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biopet.biopet
Commits
0e95e90f
Commit
0e95e90f
authored
Sep 15, 2016
by
Peter van 't Hof
Browse files
Added pre_command to executable check
parent
5a9c3ce9
Changes
1
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Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
0e95e90f
...
...
@@ -113,7 +113,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
* Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
*/
protected
[
core
]
def
preProcessExecutable
()
{
val
exe
=
BiopetCommandLineFunction
.
preProcessExecutable
(
executable
)
val
exe
=
BiopetCommandLineFunction
.
preProcessExecutable
(
executable
,
preCommands
)
exe
.
path
.
foreach
(
executable
=
_
)
addJobReportBinding
(
"md5sum_exe"
,
exe
.
md5
.
getOrElse
(
"N/A"
))
}
...
...
@@ -243,13 +243,18 @@ object BiopetCommandLineFunction extends Logging {
private
[
core
]
val
executableCache
:
mutable.Map
[
String
,
String
]
=
mutable
.
Map
()
case
class
Executable
(
path
:
Option
[
String
],
md5
:
Option
[
String
])
def
preProcessExecutable
(
executable
:
String
)
:
Executable
=
{
def
preProcessExecutable
(
executable
:
String
,
pre_commands
:
List
[
String
]
=
Nil
)
:
Executable
=
{
if
(!
BiopetCommandLineFunction
.
executableMd5Cache
.
contains
(
executable
))
{
if
(
executable
!=
null
)
{
if
(!
BiopetCommandLineFunction
.
executableCache
.
contains
(
executable
))
{
try
{
val
buffer
=
new
StringBuffer
()
val
cmd
=
Seq
(
"which"
,
executable
)
val
tempFile
=
File
.
createTempFile
(
"which."
,
".sh"
)
val
writer
=
new
PrintWriter
(
tempFile
)
pre_commands
.
foreach
(
cmd
=>
writer
.
println
(
cmd
+
" > /dev/null 2> /dev/null"
))
writer
.
println
(
s
"which $executable"
)
writer
.
close
()
val
cmd
=
Seq
(
"bash"
,
tempFile
.
getAbsolutePath
)
val
process
=
Process
(
cmd
).
run
(
ProcessLogger
(
buffer
.
append
(
_
)))
if
(
process
.
exitValue
==
0
)
{
val
file
=
new
File
(
buffer
.
toString
)
...
...
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