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biopet.biopet
Commits
5a7b30eb
Commit
5a7b30eb
authored
Aug 26, 2016
by
Peter van 't Hof
Browse files
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Merge remote-tracking branch 'remotes/origin/release-0.7.0' into develop
parents
2a6a08ee
e8783392
Changes
41
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41 changed files
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243 additions
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30 deletions
+243
-30
bam2wig/pom.xml
bam2wig/pom.xml
+1
-1
bammetrics/pom.xml
bammetrics/pom.xml
+1
-1
basty/pom.xml
basty/pom.xml
+1
-1
biopet-core/pom.xml
biopet-core/pom.xml
+1
-1
biopet-extensions/pom.xml
biopet-extensions/pom.xml
+1
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
...l/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
+14
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
...la/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
+14
-0
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala
...t/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala
+14
-0
biopet-package/pom.xml
biopet-package/pom.xml
+1
-1
biopet-tools-extensions/pom.xml
biopet-tools-extensions/pom.xml
+1
-1
biopet-tools-package/pom.xml
biopet-tools-package/pom.xml
+1
-1
biopet-tools/pom.xml
biopet-tools/pom.xml
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
...scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
...n/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala
.../scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
...main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
+14
-0
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
...l/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
+14
-0
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.scala
...ala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.scala
+14
-0
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala
...scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala
+14
-0
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala
...la/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala
+14
-0
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/StatsTest.scala
.../scala/nl/lumc/sasc/biopet/tools/bamstats/StatsTest.scala
+14
-0
biopet-utils/pom.xml
biopet-utils/pom.xml
+1
-1
carp/pom.xml
carp/pom.xml
+1
-1
docs/examples/pom.xml
docs/examples/pom.xml
+17
-1
docs/releasenotes/release_notes_0.7.0.md
docs/releasenotes/release_notes_0.7.0.md
+2
-1
external-example/pom.xml
external-example/pom.xml
+4
-4
flexiprep/pom.xml
flexiprep/pom.xml
+1
-1
gears/pom.xml
gears/pom.xml
+1
-1
generate-indexes/pom.xml
generate-indexes/pom.xml
+1
-1
gentrap/pom.xml
gentrap/pom.xml
+1
-1
gwas-test/pom.xml
gwas-test/pom.xml
+1
-1
gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2Vcf.scala
...mc/sasc/biopet/pipelines/gwastest/impute/Impute2Vcf.scala
+14
-0
gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
...asc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
+14
-0
kopisu/pom.xml
kopisu/pom.xml
+1
-1
mapping/pom.xml
mapping/pom.xml
+1
-1
pom.xml
pom.xml
+1
-1
sage/pom.xml
sage/pom.xml
+1
-1
shiva/pom.xml
shiva/pom.xml
+1
-1
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
...elines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
+14
-0
tinycap/pom.xml
tinycap/pom.xml
+1
-1
toucan/pom.xml
toucan/pom.xml
+1
-1
No files found.
bam2wig/pom.xml
View file @
5a7b30eb
...
...
@@ -26,7 +26,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
bammetrics/pom.xml
View file @
5a7b30eb
...
...
@@ -24,7 +24,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
basty/pom.xml
View file @
5a7b30eb
...
...
@@ -31,7 +31,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
biopet-core/pom.xml
View file @
5a7b30eb
...
...
@@ -21,7 +21,7 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
<modelVersion>
4.0.0
</modelVersion>
...
...
biopet-extensions/pom.xml
View file @
5a7b30eb
...
...
@@ -21,7 +21,7 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
</parent>
<modelVersion>
4.0.0
</modelVersion>
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
View file @
5a7b30eb
/**
* 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 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.bedtools
import
java.io.File
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
View file @
5a7b30eb
/**
* 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 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.hisat
import
java.io.File
...
...
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala
View file @
5a7b30eb
/**
* 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 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
import
java.io.File
...
...
biopet-package/pom.xml
View file @
5a7b30eb
...
...
@@ -24,7 +24,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
biopet-tools-extensions/pom.xml
View file @
5a7b30eb
...
...
@@ -21,7 +21,7 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
</parent>
<modelVersion>
4.0.0
</modelVersion>
...
...
biopet-tools-package/pom.xml
View file @
5a7b30eb
...
...
@@ -21,7 +21,7 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
</parent>
<modelVersion>
4.0.0
</modelVersion>
...
...
biopet-tools/pom.xml
View file @
5a7b30eb
...
...
@@ -21,7 +21,7 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
<modelVersion>
4.0.0
</modelVersion>
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
View file @
5a7b30eb
...
...
@@ -63,7 +63,7 @@ object ExtractAlignedFastq extends ToolCommand {
def
intFromCoord
(
s
:
String
)
:
Int
=
s
.
replaceAll
(
","
,
""
).
replaceAll
(
"\\."
,
""
).
toInt
inStrings
.
map
{
case
ptn1
(
chr
,
start
,
end
)
if
intFromCoord
(
end
)
>=
intFromCoord
(
start
)
=>
new
Interval
(
chr
,
intFromCoord
(
start
),
intFromCoord
(
end
))
case
ptn1
(
chr
,
start
,
end
)
if
intFromCoord
(
end
)
>=
intFromCoord
(
start
)
=>
new
Interval
(
chr
,
intFromCoord
(
start
),
intFromCoord
(
end
))
case
ptn2
(
chr
,
start
)
=>
val
startCoord
=
intFromCoord
(
start
)
new
Interval
(
chr
,
startCoord
,
startCoord
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
View file @
5a7b30eb
/**
* 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 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.tools.bamstats
import
java.io.File
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala
View file @
5a7b30eb
/**
* 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 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.tools.bamstats
import
java.io.
{
File
,
PrintWriter
}
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
View file @
5a7b30eb
/**
* 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 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.tools.bamstats
import
java.io.File
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
View file @
5a7b30eb
/**
* 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 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.tools.flagstat
import
java.io.
{
File
,
PrintWriter
}
...
...
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.scala
View file @
5a7b30eb
/**
* 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 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.tools.bamstats
import
java.io.File
...
...
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala
View file @
5a7b30eb
/**
* 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 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.tools.bamstats
import
java.io.File
...
...
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala
View file @
5a7b30eb
/**
* 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 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.tools.bamstats
import
java.io.File
...
...
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/StatsTest.scala
View file @
5a7b30eb
/**
* 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 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.tools.bamstats
import
org.scalatest.Matchers
...
...
biopet-utils/pom.xml
View file @
5a7b30eb
...
...
@@ -21,7 +21,7 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
<modelVersion>
4.0.0
</modelVersion>
...
...
carp/pom.xml
View file @
5a7b30eb
...
...
@@ -24,7 +24,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
docs/examples/pom.xml
View file @
5a7b30eb
<?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 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"
>
...
...
@@ -6,7 +22,7 @@
<groupId>
path.to.your
</groupId>
<artifactId>
MyProject
</artifactId>
<version>
YourVersion1.0
</version>
<version>
0.8.0-SNAPSHOT
</version>
<properties>
<project.build.sourceEncoding>
UTF-8
</project.build.sourceEncoding>
...
...
docs/releasenotes/release_notes_0.7.0.md
View file @
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# Release notes Biopet version 0.
6
.0
# Release notes Biopet version 0.
7
.0
## General Code changes
...
...
@@ -24,6 +24,7 @@
*
Utils - BamUtils is now estimating insert size by sampling the bam-file taking all parts of the available contigs.
*
Fix in VCF filter (#370)[https://git.lumc.nl/biopet/biopet/merge_requests/370]
*
Fix Star wrapper - added full functionality in wrapper.
*
Added a new tools: BamStats
## Reporting
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external-example/pom.xml
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@@ -27,7 +27,7 @@
<artifactId>
ExternalExample
</artifactId>
<!--TODO: replace version, for a new pipeline it's advised to start with '0.1.0-SNAPSHOT' -->
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<properties>
<project.build.sourceEncoding>
UTF-8
</project.build.sourceEncoding>
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@@ -56,19 +56,19 @@
<artifactId>
BiopetCore
</artifactId>
<!--TODO: replace version of pipeline to a fixed version -->
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetExtensions
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Shiva
</artifactId>
<!--TODO: replace version of pipeline to a fixed version -->
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
</dependency>
</dependencies>
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flexiprep/pom.xml
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@@ -24,7 +24,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
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gears/pom.xml
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@@ -21,7 +21,7 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
<modelVersion>
4.0.0
</modelVersion>
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generate-indexes/pom.xml
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@@ -26,7 +26,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
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gentrap/pom.xml
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@@ -24,7 +24,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
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gwas-test/pom.xml
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@@ -26,7 +26,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
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...
gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2Vcf.scala
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/**
* 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 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.gwastest.impute
import
java.io.File
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...
gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
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/**
* 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 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.gwastest.impute
import
java.io.File
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kopisu/pom.xml
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@@ -24,7 +24,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
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mapping/pom.xml
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@@ -24,7 +24,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
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pom.xml
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@@ -21,7 +21,7 @@
<groupId>
nl.lumc.sasc
</groupId>
<name>
Biopet
</name>
<packaging>
pom
</packaging>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<modules>
<module>
biopet-package
</module>
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sage/pom.xml
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@@ -24,7 +24,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
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shiva/pom.xml
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@@ -21,7 +21,7 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
</parent>
<modelVersion>
4.0.0
</modelVersion>
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shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
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/**
* 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 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.shiva.variantcallers
import
java.io.File
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tinycap/pom.xml
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@@ -21,7 +21,7 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
</parent>
<modelVersion>
4.0.0
</modelVersion>
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toucan/pom.xml
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@@ -24,7 +24,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.
7
.0-SNAPSHOT
</version>
<version>
0.
8
.0-SNAPSHOT
</version>
<relativePath>
../
</relativePath>
</parent>
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