thefolder *.after.xml .bpipe/outputs
| zxd06407-bpipe | tests/folderasoutput/cleanup.sh | Shell | bsd | 44 |
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 ] &... | zxd06407-bpipe | tests/filter_input_ext/run.sh | Shell | bsd | 378 |
/*
* Test that inputs with extensions find the correct file
* (regression test for bug where output file is found as input)
*/
hello = {
exec "echo foo > test.vcf"
}
filter_with_ext = {
filter("fix") {
msg "input = $input.vcf output = $output"
exec "cp $input.vcf $output"
}
}
Bpipe.run... | zxd06407-bpipe | tests/filter_input_ext/test.groovy | Groovy | bsd | 351 |
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... | zxd06407-bpipe | tests/transform/run.sh | Shell | bsd | 358 |
/*
* Simplest possible test - just execute a couple of commands and
* join them together in a pipeline, with transform.
*/
hello = {
transform("csv") {
exec "cp $input $output"
}
}
@Transform("xml")
world = {
exec "cp $input $output"
}
Bpipe.run {
hello + world
}
| zxd06407-bpipe | tests/transform/test.groovy | Groovy | bsd | 277 |
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... | zxd06407-bpipe | tests/produce_glob/run.sh | Shell | bsd | 698 |
hello = {
produce("test.csv", "test*.xml") {
exec "cp $input $output.csv"
for(def i in 1..3) {
exec "cp $input ${input.replaceAll('.txt',i+'.xml')}"
}
}
}
world = {
msg "Inputs are $inputs"
}
run { hello + world }
| zxd06407-bpipe | tests/produce_glob/test.groovy | Groovy | bsd | 241 |
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
| zxd06407-bpipe | tests/paired_end/run.sh | Shell | bsd | 212 |
REF="ref.fa"
paired = {
from("fastq","fastq","fa") {
exec "cat $input1 $input2 $input3 > $output.bam"
}
}
run { paired }
| zxd06407-bpipe | tests/paired_end/test.groovy | Groovy | bsd | 140 |
rm -f *.bam
| zxd06407-bpipe | tests/paired_end/cleanup.sh | Shell | bsd | 12 |
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... | zxd06407-bpipe | tests/from/run.sh | Shell | bsd | 419 |
/*
* Test that from correctly finds an input from backwards in the pipeline
* and makes it referencable via $input
*/
hello = {
from("txt") {
exec "cp $input $output"
}
}
world = {
from("csv") {
msg "$input => $output"
exec "cp $input $output"
}
}
Bpipe.run {
hello + world
}
| zxd06407-bpipe | tests/from/test.groovy | Groovy | bsd | 293 |
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... | zxd06407-bpipe | tests/filter/run.sh | Shell | bsd | 394 |
/*
* Simplest possible test - just execute a couple of commands and
* join them together in a pipeline
*/
hello = {
filter("foo") {
exec "cp $input $output"
}
}
@Filter("bar")
world = {
exec "cp $input $output"
}
Bpipe.run {
hello + world
}
| zxd06407-bpipe | tests/filter/test.groovy | Groovy | bsd | 254 |
source ../testsupport.sh
run
exists test2.csv
| zxd06407-bpipe | tests/output_with_index_ext_and_produce/run.sh | Shell | bsd | 48 |
hello = {
produce("test1.csv", "test2.csv") {
exec "touch $output2.csv"
}
}
run { hello }
| zxd06407-bpipe | tests/output_with_index_ext_and_produce/test.groovy | Groovy | bsd | 99 |
rm -rf *.csv .bpipe
| zxd06407-bpipe | tests/output_with_index_ext_and_produce/cleanup.sh | Shell | bsd | 20 |
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... | zxd06407-bpipe | tests/outputextsame/run.sh | Shell | bsd | 493 |
// When multiple input types are provided
// and both input and output extension are used with the same ext,
// the output should be a transform of the input used
test = {
msg "input bam is $input.bam => $output.bam"
}
run {
".chr%."* [
test
]
}
| zxd06407-bpipe | tests/outputextsame/test.groovy | Groovy | bsd | 306 |
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_... | zxd06407-bpipe | tests/persample2/run.sh | Shell | bsd | 466 |
echo = {
exec "echo $inputs"
}
Bpipe.run {
// eg: SureSelect_Capture_11MG2107_AD0AN0ACXX_GATCAG_L002_R1.fastq
"CXX_%_*.fastq" * [
echo
]
}
| zxd06407-bpipe | tests/persample2/test.groovy | Groovy | bsd | 169 |
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 || ... | zxd06407-bpipe | tests/double_parallel/run.sh | Shell | bsd | 744 |
/*
* Simplest possible test using inputs and outputs
* join them together in a pipeline
*/
hello = {
exec "cp $input $output"
}
world = {
exec "cp $input $output"
}
world2 = {
// produce("anotheroutput.txt") {
exec "cp $input $output"
// }
}
how_are_you = {
exec "sed 's/f/b/g' $input > $output"
}
tak... | zxd06407-bpipe | tests/double_parallel/test.groovy | Groovy | bsd | 642 |
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
| zxd06407-bpipe | tests/multi_input_split/run.sh | Shell | bsd | 161 |
hello = {
msg "inputs are ${inputs.txt.split()}"
}
run { hello }
| zxd06407-bpipe | tests/multi_input_split/test.groovy | Groovy | bsd | 70 |
source ../testsupport.sh
run foo.txt bar.txt
exists foo.txt.hello
| zxd06407-bpipe | tests/from_list/run.sh | Shell | bsd | 68 |
// Check that using the array / list form of from works
hello = {
from(["foo.txt","bar.txt"]) {
exec "echo $input1 $input2 > $output"
}
}
run { hello }
| zxd06407-bpipe | tests/from_list/test.groovy | Groovy | bsd | 169 |
rm -f foo.txt.hello
| zxd06407-bpipe | tests/from_list/cleanup.sh | Shell | bsd | 20 |
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 "... | zxd06407-bpipe | tests/forward/run.sh | Shell | bsd | 379 |
/*
* Simplest possible test using inputs and outputs
* join them together in a pipeline
*/
hello = {
msg " $input => $output"
exec "cp $input $output"
}
fine = {
msg " $input => $output"
exec "cp $input $output"
forward input
}
world = {
msg " $input => $output"
exec "if [ $input != 'test.txt.hello' ]... | zxd06407-bpipe | tests/forward/test.groovy | Groovy | bsd | 400 |
rm -f test.txt.*
| zxd06407-bpipe | tests/forward/cleanup.sh | Shell | bsd | 17 |
source ../testsupport.sh
run test.vcf test.bam
exists test.extract.bam
true
| zxd06407-bpipe | tests/filter_output_second_input/run.sh | Shell | bsd | 79 |
/**
* Test that when an outer filter is specified, that filter
* can then still resolve on inputs that are only specified inside
* an inner statement (effectively, one that is resolved after the
* initial filter occurred.
*/
@transform("bed")
vcf_to_bed = {
exec """
cat $input.vcf > $output.be... | zxd06407-bpipe | tests/filter_output_second_input/test.groovy | Groovy | bsd | 791 |
rm -f *.extract.* test.bed
| zxd06407-bpipe | tests/filter_output_second_input/cleanup.sh | Shell | bsd | 27 |
source ../testsupport.sh
run s_*.txt
grep -q "Stage dedupe" test.out || err "Failed to find expected stage dedupe"
grep -q "Stage align" test.out || err "Failed to find expected stage align"
[ ! -f s_2_1.foo.txt ] && err "Failed to find expected output s_2_1.foo.txt"
[ ! -f s_3_1.foo.txt ] && err "Failed to find ex... | zxd06407-bpipe | tests/persamplefrom/run.sh | Shell | bsd | 355 |
/*
@SplitBy("-%")
copy_to_resource_folder = {
produce("output/$input") {
exec "cp $input $output"
}
}
*/
align = {
exec "cat $input1 $input2 > $output"
}
dedupe = {
from("txt") {
filter("foo") {
msg "$input => $output"
exec "cp $input $output"
}
}
}
Bpipe.run {
"s_%_*.txt" * [ align + ded... | zxd06407-bpipe | tests/persamplefrom/test.groovy | Groovy | bsd | 329 |
rm -f *align* *foo*
| zxd06407-bpipe | tests/persamplefrom/cleanup.sh | Shell | bsd | 20 |
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
| zxd06407-bpipe | tests/outputext2/run.sh | Shell | bsd | 198 |
check = {
exec "echo foo > $output.txt"
}
run { check }
| zxd06407-bpipe | tests/outputext2/test.groovy | Groovy | bsd | 60 |
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... | zxd06407-bpipe | tests/produce/run.sh | Shell | bsd | 459 |
/*
* Test the produce construct and the Produce annotation
*/
hello = {
produce('test.out_1') {
exec "cp $input $output"
}
}
@Produce("test.out_2")
world = {
exec "cp $input $output"
}
Bpipe.run {
hello + world
}
| zxd06407-bpipe | tests/produce/test.groovy | Groovy | bsd | 225 |
rm test.f*
| zxd06407-bpipe | tests/filter_multi/clean.sh | Shell | bsd | 11 |
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... | zxd06407-bpipe | tests/filter_multi/run.sh | Shell | bsd | 444 |
/*
* Simplest possible test using inputs and outputs
* join them together in a pipeline
*/
hello = {
filter("f1") {
exec "cp $input $output"
}
}
world = {
filter(["f2", "f3"]) {
exec "cp $input $output1"
exec "cp $input $output2"
}
}
world2 = {
filter("f2", "f3") {
exec "cp $input $output... | zxd06407-bpipe | tests/filter_multi/test.groovy | Groovy | bsd | 390 |
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 ... | zxd06407-bpipe | tests/intermediate/run.sh | Shell | bsd | 431 |
/*
* Test that when an @intermediate annotation is applied,
* the outputs it applies to are cleaned up by the cleanup command,
* EVEN when they appear to be "final" outputs, ie: they are
* leaf nodes in the output graph.
*/
hello = {
exec "cat $input.txt > $output.csv"
}
@intermediate
world = {
exec "cat $inp... | zxd06407-bpipe | tests/intermediate/test.groovy | Groovy | bsd | 600 |
rm -rf .bpipe *.xml *.csv
| zxd06407-bpipe | tests/intermediate/cleanup.sh | Shell | bsd | 26 |
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... | zxd06407-bpipe | tests/parallel_parallel/run.sh | Shell | bsd | 449 |
hello = {
exec "cp $input $output"
}
there = {
exec "cp $input $output.xls"
}
help = {
exec "cp $input $output"
}
me = {
exec "cp $input $output.xml"
}
world = {
msg "ls $inputs.xls $inputs.xml > result.out"
exec "ls $inputs.xls $inputs.xml > result.out"
}
run {
"*" * [
"%.csv" * [ hello + ther... | zxd06407-bpipe | tests/parallel_parallel/test.groovy | Groovy | bsd | 368 |
rm -rf *.hello* *.help* *world *.xml *.xls commandlog.txt
| zxd06407-bpipe | tests/parallel_parallel/cleanup.sh | Shell | bsd | 58 |
source ../testsupport.sh
run test.txt test.csv
exists test.over.csv
true
| zxd06407-bpipe | tests/output_ext_override_filter/run.sh | Shell | bsd | 76 |
/**
* This is testing the case where the output expected from the filter
* (in this case, test.over.txt) conflicts with the output actually referenced
* by the user. In that case we should go with what the user said, as long
* as there was actualy an alternative input that could have created
* the output they ex... | zxd06407-bpipe | tests/output_ext_override_filter/test.groovy | Groovy | bsd | 551 |
rm -f *.over.*
| zxd06407-bpipe | tests/output_ext_override_filter/cleanup.sh | Shell | bsd | 15 |
source ../testsupport.sh
run test.bam test.vcf
exists test.clean.vcf
true
| zxd06407-bpipe | tests/from_with_filter_different_input/run.sh | Shell | bsd | 77 |
/*
* In this test, we declare a filter which by default operates on the first input,
* resulting in an expectation that a "bam" is being filtered to a "bam" output.
* However then in the actual command the output is declared to be a different type
* (vcf). Bpipe should accept this *only* because vcf was an input th... | zxd06407-bpipe | tests/from_with_filter_different_input/test.groovy | Groovy | bsd | 517 |
rm -f *.hello.* *.clean.*
| zxd06407-bpipe | tests/from_with_filter_different_input/cleanup.sh | Shell | bsd | 26 |
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 ... | zxd06407-bpipe | tests/parallel_same_stage_outputs/run.sh | Shell | bsd | 552 |
/*
* Parallel segments that use the *same* stage
* should work independently even though they are both running
* the same stage, using the same thread (in this test,
* Bpipe is run using -n 1 to force a single thread).
*/
how_are_you = {
msg "how_are inputs=$inputs"
exec "sed 's/f/b/g' $input > $output"
}
ta... | zxd06407-bpipe | tests/parallel_same_stage_outputs/test.groovy | Groovy | bsd | 658 |
rm -f s_1.txt.*
| zxd06407-bpipe | tests/parallel_same_stage_outputs/cleanup.sh | Shell | bsd | 16 |
package bpipe
import org.junit.Test
import static org.junit.Assert.*
import org.junit.Before
/**
*
* @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
*/
class EventManagerTest {
@Before
def void clear() {
EventManager.instance.listeners.clear()
}
@Test
def void testAddListener()... | zxd06407-bpipe | test-src/bpipe/EventManagerTest.groovy | Groovy | bsd | 1,381 |
package bpipe;
import static org.junit.Assert.*;
import org.junit.Test;
class ForwarderTest {
@Test
void testForward() {
def forwarder = new Forwarder()
File f = new File("test.src.out")
File outFile = new File("test.out")
forwarder.forward(f, new FileOutputStream(ou... | zxd06407-bpipe | test-src/bpipe/ForwarderTest.groovy | Groovy | bsd | 884 |
package bpipe;
import static org.junit.Assert.*;
import static FastUtils.globToRegex as gtr
import org.junit.Before;
import org.junit.Test;
class FastUtilsTest {
@Before
public void setUp() throws Exception {
}
@Test
void testGlobToRegex() {
def x = "hello.world.txt";
... | zxd06407-bpipe | test-src/bpipe/FastUtilsTest.groovy | Groovy | bsd | 825 |
package bpipe;
import static org.junit.Assert.*;
import static Utils.joinShellLines as jsl
import static Utils.splitShellArgs as sp
import org.junit.Test;
class UtilsTest {
@Test
public void testJoinShellLines() {
// A simple command should not be changed!
assert jsl("ls -l hello w... | zxd06407-bpipe | test-src/bpipe/UtilsTest.groovy | Groovy | bsd | 1,736 |
package bpipe;
import static org.junit.Assert.*;
import org.junit.Test;
class InputSplitterTest {
InputSplitter splitter = new InputSplitter()
/**
* A real example from bpipe user Rory
*/
@Test
void testMixedEndings() {
def inputs = [
"... | zxd06407-bpipe | test-src/bpipe/InputSplitterTest.groovy | Groovy | bsd | 7,451 |
package bpipe.executor
import org.junit.Test
import static org.junit.Assert.assertTrue
import static org.junit.Assert.assertFalse
/**
*
* @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
*/
class GridgainCommandExecutorTest {
@Test
public void testAcceptList() {
assertTrue( GridgainCommand... | zxd06407-bpipe | test-src/bpipe/executor/GridgainCommandExecutorTest.groovy | Groovy | bsd | 683 |
package bpipe
import org.junit.Before;
import org.junit.Test
class DependenciesTest {
Properties a,b,c,d
static {
Runner.initializeLogging("tests")
}
@Before
void setUp() {
//
// A =>
// B
// C =>
// D
pr... | zxd06407-bpipe | test-src/bpipe/DependenciesTest.groovy | Groovy | bsd | 8,200 |
package bpipe
import org.junit.Test
import static org.junit.Assert.*
/**
*
* @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
*/
class RunnerTest {
@Test def void testParseParameter() {
// integer
def entry = ParamsBinding.parseParam('x=100')
assertEquals 'x', entry.key
as... | zxd06407-bpipe | test-src/bpipe/RunnerTest.groovy | Groovy | bsd | 3,247 |
package bpipe;
import static org.junit.Assert.*;
import org.junit.Test;
class ToolDatabaseTest {
/**
* We want tools to NOT be identified
* as substrings of other commands/tools. In other
* words, a command should only be identified if it
* is surrounded by tokens that bash would consider
... | zxd06407-bpipe | test-src/bpipe/ToolDatabaseTest.groovy | Groovy | bsd | 1,940 |
package bpipe;
import static org.junit.Assert.*;
import org.junit.Test
import bpipe.executor.LocalCommandExecutor;
class LocalJobTest {
@Test
public void testStart() {
LocalCommandExecutor job = new LocalCommandExecutor()
job.start("ls")
}
@Test
public void testWaitFor() {
... | zxd06407-bpipe | test-src/bpipe/LocalJobTest.groovy | Groovy | bsd | 1,051 |
package bpipe;
import static org.junit.Assert.*;
import org.junit.Test;
class PipelineInputTest {
@Test
public void testPlusOperator() {
PipelineInput inp = new PipelineInput("foo.txt", [])
println( inp + ".bar")
}
}
| zxd06407-bpipe | test-src/bpipe/PipelineInputTest.groovy | Groovy | bsd | 268 |
//
// A hack script that converts "live" examples into Wiki format
// so that examples can be edited in place and updated on the wiki
// easily.
//
new File("../../examples").eachDir { exampleDir ->
println " Processing $exampleDir ".center(80,'-')
println "\n"
def lines = new File(exampleDir, "pipeline.groovy... | zxd06407-bpipe | src/misc/create_examples.groovy | Groovy | bsd | 1,434 |
<!DOCTYPE html>
<% def dateFormat = new java.text.SimpleDateFormat("yyyy-M-d H:m:s") %>
<html>
<head>
<style type='text/css'>
body {
font-family: arial;
margin: 0;
padding: 0;
color: #333;
}
#hd {
... | zxd06407-bpipe | src/main/html/bpipe/index.html | HTML | bsd | 15,526 |
<!DOCTYPE html>
<% def dateFormat = new java.text.SimpleDateFormat("yyyy-M-d H:m:s") %>
<html>
<head>
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... | zxd06407-bpipe | src/main/html/bpipe/softwareschedule.html | HTML | bsd | 2,388 |
/*
* Copyright (c) Murdoch Childrens Research Institute and Contributers
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* Redistributions of source code must retain the above copyright n... | zxd06407-bpipe | src/main/groovy/Preserve.groovy | Groovy | bsd | 1,947 |
package bpipe
import groovy.util.logging.Log;
import static bpipe.GenomicRange.range
/**
* A simple data structure to hold information about a gene
*
* @TODO: rename this to 'Feature' so as to generalise
* @author ssadedin
*/
class Gene implements Serializable {
private static final long serialV... | zxd06407-bpipe | src/main/groovy/bpipe/Sequence.groovy | Groovy | bsd | 4,926 |
/*
* Copyright (c) 2012 MCRI, authors
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, me... | zxd06407-bpipe | src/main/groovy/bpipe/Concurrency.groovy | Groovy | bsd | 9,438 |
/*
* Copyright (c) 2012 MCRI, authors
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, pu... | zxd06407-bpipe | src/main/groovy/bpipe/ReportStatisticsListener.groovy | Groovy | bsd | 1,943 |
/*
* Copyright (c) Murdoch Childrens Research Institute and Contributers
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* Redistributions of source code must retain the above copyright... | zxd06407-bpipe | src/main/groovy/bpipe/PipelineStage.groovy | Groovy | bsd | 17,512 |
/*
* Copyright (c) Murdoch Childrens Research Institute and Contributers
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* Redistributions of source code must retain the above copyright n... | zxd06407-bpipe | src/main/groovy/bpipe/BpipeLogFormatter.groovy | Groovy | bsd | 2,517 |
/*
* Copyright (c) Murdoch Childrens Research Institute and Contributers
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* Redistributions of source code must retain the above copyright n... | zxd06407-bpipe | src/main/groovy/bpipe/MultiPipelineInput.groovy | Groovy | bsd | 3,465 |
/*
* Copyright (c) 2013 MCRI, authors
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, pu... | zxd06407-bpipe | src/main/groovy/bpipe/Chr.groovy | Groovy | bsd | 2,428 |
/*
* Copyright (c) 2011 MCRI, authors
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, pu... | zxd06407-bpipe | src/main/groovy/bpipe/CommandManager.groovy | Groovy | bsd | 10,341 |
package bpipe
import groovy.util.logging.Log;
/**
* Forwards all calls through to a thread specific context.
*
* @author simon.sadedin@mcri.edu.au
*/
@Log
class PipelineDelegate {
PipelineDelegate(PipelineContext ctx) {
if(ctx == null)
throw new IllegalArgumentException("Attempt to s... | zxd06407-bpipe | src/main/groovy/bpipe/PipelineDelegate.groovy | Groovy | bsd | 5,199 |
/*
* Copyright (c) 2012 MCRI, authors
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, pu... | zxd06407-bpipe | src/main/groovy/bpipe/Utils.groovy | Groovy | bsd | 19,058 |
/*
* Copyright (c) 2012 MCRI, authors
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, ... | zxd06407-bpipe | src/main/groovy/bpipe/graph/Graph.groovy | Groovy | bsd | 6,429 |
/*
* Copyright (c) 2012 MCRI, authors
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, me... | zxd06407-bpipe | src/main/groovy/bpipe/NotificationChannel.java | Java | bsd | 1,320 |
/*
* Copyright (c) 2012 MCRI, authors
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, pu... | zxd06407-bpipe | src/main/groovy/bpipe/PipelineCategory.groovy | Groovy | bsd | 22,475 |
package bpipe
/**
* A wrapper for either a RegionSet or a Chr that
* enables them to be used as either string values or to support a ".bed"
* extension.
*/
class RegionValue {
String value
def propertyMissing(String name) {
if(name == "bed") {
def fn = new File(".bp... | zxd06407-bpipe | src/main/groovy/bpipe/RegionValue.groovy | Groovy | bsd | 1,136 |
/*
* Copyright (c) 2011 MCRI, authors
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, ... | zxd06407-bpipe | src/main/groovy/bpipe/PipelineError.java | Java | bsd | 1,717 |
/*
* Copyright (c) 2012 MCRI, authors
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, pu... | zxd06407-bpipe | src/main/groovy/bpipe/PipelineInput.groovy | Groovy | bsd | 8,867 |
/*
* Copyright (c) Murdoch Childrens Research Institute and Contributers
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* Redistributions of source code must retain the above copyright n... | zxd06407-bpipe | src/main/groovy/bpipe/executor/HazelcastGridProvider.groovy | Groovy | bsd | 3,308 |
package bpipe.executor
import groovy.util.logging.Log;
import bpipe.Concurrency;
import bpipe.PipelineContext;
import bpipe.ResourceUnit;
/**
* Wraps another CommandExecutor and adds concurrency control to it
* so that the command will not execute if it would violate the concurrency
* restrictions confi... | zxd06407-bpipe | src/main/groovy/bpipe/executor/ThrottledDelegatingCommandExecutor.groovy | Groovy | bsd | 3,710 |
/*
* Copyright (c) 2012 MCRI, authors
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, pu... | zxd06407-bpipe | src/main/groovy/bpipe/executor/SgeCommandExecutor.groovy | Groovy | bsd | 8,741 |
/*
* Copyright (c) Murdoch Childrens Research Institute and Contributers
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* Redistributions of source code must retain the above copyright n... | zxd06407-bpipe | src/main/groovy/bpipe/executor/AbstractGridBashExecutor.groovy | Groovy | bsd | 3,557 |
/*
* Copyright (c) 2011 MCRI, authors
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, pu... | zxd06407-bpipe | src/main/groovy/bpipe/executor/CustomCommandExecutor.groovy | Groovy | bsd | 14,098 |
/*
* Copyright (c) 2012 MCRI, authors
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, pu... | zxd06407-bpipe | src/main/groovy/bpipe/executor/CommandExecutor.java | Java | bsd | 2,490 |
/*
* Copyright (c) Murdoch Childrens Research Institute and Contributers
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* Redistributions of source code must retain the above copyright n... | zxd06407-bpipe | src/main/groovy/bpipe/executor/LocalCommandExecutor.groovy | Groovy | bsd | 4,200 |