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biopet.biopet
Commits
e42e39c6
Commit
e42e39c6
authored
Feb 16, 2015
by
Peter van 't Hof
Browse files
Fix outputDirs
parent
1865f3b0
Changes
2
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Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
View file @
e42e39c6
...
...
@@ -48,7 +48,7 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
var
f
:
String
=
"d"
@Argument
(
doc
=
"Output directory"
,
required
=
true
)
var
w
:
String
=
_
var
w
:
File
=
null
var
noBfgs
:
Boolean
=
config
(
"no_bfgs"
,
default
=
false
)
...
...
@@ -65,6 +65,7 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
var
executableThreads
:
Option
[
String
]
=
config
(
"exe_pthreads"
)
override
def
beforeGraph
{
require
(
w
!=
null
)
if
(
threads
==
0
)
threads
=
getThreads
(
defaultThreads
)
executable
=
if
(
threads
>
1
&&
executableThreads
.
isDefined
)
executableThreads
.
get
else
executableNonThreads
super
.
beforeGraph
...
...
@@ -73,24 +74,24 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
case
"d"
if
b
.
isEmpty
=>
{
out
+:=
getBestTreeFile
for
(
t
<-
0
until
N
.
getOrElse
(
1
))
{
out
+:=
new
File
(
w
+
File
.
separator
+
"RAxML_log."
+
n
+
".RUN."
+
t
)
out
+:=
new
File
(
w
+
File
.
separator
+
"RAxML_parsimonyTree."
+
n
+
".RUN."
+
t
)
out
+:=
new
File
(
w
+
File
.
separator
+
"RAxML_result."
+
n
+
".RUN."
+
t
)
out
+:=
new
File
(
w
,
"RAxML_log."
+
n
+
".RUN."
+
t
)
out
+:=
new
File
(
w
,
"RAxML_parsimonyTree."
+
n
+
".RUN."
+
t
)
out
+:=
new
File
(
w
,
"RAxML_result."
+
n
+
".RUN."
+
t
)
}
}
case
"d"
if
b
.
isDefined
=>
out
+:=
getBootstrapFile
case
"b"
=>
{
out
+:=
new
File
(
w
+
File
.
separator
+
"RAxML_bipartitionsBranchLabels."
+
n
)
out
+:=
new
File
(
w
+
File
.
separator
+
"RAxML_bipartitions."
+
n
)
out
+:=
new
File
(
w
,
"RAxML_bipartitionsBranchLabels."
+
n
)
out
+:=
new
File
(
w
,
"RAxML_bipartitions."
+
n
)
}
case
_
=>
}
}
def
getBestTreeFile
:
File
=
new
File
(
w
+
File
.
separator
+
"RAxML_bestTree."
+
n
)
def
getBootstrapFile
:
File
=
new
File
(
w
+
File
.
separator
+
"RAxML_bootstrap."
+
n
)
def
getBipartitionsFile
:
File
=
new
File
(
w
+
File
.
separator
+
"RAxML_bipartitions."
+
n
)
def
getInfoFile
:
File
=
new
File
(
w
+
File
.
separator
+
"RAxML_info."
+
n
)
def
getBestTreeFile
:
File
=
new
File
(
w
,
"RAxML_bestTree."
+
n
)
def
getBootstrapFile
:
File
=
new
File
(
w
,
"RAxML_bootstrap."
+
n
)
def
getBipartitionsFile
:
File
=
new
File
(
w
,
"RAxML_bipartitions."
+
n
)
def
getInfoFile
:
File
=
new
File
(
w
,
"RAxML_info."
+
n
)
def
cmdLine
=
required
(
executable
)
+
required
(
"-m"
,
m
)
+
...
...
@@ -103,6 +104,6 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
optional
(
"-f"
,
f
)
+
optional
(
"-t"
,
t
)
+
optional
(
"-z"
,
z
)
+
conditional
(
noBfgs
,
"--no-b
g
fs"
)
+
conditional
(
noBfgs
,
"--no-bf
g
s"
)
+
required
(
"-T"
,
threads
)
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
View file @
e42e39c6
...
...
@@ -33,7 +33,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
var
outputFiles
:
List
[
File
]
=
Nil
@Argument
(
required
=
true
)
var
outputDirectory
:
String
=
_
var
outputDirectory
:
File
=
null
executable
=
config
(
"exe"
,
default
=
"run_gubbins.py"
)
var
outgroup
:
Option
[
String
]
=
config
(
"outgroup"
)
...
...
@@ -49,7 +49,8 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
jobLocalDir
=
new
File
(
outputDirectory
)
require
(
outputDirectory
!=
null
)
jobLocalDir
=
outputDirectory
if
(
prefix
.
isEmpty
)
prefix
=
Some
(
fastafile
.
getName
)
val
out
:
List
[
String
]
=
List
(
".recombination_predictions.embl"
,
".recombination_predictions.gff"
,
...
...
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