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biopet.biopet
Commits
9156f68c
Commit
9156f68c
authored
Oct 26, 2015
by
Peter van 't Hof
Browse files
Fixed unknown executables
parent
db4dcbca
Changes
2
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
View file @
9156f68c
...
...
@@ -43,7 +43,7 @@ trait GatkGeneral extends CommandLineGATK with CommandLineResources with Referen
def
versionCommand
=
"java"
+
" -jar "
+
jarFile
+
" -version"
override
def
getVersion
=
{
executable
=
BiopetCommandLineFunction
.
preProcessExecutable
(
executable
).
path
BiopetCommandLineFunction
.
preProcessExecutable
(
executable
).
path
.
foreach
(
executable
=
_
)
super
.
getVersion
.
collect
{
case
v
=>
"Gatk "
+
v
}
}
}
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
9156f68c
...
...
@@ -99,7 +99,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
*/
protected
[
core
]
def
preProcessExecutable
()
{
val
exe
=
BiopetCommandLineFunction
.
preProcessExecutable
(
executable
)
executable
=
exe
.
path
exe
.
path
.
foreach
(
executable
=
_
)
addJobReportBinding
(
"md5sum_exe"
,
exe
.
md5
.
getOrElse
(
"N/A"
))
}
...
...
@@ -199,7 +199,7 @@ object BiopetCommandLineFunction extends Logging {
private
[
core
]
val
executableMd5Cache
:
mutable.Map
[
String
,
String
]
=
mutable
.
Map
()
private
[
core
]
val
executableCache
:
mutable.Map
[
String
,
String
]
=
mutable
.
Map
()
case
class
Executable
(
path
:
String
,
md5
:
Option
[
String
])
case
class
Executable
(
path
:
Option
[
String
]
,
md5
:
Option
[
String
])
def
preProcessExecutable
(
executable
:
String
)
:
Executable
=
{
if
(!
BiopetCommandLineFunction
.
executableMd5Cache
.
contains
(
executable
))
{
if
(
executable
!=
null
)
{
...
...
@@ -236,7 +236,7 @@ object BiopetCommandLineFunction extends Logging {
}
}
}
Executable
(
BiopetCommandLineFunction
.
executableCache
(
executable
),
Executable
(
BiopetCommandLineFunction
.
executableCache
.
get
(
executable
),
BiopetCommandLineFunction
.
executableMd5Cache
.
get
(
executable
))
}
}
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