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biopet.biopet
Commits
e371afc7
Commit
e371afc7
authored
Feb 16, 2017
by
Peter van 't Hof
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Config report now happens in the background
parent
65f98276
Changes
4
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4 changed files
with
16 additions
and
9 deletions
+16
-9
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+6
-3
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+2
-2
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
.../main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
+6
-2
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
...cala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
+2
-2
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
e371afc7
...
...
@@ -24,6 +24,8 @@ import org.broadinstitute.gatk.queue.{ QScript, QSettings }
import
org.broadinstitute.gatk.queue.function.QFunction
import
org.broadinstitute.gatk.queue.util.
{
Logging
=>
GatkLogging
}
import
scala.collection.mutable.ListBuffer
/** Base for biopet pipeline */
trait
BiopetQScript
extends
Configurable
with
GatkLogging
{
qscript
:
QScript
=>
...
...
@@ -95,6 +97,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
logger
.
info
(
"Running pre commands"
)
var
count
=
0
val
totalCount
=
functions
.
size
for
(
function
<-
functions
)
{
function
match
{
case
f
:
BiopetCommandLineFunction
=>
...
...
@@ -106,15 +109,15 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
case
_
=>
}
count
+=
1
if
(
count
%
500
==
0
)
logger
.
info
(
s
"Preprocessing done for $
{count} jobs out of ${functions.length}
total"
)
if
(
count
%
500
==
0
)
logger
.
info
(
s
"Preprocessing done for $
count jobs out of $totalCount
total"
)
}
logger
.
info
(
s
"Preprocessing done for $
{functions.length}
functions"
)
logger
.
info
(
s
"Preprocessing done for $
totalCount
functions"
)
val
logDir
=
new
File
(
outputDir
,
".log"
+
File
.
separator
+
qSettings
.
runName
.
toLowerCase
)
if
(
outputDir
.
getParentFile
.
canWrite
||
(
outputDir
.
exists
&&
outputDir
.
canWrite
))
globalConfig
.
writeReport
(
new
File
(
logDir
,
"config"
))
else
Logging
.
addError
(
"Parent of output dir: '"
+
outputDir
.
getParent
+
"' is not writ
e
able, output directory cannot be created"
)
else
Logging
.
addError
(
"Parent of output dir: '"
+
outputDir
.
getParent
+
"' is not writable, output directory cannot be created"
)
logger
.
info
(
"Checking input files"
)
inputFiles
.
par
.
foreach
{
i
=>
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
e371afc7
...
...
@@ -14,11 +14,11 @@
*/
package
nl.lumc.sasc.biopet.core.summary
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
java.sql.Date
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.extensions.
{
CheckChecksum
,
Md5sum
}
import
nl.lumc.sasc.biopet.core.extensions.
{
CheckChecksum
,
Md5sum
}
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
org.broadinstitute.gatk.queue.QScript
import
nl.lumc.sasc.biopet.LastCommitHash
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
View file @
e371afc7
...
...
@@ -15,9 +15,13 @@
package
nl.lumc.sasc.biopet.utils.config
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.
{
Logging
,
ConfigUtils
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils._
import
scala.concurrent.Future
import
scala.concurrent.ExecutionContext.Implicits.global
/**
* This class can store nested config values
* @param _map Map with value for new config
...
...
@@ -189,7 +193,7 @@ class Config(protected var _map: Map[String, Any],
}
else
ConfigValue
(
requestedIndex
,
null
,
null
,
freeVar
)
}
def
writeReport
(
directory
:
File
)
:
Unit
=
{
def
writeReport
(
directory
:
File
)
:
Future
[
Unit
]
=
Future
{
directory
.
mkdirs
()
def
convertIndexValuesToMap
(
input
:
List
[(
ConfigValueIndex
,
Any
)],
forceFreeVar
:
Option
[
Boolean
]
=
None
)
:
Map
[
String
,
Any
]
=
{
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
View file @
e371afc7
...
...
@@ -6,8 +6,8 @@ import slick.driver.H2Driver.api._
import
scala.concurrent.ExecutionContext.Implicits.global
import
scala.concurrent.duration.Duration
import
scala.concurrent.
{
Await
,
Future
}
import
java.io.
{
Closeable
,
File
}
import
scala.concurrent.
{
Await
,
Future
}
import
java.io.
{
Closeable
,
File
}
import
java.sql.Date
/**
...
...
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