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biopet.biopet
Commits
6bb6b014
Commit
6bb6b014
authored
Jan 15, 2015
by
Sander Bollen
Browse files
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Adding toucan pipeline stub
parent
7ff4c9b0
Changes
12
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12 changed files
with
423 additions
and
7 deletions
+423
-7
protected/biopet-protected-package/BiopetProtectedPackage.iml
...ected/biopet-protected-package/BiopetProtectedPackage.iml
+1
-0
public/biopet-framework/BiopetFramework.iml
public/biopet-framework/BiopetFramework.iml
+1
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+226
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala
.../main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala
+10
-5
public/biopet-public-package/BiopetPublicPackage.iml
public/biopet-public-package/BiopetPublicPackage.iml
+1
-0
public/biopet-public-package/pom.xml
public/biopet-public-package/pom.xml
+5
-0
public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
...ala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
+2
-1
public/pom.xml
public/pom.xml
+1
-0
public/toucan/.gitignore
public/toucan/.gitignore
+1
-0
public/toucan/Flexiprep.iml
public/toucan/Flexiprep.iml
+92
-0
public/toucan/pom.xml
public/toucan/pom.xml
+43
-0
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+40
-0
No files found.
protected/biopet-protected-package/BiopetProtectedPackage.iml
View file @
6bb6b014
...
...
@@ -95,6 +95,7 @@
<orderEntry
type=
"module"
module-name=
"Gentrap"
/>
<orderEntry
type=
"module"
module-name=
"Sage"
/>
<orderEntry
type=
"module"
module-name=
"Yamsvp"
/>
<orderEntry
type=
"module"
module-name=
"Toucan"
/>
<orderEntry
type=
"module"
module-name=
"BiopetGatkPipelines"
/>
<orderEntry
type=
"module"
module-name=
"BiopetGatkExtensions"
/>
<orderEntry
type=
"module"
module-name=
"Basty"
/>
...
...
public/biopet-framework/BiopetFramework.iml
View file @
6bb6b014
...
...
@@ -5,8 +5,8 @@
<output-test
url=
"file://$MODULE_DIR$/target/test-classes"
/>
<content
url=
"file://$MODULE_DIR$"
>
<sourceFolder
url=
"file://$MODULE_DIR$/src/main/resources"
type=
"java-resource"
/>
<sourceFolder
url=
"file://$MODULE_DIR$/src/test/resources"
type=
"java-test-resource"
/>
<sourceFolder
url=
"file://$MODULE_DIR$/src/main/scala"
isTestSource=
"false"
/>
<sourceFolder
url=
"file://$MODULE_DIR$/src/test/resources"
type=
"java-test-resource"
/>
<sourceFolder
url=
"file://$MODULE_DIR$/src/test/scala"
isTestSource=
"true"
/>
<excludeFolder
url=
"file://$MODULE_DIR$/target"
/>
</content>
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
0 → 100644
View file @
6bb6b014
package
nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Created by ahbbollen on 15-1-15.
*/
class
VariantEffectPredictor
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
executable
=
config
(
"exe"
,
submodule
=
"perl"
,
default
=
"perl"
)
var
vep_script
:
String
=
config
(
"vep_script"
,
required
=
true
)
@Input
(
doc
=
"input VCF"
,
required
=
true
)
var
input
:
File
=
_
@Output
(
doc
=
"output file"
,
required
=
true
)
var
output
:
File
=
_
override
val
versionRegex
=
"""version (\d*)"""
.
r
override
def
versionCommand
=
executable
+
" "
+
vep_script
+
" --help"
//Boolean vars
var
v
:
Boolean
=
config
(
"v"
)
var
q
:
Boolean
=
config
(
"q"
)
var
no_progress
:
Boolean
=
config
(
"no_progress"
)
var
everything
:
Boolean
=
config
(
"everything"
)
var
force
:
Boolean
=
config
(
"force"
)
var
no_stats
:
Boolean
=
config
(
"no_stats"
)
var
stats_text
:
Boolean
=
config
(
"stats_text"
)
var
html
:
Boolean
=
config
(
"html"
)
var
cache
:
Boolean
=
config
(
"cache"
)
var
humdiv
:
Boolean
=
config
(
"humdiv"
)
var
regulatory
:
Boolean
=
config
(
"regulatory"
)
var
cell_type
:
Boolean
=
config
(
"cell_type"
)
var
phased
:
Boolean
=
config
(
"phased"
)
var
allele_number
:
Boolean
=
config
(
"allele_number"
)
var
numbers
:
Boolean
=
config
(
"numbers"
)
var
domains
:
Boolean
=
config
(
"domains"
)
var
no_escape
:
Boolean
=
config
(
"no_escape"
)
var
hgvs
:
Boolean
=
config
(
"hgvs"
)
var
protein
:
Boolean
=
config
(
"protein"
)
var
symbol
:
Boolean
=
config
(
"symbol"
)
var
ccds
:
Boolean
=
config
(
"ccds"
)
var
uniprot
:
Boolean
=
config
(
"uniprot"
)
var
tsl
:
Boolean
=
config
(
"tsl"
)
var
canonical
:
Boolean
=
config
(
"canonical"
)
var
biotype
:
Boolean
=
config
(
"biotype"
)
var
xref_refseq
:
Boolean
=
config
(
"xref_refseq"
)
var
check_existing
:
Boolean
=
config
(
"check_existing"
)
var
check_alleles
:
Boolean
=
config
(
"check_alleles"
)
var
check_svs
:
Boolean
=
config
(
"svs"
)
var
gmaf
:
Boolean
=
config
(
"gmaf"
)
var
maf_1kg
:
Boolean
=
config
(
"maf_1kg"
)
var
maf_esp
:
Boolean
=
config
(
"maf_esp"
)
var
old_map
:
Boolean
=
config
(
"old_maf"
)
var
pubmed
:
Boolean
=
config
(
"pubmed"
)
var
failed
:
Boolean
=
config
(
"failed"
)
var
vcf
:
Boolean
=
config
(
"vcf"
,
default
=
true
)
var
json
:
Boolean
=
config
(
"json"
)
var
gvf
:
Boolean
=
config
(
"gvf"
)
var
check_ref
:
Boolean
=
config
(
"check_ref"
)
var
coding_only
:
Boolean
=
config
(
"coding_only"
)
var
no_intergenic
:
Boolean
=
config
(
"no_intergenic"
)
var
pick
:
Boolean
=
config
(
"pick"
)
var
pick_allele
:
Boolean
=
config
(
"pick_allele"
)
var
flag_pick
:
Boolean
=
config
(
"flag_pick"
)
var
flag_pick_allele
:
Boolean
=
config
(
"flag_pick_allele"
)
var
per_gene
:
Boolean
=
config
(
"per_gene"
)
var
most_severe
:
Boolean
=
config
(
"most_severe"
)
var
summary
:
Boolean
=
config
(
"summary"
)
var
filter_common
:
Boolean
=
config
(
"filter_common"
)
var
check_frequency
:
Boolean
=
config
(
"check_frequency"
)
var
allow_non_variant
:
Boolean
=
config
(
"allow_non_variant"
)
var
database
:
Boolean
=
config
(
"database"
)
var
genomes
:
Boolean
=
config
(
"genomes"
)
var
gencode_basic
:
Boolean
=
config
(
"gencode_basic"
)
var
refseq
:
Boolean
=
config
(
"refseq"
)
var
merged
:
Boolean
=
config
(
"merged"
)
var
all_refseq
:
Boolean
=
config
(
"all_refseq"
)
var
lrg
:
Boolean
=
config
(
"lrg"
)
var
no_whole_genome
:
Boolean
=
config
(
"no_whole_genome"
)
var
skip_db_check
:
Boolean
=
config
(
"skip_db_check"
)
// Textual args
var
vep_config
:
String
=
config
(
"config"
)
var
species
:
String
=
config
(
"species"
)
var
assembly
:
String
=
config
(
"assembly"
)
var
format
:
String
=
config
(
"format"
)
var
dir
:
String
=
config
(
"dir"
)
var
dir_cache
:
String
=
config
(
"dir_cache"
)
var
dir_plugins
:
String
=
config
(
"dir_plugins"
)
var
fasta
:
File
=
config
(
"fasta"
)
var
sift
:
String
=
config
(
"sift"
)
var
polyphen
:
String
=
config
(
"polyphen"
)
var
custom
:
String
=
config
(
"custom"
)
var
plugin
:
List
[
String
]
=
config
(
"plugin"
)
var
individual
:
String
=
config
(
"individual"
)
var
fields
:
String
=
config
(
"fields"
)
var
convert
:
String
=
config
(
"convert"
)
var
terms
:
String
=
config
(
"terms"
)
var
chr
:
String
=
config
(
"chr"
)
var
pick_order
:
String
=
config
(
"pick_order"
)
var
freq_pop
:
String
=
config
(
"check_pop"
)
var
freq_gt_lt
:
String
=
config
(
"freq_gt_lt"
)
var
freq_filter
:
String
=
config
(
"freq_filter"
)
var
filter
:
String
=
config
(
"filter"
)
var
host
:
String
=
config
(
"host"
)
var
user
:
String
=
config
(
"user"
)
var
password
:
String
=
config
(
"password"
)
var
registry
:
String
=
config
(
"registry"
)
var
build
:
String
=
config
(
"build"
)
var
compress
:
String
=
config
(
"compress"
)
var
cache_region_size
:
String
=
config
(
"cache_region_size"
)
// Numeric args
var
fork
:
Option
[
Int
]
=
config
(
"fork"
)
var
cache_version
:
Option
[
Int
]
=
config
(
"cache_version"
)
var
freq_freq
:
Option
[
Float
]
=
config
(
"freq_freq"
)
var
port
:
Option
[
Int
]
=
config
(
"port"
)
var
db_version
:
Option
[
Int
]
=
config
(
"db_version"
)
var
buffer_size
:
Option
[
Int
]
=
config
(
"buffer_size"
)
def
cmdLine
=
required
(
executable
)
+
required
(
vep_script
)
+
required
(
"-i"
,
input
)
+
required
(
"-o"
,
output
)
+
conditional
(
v
,
"-v"
)
+
conditional
(
q
,
"-q"
)
+
conditional
(
no_progress
,
"--no_progress"
)
+
conditional
(
everything
,
"--everything"
)
+
conditional
(
force
,
"--force_overwrite"
)
+
conditional
(
no_stats
,
"--no_stats"
)
+
conditional
(
stats_text
,
"--stats_text"
)
+
conditional
(
html
,
"--html"
)
+
conditional
(
cache
,
"--cache"
)
+
conditional
(
humdiv
,
"--humdiv"
)
+
conditional
(
regulatory
,
"--regulatory"
)
+
conditional
(
cell_type
,
"--cel_type"
)
+
conditional
(
phased
,
"--phased"
)
+
conditional
(
allele_number
,
"--allele_number"
)
+
conditional
(
numbers
,
"--numbers"
)
+
conditional
(
domains
,
"--domains"
)
+
conditional
(
no_escape
,
"--no_escape"
)
+
conditional
(
hgvs
,
"--hgvs"
)
+
conditional
(
protein
,
"--protein"
)
+
conditional
(
symbol
,
"--symbol"
)
+
conditional
(
ccds
,
"--ccds"
)
+
conditional
(
uniprot
,
"--uniprot"
)
+
conditional
(
tsl
,
"--tsl"
)
+
conditional
(
canonical
,
"--canonical"
)
+
conditional
(
biotype
,
"--biotype"
)
+
conditional
(
xref_refseq
,
"--xref_refseq"
)
+
conditional
(
check_existing
,
"--check_existing"
)
+
conditional
(
check_alleles
,
"--check_alleles"
)
+
conditional
(
check_svs
,
"--check_svs"
)
+
conditional
(
gmaf
,
"--gmaf"
)
+
conditional
(
maf_1kg
,
"--maf_1kg"
)
+
conditional
(
maf_esp
,
"--maf_esp"
)
+
conditional
(
pubmed
,
"--pubmed"
)
+
conditional
(
failed
,
"--failed"
)
+
conditional
(
vcf
,
"--vcf"
)
+
conditional
(
json
,
"--json"
)
+
conditional
(
gvf
,
"--gvf"
)
+
conditional
(
check_ref
,
"--check_ref"
)
+
conditional
(
coding_only
,
"--coding_only"
)
+
conditional
(
no_intergenic
,
"--no_intergenic"
)
+
conditional
(
pick
,
"--pick"
)
+
conditional
(
pick_allele
,
"--pick_allele"
)
+
conditional
(
flag_pick
,
"--flag_pick"
)
+
conditional
(
flag_pick_allele
,
"--flag_pick_allele"
)
+
conditional
(
per_gene
,
"--per_gene"
)
+
conditional
(
most_severe
,
"--most_severe"
)
+
conditional
(
summary
,
"--summary"
)
+
conditional
(
filter_common
,
"--filter_common"
)
+
conditional
(
check_frequency
,
"--check_frequency"
)
+
conditional
(
allow_non_variant
,
"--allow_non_variant"
)
+
conditional
(
database
,
"--database"
)
+
conditional
(
genomes
,
"--genomes"
)
+
conditional
(
gencode_basic
,
"--gencode_basic"
)
+
conditional
(
refseq
,
"--refseq"
)
+
conditional
(
merged
,
"--merged"
)
+
conditional
(
all_refseq
,
"--all_refseq"
)
+
conditional
(
lrg
,
"--lrg"
)
+
conditional
(
no_whole_genome
,
"--no_whole_genome"
)
+
conditional
(
skip_db_check
,
"--skip_db_check"
)
+
optional
(
"--config"
,
vep_config
)
+
optional
(
"--species"
,
species
)
+
optional
(
"--assembly"
,
assembly
)
+
optional
(
"--format"
,
format
)
+
optional
(
"--dir"
,
dir
)
+
optional
(
"--dir_cache"
,
dir_cache
)
+
optional
(
"--dir_plugins"
,
dir_plugins
)
+
optional
(
"--fasta"
,
fasta
)
+
optional
(
"--sift"
,
sift
)
+
optional
(
"--polyphen"
,
polyphen
)
+
optional
(
"--custom"
,
custom
)
+
repeat
(
"--plugin"
,
plugin
)
+
optional
(
"--individual"
,
individual
)
+
optional
(
"--fields"
,
fields
)
+
optional
(
"--convert"
,
convert
)
+
optional
(
"--terms"
,
terms
)
+
optional
(
"--chr"
,
chr
)
+
optional
(
"--pick_order"
,
pick_order
)
+
optional
(
"--freq_pop"
,
freq_pop
)
+
optional
(
"--freq_gt_lt"
,
freq_gt_lt
)
+
optional
(
"--freq_filter"
,
freq_filter
)
+
optional
(
"--filter"
,
filter
)
+
optional
(
"--host"
,
host
)
+
optional
(
"--user"
,
user
)
+
optional
(
"--password"
,
password
)
+
optional
(
"--registry"
,
registry
)
+
optional
(
"--build"
,
build
)
+
optional
(
"--compress"
,
compress
)
+
optional
(
"--cache_region_size"
,
cache_region_size
)
+
optional
(
"--fork"
,
fork
)
+
optional
(
"--cache_version"
,
cache_version
)
+
optional
(
"--freq_freq"
,
freq_freq
)
+
optional
(
"--port"
,
port
)
+
optional
(
"--db_version"
,
db_version
)
+
optional
(
"--buffer_size"
,
buffer_size
)
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala
View file @
6bb6b014
...
...
@@ -25,12 +25,17 @@ class VEPNormalizer(val root: Configurable) extends BiopetJavaCommandLineFunctio
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input VCF, may be indexed"
,
shortName
=
"InputFile"
,
required
=
true
)
var
InputVCF
:
File
=
_
//TODO: Add flags?
var
inputVCF
:
File
=
_
@Output
(
doc
=
"Output VCF"
,
shortName
=
"OutputFile"
,
required
=
true
)
var
OutputVCF
:
File
=
_
var
outputVCF
:
File
=
_
var
mode
:
String
=
config
(
"mode"
,
default
=
"explode"
)
override
def
commandLine
=
super
.
commandLine
+
required
(
"-I"
,
inputVCF
)
+
required
(
"-O"
,
outputVCF
)
+
required
(
"-m"
,
mode
)
}
object
VEPNormalizer
extends
ToolCommand
{
...
...
@@ -280,7 +285,7 @@ object VEPNormalizer extends ToolCommand {
case
class
Args
(
inputVCF
:
File
=
null
,
outputVCF
:
File
=
null
,
mode
:
String
=
"standard"
)
extends
AbstractArgs
mode
:
String
=
null
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
...
...
public/biopet-public-package/BiopetPublicPackage.iml
View file @
6bb6b014
...
...
@@ -94,5 +94,6 @@
<orderEntry
type=
"module"
module-name=
"Gentrap"
/>
<orderEntry
type=
"module"
module-name=
"Sage"
/>
<orderEntry
type=
"module"
module-name=
"Yamsvp"
/>
<orderEntry
type=
"module"
module-name=
"Toucan"
/>
</component>
</module>
\ No newline at end of file
public/biopet-public-package/pom.xml
View file @
6bb6b014
...
...
@@ -75,6 +75,11 @@
<artifactId>
Yamsvp
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Toucan
</artifactId>
<version>
${project.version}
</version>
</dependency>
</dependencies>
<build>
<plugins>
...
...
public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
View file @
6bb6b014
...
...
@@ -22,7 +22,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gentrap
.
Gentrap
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
bammetrics
.
BamMetrics
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
yamsvp
.
Yamsvp
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
sage
.
Sage
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
sage
.
Sage
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
toucan
.
Toucan
)
def
tools
:
List
[
MainCommand
]
=
List
(
...
...
public/pom.xml
View file @
6bb6b014
...
...
@@ -33,6 +33,7 @@
<module>
mapping
</module>
<module>
sage
</module>
<module>
yamsvp
</module>
<module>
toucan
</module>
</modules>
<properties>
...
...
public/toucan/.gitignore
0 → 100644
View file @
6bb6b014
/target/
\ No newline at end of file
public/toucan/Flexiprep.iml
0 → 100644
View file @
6bb6b014
<?xml version="1.0" encoding="UTF-8"?>
<module
org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule=
"true"
type=
"JAVA_MODULE"
version=
"4"
>
<component
name=
"NewModuleRootManager"
inherit-compiler-output=
"false"
>
<output
url=
"file://$MODULE_DIR$/target/classes"
/>
<output-test
url=
"file://$MODULE_DIR$/target/test-classes"
/>
<content
url=
"file://$MODULE_DIR$"
>
<sourceFolder
url=
"file://$MODULE_DIR$/src/main/resources"
type=
"java-resource"
/>
<sourceFolder
url=
"file://$MODULE_DIR$/src/main/scala"
isTestSource=
"false"
/>
<excludeFolder
url=
"file://$MODULE_DIR$/target"
/>
</content>
<orderEntry
type=
"inheritedJdk"
/>
<orderEntry
type=
"sourceFolder"
forTests=
"false"
/>
<orderEntry
type=
"module"
module-name=
"BiopetFramework"
/>
<orderEntry
type=
"library"
name=
"Maven: org.scala-lang:scala-library:2.11.2"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.broadinstitute.gatk:gatk-queue:3.3"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.broadinstitute.gatk:gatk-tools-public:3.3"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.broadinstitute.gatk:gatk-engine:3.3"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.scala-lang:scala-compiler:2.10.2"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.scala-lang:scala-reflect:2.10.2"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: log4j:log4j:1.2.15"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: net.sf.jgrapht:jgrapht:0.8.3"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.apache.commons:commons-email:1.2"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: javax.activation:activation:1.1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: javax.mail:mail:1.4.4"
level=
"project"
/>
<orderEntry
type=
"module-library"
>
<library
name=
"Maven: com.sun:tools:1.4.2"
>
<CLASSES>
<root
url=
"jar:///usr/lib/jvm/java-1.7.0-openjdk-amd64/lib/tools.jar!/"
/>
</CLASSES>
<JAVADOC
/>
<SOURCES
/>
</library>
</orderEntry>
<orderEntry
type=
"library"
name=
"Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: gov.nist.math:jama:1.0.2"
level=
"project"
/>
<orderEntry
type=
"library"
scope=
"RUNTIME"
name=
"Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.broadinstitute.gatk:gatk-utils:3.3"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: samtools:htsjdk:1.120.1620"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.xerial.snappy:snappy-java:1.0.3-rc3"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: picard:picard:1.120.1579"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.apache.ant:ant:1.8.2"
level=
"project"
/>
<orderEntry
type=
"module-library"
>
<library
name=
"Maven: com.sun:tools.jar:1.5"
>
<CLASSES>
<root
url=
"jar:///usr/lib/jvm/java-1.7.0-openjdk-amd64/lib/tools.jar!/"
/>
</CLASSES>
<JAVADOC
/>
<SOURCES
/>
</library>
</orderEntry>
<orderEntry
type=
"library"
name=
"Maven: colt:colt:1.2.0"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: concurrent:concurrent:1.3.4"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: it.unimi.dsi:fastutil:6.5.3"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.simpleframework:simple-xml:2.0.4"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: stax:stax-api:1.0.1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: stax:stax:1.2.0"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.reflections:reflections:0.9.9-RC1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.javassist:javassist:3.16.1-GA"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: dom4j:dom4j:1.6.1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: xml-apis:xml-apis:1.0.b2"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.slf4j:slf4j-log4j12:1.6.1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.slf4j:slf4j-api:1.6.1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.freemarker:freemarker:2.3.18"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.apache.commons:commons-jexl:2.1.1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: commons-logging:commons-logging:1.1.1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: commons-lang:commons-lang:2.5"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: commons-io:commons-io:2.1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: commons-collections:commons-collections:3.2.1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.apache.commons:commons-math:2.2"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: net.java.dev.jna:jna:3.2.7"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: net.java.dev.jets3t:jets3t:0.8.1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: commons-codec:commons-codec:1.3"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: commons-httpclient:commons-httpclient:3.1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: com.jamesmurty.utils:java-xmlbuilder:0.4"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: us.levk:drmaa-gridengine:6.2u5"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: us.levk:drmaa-common:1.0"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: com.google.code.gson:gson:2.2.2"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.apache.httpcomponents:httpclient:4.1.1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.apache.httpcomponents:httpcore:4.1"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: com.google.code.cofoja:cofoja:1.0-r139"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: io.argonaut:argonaut_2.11:6.1-M4"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.scalaz:scalaz-core_2.11:7.1.0"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.biojava:biojava3-core:3.1.0"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: org.biojava:biojava3-sequencing:3.1.0"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: com.google.guava:guava:18.0"
level=
"project"
/>
<orderEntry
type=
"library"
name=
"Maven: com.github.scopt:scopt_2.10:3.2.0"
level=
"project"
/>
</component>
</module>
\ No newline at end of file
public/toucan/pom.xml
0 → 100644
View file @
6bb6b014
<!--
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>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Toucan
</artifactId>
<packaging>
jar
</packaging>
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.3.0-DEV
</version>
<relativePath>
../
</relativePath>
</parent>
<inceptionYear>
2014
</inceptionYear>
<name>
Toucan
</name>
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetFramework
</artifactId>
<version>
${project.version}
</version>
</dependency>
</dependencies>
</project>
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
0 → 100644
View file @
6bb6b014
package
nl.lumc.sasc.biopet.pipelines.toucan
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
BiopetQScript
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
import
nl.lumc.sasc.biopet.tools.VEPNormalizer
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Argument
}
/**
* Created by ahbbollen on 15-1-15.
*/
class
Toucan
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
def
this
()
=
this
(
null
)
@Input
(
doc
=
"Input VCF file"
,
shortName
=
"Input"
,
required
=
true
)
var
inputVCF
:
File
=
_
def
init
()
:
Unit
=
{
}
defaults
++=
Map
(
"varianteffectpredictor"
->
Map
(
"everything"
->
true
))
def
biopetScript
()
:
Unit
=
{
val
vep
=
new
VariantEffectPredictor
(
this
)
vep
.
input
=
inputVCF
vep
.
output
=
outputDir
+
inputVCF
.
getName
.
stripSuffix
(
".gz"
).
stripSuffix
(
".vcf"
)
+
".vep.vcf"
vep
.
isIntermediate
=
true
add
(
vep
)
val
normalizer
=
new
VEPNormalizer
(
this
)
normalizer
.
inputVCF
=
vep
.
output
normalizer
.
outputVCF
=
swapExt
(
vep
.
output
,
".vcf"
,
".normalized.vcf.gz"
)
add
(
normalizer
)
}
}
object
Toucan
extends
PipelineCommand
\ No newline at end of file
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