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biopet.biopet
Commits
079ac31b
Commit
079ac31b
authored
Jun 10, 2015
by
Peter van 't Hof
Browse files
Adding versions
parent
1ee97e08
Changes
3
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
View file @
079ac31b
...
...
@@ -29,6 +29,9 @@ class Gzip(val root: Configurable) extends BiopetCommandLineFunction {
executable
=
config
(
"exe"
,
default
=
"gzip"
)
override
val
versionRegex
=
"""gzip (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
def
cmdLine
=
required
(
executable
)
+
" -c "
+
repeat
(
input
)
+
" > "
+
required
(
output
)
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
View file @
079ac31b
...
...
@@ -33,6 +33,9 @@ class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
executable
=
config
(
"exe"
,
default
=
"md5sum"
)
override
val
versionRegex
=
"""md5sum \(GNU coreutils\) (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
/** return commandline to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
input
)
+
" > "
+
required
(
output
)
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
View file @
079ac31b
...
...
@@ -30,6 +30,9 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
executable
=
config
(
"exe"
,
default
=
"zcat"
)
override
val
versionRegex
=
"""zcat \(gzip\) (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
input
)
+
" > "
+
required
(
output
)
}
...
...
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