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biopet.biopet
Commits
488594e1
Commit
488594e1
authored
Jan 06, 2016
by
Wai Yi Leung
Browse files
Merge branch 'feature-generate_indexes' into 'develop'
Feature generate indexes see also #187 See merge request !211
parents
1921f894
244653f5
Changes
21
Hide whitespace changes
Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
View file @
488594e1
...
...
@@ -31,12 +31,14 @@ class Cat(val root: Configurable) extends BiopetCommandLineFunction {
@Output
(
doc
=
"Unzipped file"
,
required
=
true
)
var
output
:
File
=
_
var
appending
=
false
executable
=
config
(
"exe"
,
default
=
"cat"
)
/** return commandline to execute */
def
cmdLine
=
required
(
executable
)
+
(
if
(
inputAsStdin
)
""
else
repeat
(
input
))
+
(
if
(
outputAsStsout
)
""
else
" > "
+
required
(
output
))
(
if
(
outputAsStsout
)
""
else
(
if
(
appending
)
" >> "
else
" > "
)
+
required
(
output
))
}
/**
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala
0 → 100644
View file @
488594e1
package
nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Output
/**
* Created by pjvan_thof on 8/11/15.
*/
class
Curl
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
@Output
var
output
:
File
=
_
var
url
:
String
=
_
executable
=
config
(
"exe"
,
default
=
"curl"
)
def
versionCommand
=
executable
+
" --version"
def
versionRegex
=
"""curl (\w+\.\w+\.\w+) .*"""
.
r
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
url
)
+
" > "
+
required
(
output
)
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
View file @
488594e1
...
...
@@ -62,7 +62,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
var
genomeDir
:
File
=
null
var
runmode
:
String
=
_
var
sjdbOverhang
:
Int
=
_
var
sjdbOverhang
:
Option
[
Int
]
=
None
var
outFileNamePrefix
:
String
=
_
var
runThreadN
:
Option
[
Int
]
=
config
(
"runThreadN"
)
...
...
@@ -73,24 +73,24 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
reference
==
null
)
reference
=
referenceFasta
()
genomeDir
=
config
(
"genomeDir"
,
new
File
(
reference
.
getAbsoluteFile
.
getParent
,
"star"
))
if
(
outFileNamePrefix
!=
null
&&
!
outFileNamePrefix
.
endsWith
(
"."
))
outFileNamePrefix
+=
"."
val
prefix
=
if
(
outFileNamePrefix
!=
null
)
outputDir
+
File
.
separator
+
outFileNamePrefix
else
outputDir
+
File
.
separator
if
(
runmode
==
null
)
{
outputSam
=
new
File
(
prefix
+
"Aligned.out.sam"
)
outputTab
=
new
File
(
prefix
+
"SJ.out.tab"
)
genomeDir
=
config
(
"genomeDir"
,
new
File
(
reference
.
getAbsoluteFile
.
getParent
,
"star"
))
}
else
if
(
runmode
==
"genomeGenerate"
)
{
genomeDir
=
outputDir
outputGenome
=
new
File
(
prefix
+
"Genome"
)
outputSA
=
new
File
(
prefix
+
"SA"
)
outputSAindex
=
new
File
(
prefix
+
"SAindex"
)
sjdbOverhang
=
config
(
"sjdboverhang"
,
75
)
sjdbOverhang
=
config
(
"sjdboverhang"
)
}
}
/** Returns command to execute */
def
cmdLine
=
{
var
cmd
:
String
=
required
(
"cd"
,
outputDir
)
+
"&&"
+
required
(
executable
)
var
cmd
:
String
=
required
(
"cd"
,
outputDir
)
+
"
&&
"
+
required
(
executable
)
if
(
runmode
!=
null
&&
runmode
==
"genomeGenerate"
)
{
// Create index
cmd
+=
required
(
"--runMode"
,
runmode
)
+
required
(
"--genomeFastaFiles"
,
reference
)
...
...
@@ -100,8 +100,8 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
cmd
+=
required
(
"--genomeDir"
,
genomeDir
)
+
optional
(
"--sjdbFileChrStartEnd"
,
sjdbFileChrStartEnd
)
+
optional
(
"--runThreadN"
,
threads
)
+
optional
(
"--outFileNamePrefix"
,
outFileNamePrefix
)
if
(
sjdbOverhang
>
0
)
cmd
+=
optional
(
"--sjdbOverhang"
,
sjdbOverhang
)
optional
(
"--outFileNamePrefix"
,
outFileNamePrefix
)
+
optional
(
"--sjdbOverhang"
,
sjdbOverhang
)
cmd
}
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
View file @
488594e1
...
...
@@ -66,6 +66,7 @@ class Tabix(val root: Configurable) extends BiopetCommandLineFunction with Versi
private
val
validFormats
:
Set
[
String
]
=
Set
(
"gff"
,
"bed"
,
"sam"
,
"vcf"
,
"psltbl"
)
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
p
match
{
case
Some
(
fmt
)
=>
require
(
validFormats
.
contains
(
fmt
),
"-p flag must be one of "
+
validFormats
.
mkString
(
", "
))
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/TarExtract.scala
0 → 100644
View file @
488594e1
package
nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
}
/**
* Created by pjvan_thof on 8/11/15.
*/
class
TarExtract
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
@Input
(
required
=
true
)
var
inputTar
:
File
=
_
@Argument
(
required
=
true
)
var
outputDir
:
File
=
_
executable
=
config
(
"exe"
,
default
=
"tar"
,
freeVar
=
false
)
def
versionCommand
=
executable
+
" --version"
def
versionRegex
=
"""tar \(GNU tar\) (.*)"""
.
r
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
jobLocalDir
=
outputDir
jobOutputFile
=
new
File
(
outputDir
,
"."
+
inputTar
.
getName
+
".tar.out"
)
}
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"-x"
)
+
required
(
"-f"
,
inputTar
)
+
required
(
"--directory"
,
outputDir
)
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
View file @
488594e1
...
...
@@ -29,6 +29,8 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction with Versio
@Output
(
doc
=
"Unzipped file"
,
required
=
true
)
var
output
:
File
=
_
var
appending
=
false
executable
=
config
(
"exe"
,
default
=
"zcat"
)
def
versionRegex
=
"""zcat \(gzip\) (.*)"""
.
r
...
...
@@ -37,7 +39,7 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction with Versio
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
(
if
(
inputAsStdin
)
""
else
repeat
(
input
))
+
(
if
(
outputAsStsout
)
""
else
" > "
+
required
(
output
))
(
if
(
outputAsStsout
)
""
else
(
if
(
appending
)
" >> "
else
" > "
)
+
required
(
output
))
}
object
Zcat
{
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
→
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/
bowtie/
Bowtie.scala
View file @
488594e1
...
...
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions
package
nl.lumc.sasc.biopet.extensions
.bowtie
import
java.io.File
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie2.scala
→
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/
bowtie/
Bowtie2.scala
View file @
488594e1
package
nl.lumc.sasc.biopet.extensions
package
nl.lumc.sasc.biopet.extensions
.bowtie
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Extension for bowtie 2
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala
0 → 100644
View file @
488594e1
package
nl.lumc.sasc.biopet.extensions.bowtie
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
}
/**
* Created by pjvan_thof on 8/15/15.
*/
class
Bowtie2Build
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
@Input
(
required
=
true
)
var
reference
:
File
=
_
@Argument
(
required
=
true
)
var
baseName
:
String
=
_
executable
=
config
(
"exe"
,
default
=
"bowtie2-build"
,
freeVar
=
false
)
def
versionRegex
=
""".*[Vv]ersion:? (\d*\.\d*\.\d*)"""
.
r
def
versionCommand
=
executable
+
" --version"
override
def
defaultCoreMemory
=
15.0
override
def
beforeGraph
:
Unit
=
{
outputFiles
::=
new
File
(
reference
.
getParentFile
,
baseName
+
".1.bt2"
)
outputFiles
::=
new
File
(
reference
.
getParentFile
,
baseName
+
".2.bt2"
)
}
def
cmdLine
=
required
(
"cd"
,
reference
.
getParentFile
)
+
" && "
+
required
(
executable
)
+
required
(
reference
)
+
required
(
baseName
)
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala
0 → 100644
View file @
488594e1
package
nl.lumc.sasc.biopet.extensions.bowtie
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
}
/**
* Created by pjvan_thof on 8/15/15.
*/
class
BowtieBuild
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
@Input
(
required
=
true
)
var
reference
:
File
=
_
@Argument
(
required
=
true
)
var
baseName
:
String
=
_
executable
=
config
(
"exe"
,
default
=
"bowtie-build"
,
freeVar
=
false
)
def
versionRegex
=
""".*[Vv]ersion:? (\d*\.\d*\.\d*)"""
.
r
def
versionCommand
=
executable
+
" --version"
override
def
defaultCoreMemory
=
15.0
override
def
beforeGraph
:
Unit
=
{
outputFiles
::=
new
File
(
reference
.
getParentFile
,
baseName
+
".1.ebwt"
)
outputFiles
::=
new
File
(
reference
.
getParentFile
,
baseName
+
".2.ebwt"
)
}
def
cmdLine
=
required
(
"cd"
,
reference
.
getParentFile
)
+
" && "
+
required
(
executable
)
+
required
(
reference
)
+
required
(
baseName
)
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala
0 → 100644
View file @
488594e1
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions.bwa
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Extension for bwa aln
*
* Based on version 0.7.12-r1039
*
* Created by pjvan_thof on 1/16/15.
*/
class
BwaIndex
(
val
root
:
Configurable
)
extends
Bwa
{
@Input
(
doc
=
"Fastq file"
,
required
=
true
)
var
reference
:
File
=
_
@Output
(
doc
=
"Index files for bwa"
,
required
=
false
)
private
var
output
:
List
[
File
]
=
Nil
var
a
:
Option
[
String
]
=
config
(
"a"
,
freeVar
=
false
)
var
p
:
Option
[
String
]
=
config
(
"p"
,
freeVar
=
false
)
var
b
:
Option
[
Int
]
=
config
(
"e"
,
freeVar
=
false
)
var
_6
:
Boolean
=
config
(
"6"
,
default
=
false
,
freeVar
=
false
)
override
def
defaultCoreMemory
=
35.0
override
def
beforeGraph
()
{
super
.
beforeGraph
()
List
(
".sa"
,
".pac"
)
.
foreach
(
ext
=>
output
::=
new
File
(
reference
.
getAbsolutePath
+
ext
))
output
=
output
.
distinct
}
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
"index"
)
+
optional
(
"-a"
,
a
)
+
optional
(
"-p"
,
p
)
+
optional
(
"-b"
,
b
)
+
conditional
(
_6
,
"-6"
)
+
required
(
reference
)
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/GmapBuild.scala
0 → 100644
View file @
488594e1
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions.gmap
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
,
Reference
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Input
/**
* Wrapper for the gsnap command line tool
* Written based on gsnap version 2014-05-15
*/
class
GmapBuild
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
with
Version
{
/** default executable */
executable
=
config
(
"exe"
,
default
=
"gmap_build"
,
freeVar
=
false
)
/** input file */
@Input
(
doc
=
"Input fasta files"
,
required
=
true
)
//var input: List[File] = _
var
fastaFiles
:
List
[
File
]
=
Nil
/** genome directory */
var
dir
:
File
=
_
/** genome database */
var
db
:
String
=
_
override
def
defaultCoreMemory
=
25.0
def
versionRegex
=
""".* version (.*)"""
.
r
def
versionCommand
=
executable
override
def
versionExitcode
=
List
(
0
,
1
,
255
)
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
jobOutputFile
=
new
File
(
dir
,
".log.out"
)
}
def
cmdLine
=
{
required
(
executable
)
+
required
(
"--dir"
,
dir
)
+
optional
(
"--db"
,
db
)
+
repeat
(
fastaFiles
)
}
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
→
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/
gmap/
Gsnap.scala
View file @
488594e1
...
...
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions
package
nl.lumc.sasc.biopet.extensions
.gmap
import
java.io.File
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CreateSequenceDictionary.scala
0 → 100644
View file @
488594e1
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
CreateSequenceDictionary
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
new
picard
.
sam
.
CreateSequenceDictionary
().
getClass
.
getName
@Input
(
required
=
true
)
var
reference
:
File
=
_
@Output
(
required
=
true
)
var
output
:
File
=
_
var
genomeAssembly
:
Option
[
String
]
=
config
(
"genomeAssembly"
)
var
uri
:
Option
[
String
]
=
config
(
"uri"
)
var
species
:
Option
[
String
]
=
config
(
"species"
)
var
truncateAtWhiteSpace
:
Boolean
=
config
(
"truncateAtWhiteSpace"
,
default
=
false
)
var
numSequences
:
Option
[
Int
]
=
config
(
"numSequences"
)
override
def
cmdLine
=
super
.
cmdLine
+
required
(
"REFERENCE="
,
reference
,
spaceSeparated
=
false
)
+
required
(
"OUTPUT="
,
output
,
spaceSeparated
=
false
)
+
optional
(
"GENOME_ASSEMBLY="
,
genomeAssembly
,
spaceSeparated
=
false
)
+
optional
(
"URI="
,
uri
,
spaceSeparated
=
false
)
+
optional
(
"SPECIES="
,
species
,
spaceSeparated
=
false
)
+
conditional
(
truncateAtWhiteSpace
,
"TRUNCATE_NAMES_AT_WHITESPACE=true"
)
+
optional
(
"NUM_SEQUENCES="
,
numSequences
,
spaceSeparated
=
false
)
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala
0 → 100644
View file @
488594e1
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions.samtools
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/** Extension for samtools flagstat */
class
SamtoolsFaidx
(
val
root
:
Configurable
)
extends
Samtools
{
@Input
(
doc
=
"Bam File"
)
var
input
:
File
=
_
@Output
(
doc
=
"output File"
)
private
var
_output
:
File
=
_
def
output
=
_output
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
_output
=
new
File
(
input
.
getParentFile
,
input
.
getName
+
".fai"
)
}
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
"faidx"
)
+
required
(
input
)
}
object
SamtoolsFaidx
{
def
apply
(
root
:
Configurable
,
input
:
File
)
:
SamtoolsFaidx
=
{
val
faidx
=
new
SamtoolsFaidx
(
root
)
faidx
.
input
=
input
faidx
.
_output
=
new
File
(
input
.
getParentFile
,
input
.
getName
+
".fai"
)
faidx
}
}
\ No newline at end of file
public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
View file @
488594e1
...
...
@@ -16,6 +16,7 @@
package
nl.lumc.sasc.biopet.extensions
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.SkipException
...
...
public/generate-indexes/pom.xml
0 → 100644
View file @
488594e1
<?xml version="1.0" encoding="UTF-8"?>
<!--
Biopet is built on top of GATK Queue for building bioinformatic
pipelines. It is mainly intended to support LUMC SHARK cluster which is running
SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
should also be able to execute Biopet tools and pipelines.
Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
-->
<project
xmlns=
"http://maven.apache.org/POM/4.0.0"
xmlns:xsi=
"http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation=
"http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
>
<modelVersion>
4.0.0
</modelVersion>
<artifactId>
GenerateIndexes
</artifactId>
<packaging>
jar
</packaging>
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.6.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
<inceptionYear>
2014
</inceptionYear>
<name>
GenerateIndexes
</name>
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetCore
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetExtensions
</artifactId>
<version>
${project.version}
</version>
</dependency>
</dependencies>
</project>
\ No newline at end of file
public/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala
0 → 100644
View file @
488594e1
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.pipelines
import
java.io.PrintWriter
import
java.util
import
nl.lumc.sasc.biopet.core.extensions.Md5sum
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie2Build
,
BowtieBuild
}
import
nl.lumc.sasc.biopet.extensions.bwa.BwaIndex
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.gmap.GmapBuild