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biopet.biopet
Commits
e653337b
Commit
e653337b
authored
Mar 08, 2015
by
bow
Browse files
Fix bug in JAR run caused by copying entire resource folder
parent
c0064f43
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Top
H
at.scala
→
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Top
h
at.scala
View file @
e653337b
...
...
@@ -22,20 +22,28 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
class
TopHat
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"FastQ file R1"
,
shortName
=
"R1"
)
var
R1
:
File
=
_
@Input
(
doc
=
"FastQ file R
2
"
,
shortName
=
"R
2"
,
required
=
false
)
var
R
2
:
File
=
_
@Input
(
doc
=
"FastQ file
(s)
R
1
"
,
shortName
=
"R
1"
)
var
R
1
:
List
[
File
]
=
List
.
empty
[
File
]
@Input
(
doc
=
"
Bowtie index"
,
shortName
=
"bti"
)
var
bowtie_index
:
File
=
config
(
"bowtie_index"
)
@Input
(
doc
=
"
FastQ file(s) R2"
,
shortName
=
"R2"
,
required
=
false
)
var
R2
:
List
[
File
]
=
List
.
empty
[
File
]
@Argument
(
doc
=
"Output Directory"
)
var
outputDir
:
String
=
_
/** output files, computed automatically from output directory */
@Output
(
doc
=
"Output file SAM"
,
shortName
=
"output"
)
var
output
:
File
=
_
@Output
(
doc
=
"Output SAM/BAM file"
)
lazy
val
outputGtf
:
File
=
{
require
(
R1
.
nonEmpty
&&
output_dir
!=
null
,
"Read 1 input(s) are defined and output directory is defined"
)
// cufflinks always outputs a transcripts.gtf file in the output directory
new
File
(
output_dir
,
"accepted_hits.bam"
)
}
@Argument
(
doc
=
"Bowtie index"
,
shortName
=
"bti"
,
required
=
true
)
var
bowtie_index
:
String
=
config
(
"bowtie_index"
)
/** write all output files to this directory [./] */
var
output_dir
:
File
=
config
(
"output_dir"
,
default
=
new
File
(
"tophat_out"
))
// options set via API or config
// var numrecords: String = config("numrecords", default = "all")
...
...
@@ -56,25 +64,18 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
// var logfile: String = config("logfile")
executable
=
config
(
"exe"
,
default
=
"tophat"
,
freeVar
=
false
)
override
val
versionRegex
=
"""TopHat v(.*)"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
override
def
versionCommand
=
executable
+
" --version"
override
val
defaultVmem
=
"4G"
override
val
defaultThreads
=
8
override
def
versionCommand
=
executable
+
" --version"
override
def
beforeGraph
()
{
if
(!
outputDir
.
endsWith
(
"/"
))
outputDir
+=
"/"
output
=
new
File
(
outputDir
+
"accepted_hits.bam"
)
}
//override def beforeGraph = {}
def
cmdLine
:
String
=
{
var
cmd
:
String
=
required
(
executable
)
+
optional
(
"-p"
,
nCoresRequest
)
+
"--no-convert-bam"
+
required
(
bowtie_index
)
+
required
(
R1
)
+
optional
(
R2
)
return
cmd
}
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
bowtie_index
)
+
required
(
R1
.
mkString
(
","
))
+
optional
(
R2
.
mkString
(
","
))
}
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/
img/
gentrap_front.png
→
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/gentrap_front.png
View file @
e653337b
File moved
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala
View file @
e653337b
...
...
@@ -6,9 +6,9 @@
package
nl.lumc.sasc.biopet.pipelines.gentrap.scripts
import
java.io.File
import
java.io.
{
File
,
FileOutputStream
}
import
org.apache.commons.io.
File
Utils
import
org.apache.commons.io.
IO
Utils
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
@@ -19,10 +19,6 @@ import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
*/
class
PdfReportTemplateWriter
(
val
root
:
Configurable
)
extends
PythonCommandLineFunction
{
val
templateResDir
:
File
=
new
File
(
getClass
.
getResource
(
"/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf"
).
toURI
)
val
templateWorkDir
:
File
=
new
File
(
".queue/tmp/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf"
)
val
imgWorkDir
:
File
=
new
File
(
templateWorkDir
,
"img"
)
@Input
(
doc
=
"Input summary file"
,
required
=
true
)
var
summaryFile
:
File
=
null
...
...
@@ -30,13 +26,34 @@ class PdfReportTemplateWriter(val root: Configurable) extends PythonCommandLineF
def
mainTemplateFile
:
File
=
new
File
(
templateWorkDir
,
"main.tex"
)
@Input
(
doc
=
"Main report logo"
,
required
=
true
)
// def since we hard-code the logo
def
logoFile
:
File
=
new
File
(
img
WorkDir
,
"gentrap_front.png"
)
def
logoFile
:
File
=
new
File
(
template
WorkDir
,
"gentrap_front.png"
)
@Output
(
doc
=
"Output file"
,
required
=
true
)
var
output
:
File
=
null
protected
def
prepTemplate
()
:
Unit
=
{
FileUtils
.
copyDirectory
(
templateResDir
,
templateWorkDir
)
val
templateWorkDir
:
File
=
new
File
(
".queue/tmp/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf"
)
val
templateFiles
:
Seq
[
String
]
=
Seq
(
"main.tex"
,
"gentrap_front.png"
,
"sample.tex"
,
"sample_mapping.tex"
,
"lib.tex"
,
"lib_seqeval.tex"
,
"lib_mapping.tex"
)
protected
def
prepTemplate
(
name
:
String
,
subPackage
:
String
=
"/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf"
)
:
Unit
=
{
val
target
=
new
File
(
".queue/tmp"
+
subPackage
,
name
)
if
(!
target
.
getParentFile
.
exists
)
target
.
getParentFile
.
mkdirs
()
val
is
=
getClass
.
getResourceAsStream
(
subPackage
+
"/"
+
name
)
val
os
=
new
FileOutputStream
(
target
)
org
.
apache
.
commons
.
io
.
IOUtils
.
copy
(
is
,
os
)
os
.
close
()
//python_script_name = script
//python_script = new File(".queue/tmp/" + subpackage + python_script_name)
//if (!python_script.getParentFile.exists) python_script.getParentFile.mkdirs
//val is = getClass.getResourceAsStream(subpackage + python_script_name)
//val os = new FileOutputStream(python_script)
//org.apache.commons.io.IOUtils.copy(is, os)
//os.close()
}
def
cmdLine
=
{
...
...
@@ -48,5 +65,5 @@ class PdfReportTemplateWriter(val root: Configurable) extends PythonCommandLineF
}
setPythonScript
(
"pdf_report.py"
)
prepTemplate
()
templateFiles
.
foreach
(
t
=>
prepTemplate
(
t
)
)
}
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