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-rw-r--r--default.nix2
-rw-r--r--lib/qsub.nix127
-rw-r--r--tools/ascat-callCNV.nix1
-rw-r--r--tools/ascat-gccorrect.nix1
-rw-r--r--tools/bowtie-align.nix1
-rw-r--r--tools/bowtie-index.nix1
-rw-r--r--tools/bwa-mem.nix1
-rw-r--r--tools/cnvkit-batch.nix1
-rw-r--r--tools/gridss-assemble.nix1
-rw-r--r--tools/gridss-callVariants.nix1
-rw-r--r--tools/gridss-softClipsToSplitReads.nix1
-rw-r--r--tools/kallisto-quant.nix1
-rw-r--r--tools/mosdepth-depth.nix1
-rw-r--r--tools/platypus-callVariants.nix1
-rw-r--r--tools/samtools-flagstat.nix1
-rw-r--r--tools/samtools-index.nix1
-rw-r--r--tools/samtools-sort.nix1
-rw-r--r--tools/strelka-call.nix1
-rw-r--r--tools/strelka-callSomatic.nix1
19 files changed, 83 insertions, 63 deletions
diff --git a/default.nix b/default.nix
index aa3d8d2..736eef0 100644
--- a/default.nix
+++ b/default.nix
@@ -63,7 +63,7 @@ let
# Export nixpkgs and standard library lib
pkgs = nixpkgs;
lib = nixpkgs.lib // { types = types; };
- stage = nixpkgs.stdenvNoCC.mkDerivation;
+ stage = x: { multicore = false; } // nixpkgs.stdenvNoCC.mkDerivation x;
# splitting/joining
splitFile = file: drv: stage {
diff --git a/lib/qsub.nix b/lib/qsub.nix
index 6b40431..6370a98 100644
--- a/lib/qsub.nix
+++ b/lib/qsub.nix
@@ -2,70 +2,73 @@
with lib;
-{ ppn, mem, walltime, queue ? null, qsubFlags ? null, tmpDir, sleepTime}: drv: lib.overrideDerivation drv ({ args, builder, name, ... }: {
- builder = "/bin/bash";
- args = let
- script = writeScript "qsub-script" ''
- #!${stdenv.shell}
- while [ ! -e ${tmpDir}/qsub-$PBS_JOBID ] ; do
- sleep ${toString sleepTime}
- done
- set -a
- . ${tmpDir}/qsub-$PBS_JOBID/nix-set
- set +a
- TMPDIR=${tmpDir}/qsub-$PBS_JOBID
- TEMP=$TMPDIR
- TMP=$TMPDIR
- NIX_BUILD_TOP=$TMPDIR
- cd $TMPDIR
- ${builder} ${lib.escapeShellArgs args} &> qsub-log
- echo $? > qsub-exit
- '';
+{ ppn, mem, walltime, queue ? null, qsubFlags ? null, tmpDir, sleepTime}:
+drv:
+ let ppnReified = if drv.multicore then ppn else 1;
+ in lib.overrideDerivation drv ({ args, builder, name, ... }: {
+ builder = "/bin/bash";
+ args = let
+ script = writeScript "qsub-script" ''
+ #!${stdenv.shell}
+ while [ ! -e ${tmpDir}/qsub-$PBS_JOBID ] ; do
+ sleep ${toString sleepTime}
+ done
+ set -a
+ . ${tmpDir}/qsub-$PBS_JOBID/nix-set
+ set +a
+ TMPDIR=${tmpDir}/qsub-$PBS_JOBID
+ TEMP=$TMPDIR
+ TMP=$TMPDIR
+ NIX_BUILD_TOP=$TMPDIR
+ cd $TMPDIR
+ ${builder} ${lib.escapeShellArgs args} &> qsub-log
+ echo $? > qsub-exit
+ '';
- qsub = writeScript "qsub" ''
- #!${stdenv.shell}
- PATH=/usr/bin:/bin:/usr/sbin:/sbin
- SHELL=/bin/sh
- NIX_BUILD_CORES=${toString ppn}
+ qsub = writeScript "qsub" ''
+ #!${stdenv.shell}
+ PATH=/usr/bin:/bin:/usr/sbin:/sbin
+ SHELL=/bin/sh
+ NIX_BUILD_CORES=${toString ppnReified}
- while : ; do
- qsub -l nodes=1:ppn=${toString ppn},mem=${toString mem}gb,walltime=${walltime} \
- -N "${name}" \
- ${optionalString (queue != null) "-q ${queue}"} \
- ${optionalString (qsubFlags != null) qsubFlags} \
- ${script} 2>&1 > id
- if [ $? -eq 0 ] ; then
- break
- fi
- if ! grep "Please retry" id > /dev/null ; then
- cat id >&2
- exit 1
- fi
- sleep ${toString sleepTime}
- done
- id=$(cat id)
- echo $id
+ while : ; do
+ qsub -l nodes=1:ppn=${toString ppnReified},mem=${toString mem}gb,walltime=${walltime} \
+ -N "${name}" \
+ ${optionalString (queue != null) "-q ${queue}"} \
+ ${optionalString (qsubFlags != null) qsubFlags} \
+ ${script} 2>&1 > id
+ if [ $? -eq 0 ] ; then
+ break
+ fi
+ if ! grep "Please retry" id > /dev/null ; then
+ cat id >&2
+ exit 1
+ fi
+ sleep ${toString sleepTime}
+ done
+ id=$(cat id)
+ echo $id
- function cleanup {
- qdel $id 2>/dev/null || true
- sleep ${toString sleepTime}
- rm -rf ${tmpDir}/qsub-$id
- }
- trap cleanup INT TERM EXIT
+ function cleanup {
+ qdel $id 2>/dev/null || true
+ sleep ${toString sleepTime}
+ rm -rf ${tmpDir}/qsub-$id
+ }
+ trap cleanup INT TERM EXIT
- cp -r $TMPDIR ${tmpDir}/qsub-$id
- set > ${tmpDir}/qsub-$id/nix-set
- until qstat -f ''${id%%.} 2>&1 | grep "\(Unknown Job\|job_state = C\)" > /dev/null ; do
- sleep ${toString sleepTime}
- done
- cat ${tmpDir}/qsub-$id/qsub-log
- if [ -e ${tmpDir}/qsub-$id/qsub-exit ]; then
- exitCode=$(cat ${tmpDir}/qsub-$id/qsub-exit)
- else
- exitCode=1
- fi
- exit $exitCode
- '';
+ cp -r $TMPDIR ${tmpDir}/qsub-$id
+ set > ${tmpDir}/qsub-$id/nix-set
+ until qstat -f ''${id%%.} 2>&1 | grep "\(Unknown Job\|job_state = C\)" > /dev/null ; do
+ sleep ${toString sleepTime}
+ done
+ cat ${tmpDir}/qsub-$id/qsub-log
+ if [ -e ${tmpDir}/qsub-$id/qsub-exit ]; then
+ exitCode=$(cat ${tmpDir}/qsub-$id/qsub-exit)
+ else
+ exitCode=1
+ fi
+ exit $exitCode
+ '';
- in [ "-c" qsub ];
-})
+ in [ "-c" qsub ];
+ })
diff --git a/tools/ascat-callCNV.nix b/tools/ascat-callCNV.nix
index 357ab8a..f74bb18 100644
--- a/tools/ascat-callCNV.nix
+++ b/tools/ascat-callCNV.nix
@@ -34,4 +34,5 @@ stage rec {
-protocol WGS \
-cpus $NIX_BUILD_CORES
'';
+ passthru.multicore = true;
}
diff --git a/tools/ascat-gccorrect.nix b/tools/ascat-gccorrect.nix
index c1838d9..584c2ae 100644
--- a/tools/ascat-gccorrect.nix
+++ b/tools/ascat-gccorrect.nix
@@ -33,4 +33,5 @@ stage rec {
sed 1d $f >> $out
done
'';
+ passthru.multicore = true;
}
diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix
index 67a1169..65d0e9f 100644
--- a/tools/bowtie-align.nix
+++ b/tools/bowtie-align.nix
@@ -32,4 +32,5 @@ in stage {
> $out
'';
passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+ passthru.multicore = true;
}
diff --git a/tools/bowtie-index.nix b/tools/bowtie-index.nix
index 4554ad1..4607995 100644
--- a/tools/bowtie-index.nix
+++ b/tools/bowtie-index.nix
@@ -18,4 +18,5 @@ stage {
mkdir $out
bowtie2-build --seed ${toString seed} --threads $NIX_BUILD_CORES ${optionalString (flags != null) flags} ${ref} $out/ref
'';
+ passthru.multicore = true;
}
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 1427b49..e58ef03 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -36,4 +36,5 @@ in stage {
> $out
'';
passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+ passthru.multicore = true;
}
diff --git a/tools/cnvkit-batch.nix b/tools/cnvkit-batch.nix
index 6fb97a4..d033dc4 100644
--- a/tools/cnvkit-batch.nix
+++ b/tools/cnvkit-batch.nix
@@ -37,4 +37,5 @@ stage {
mkdir $out
cp * $out
'';
+ passthru.multicore = true;
}
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index e5cb3ca..27bbe32 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -57,4 +57,5 @@ stage rec {
TMP_DIR=$TMPDIR/
'';
passthru.filetype = filetype.bam { ref = ref; sorting = sort.name {}; };
+ passthru.multicore = true;
}
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index 4117126..1ec9206 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -50,4 +50,5 @@ stage rec {
${optionalString (blacklist != null) ("BLACKLIST=" + blacklist)} \
${optionalString (flags != null) flags}
'';
+ passthru.multicore = true;
}
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 315fbf9..4a73e3c 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -37,4 +37,5 @@ stage rec {
WORKER_THREADS=$NIX_BUILD_CORES
'';
passthru.filetype = filetype.bam { ref = ref; sorting = sort.none {}; };
+ passthru.multicore = true;
}
diff --git a/tools/kallisto-quant.nix b/tools/kallisto-quant.nix
index 1deab67..9f0ab57 100644
--- a/tools/kallisto-quant.nix
+++ b/tools/kallisto-quant.nix
@@ -44,4 +44,5 @@ stage {
-t $NIX_BUILD_CORES \
${concatStringsSep " " inputs}
'';
+ passthru.multicore = true;
}
diff --git a/tools/mosdepth-depth.nix b/tools/mosdepth-depth.nix
index 448da11..2dbfc8d 100644
--- a/tools/mosdepth-depth.nix
+++ b/tools/mosdepth-depth.nix
@@ -17,4 +17,5 @@ stage {
ln -s ${bionix.samtools.index indexAttrs input} input.bam.bai
mosdepth -t $NIX_BUILD_CORES ${optionalString (flags != null) flags} $out/out input.bam
'';
+ passthru.multicore = true;
}
diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
index a5e497e..f3b3e7c 100644
--- a/tools/platypus-callVariants.nix
+++ b/tools/platypus-callVariants.nix
@@ -37,4 +37,5 @@ stage {
--bamFiles=${concatMapStringsSep "," (p: "${filename p}.bam") inputs}
'';
passthru.filetype = filetype.vcf {ref = ref;};
+ passthru.multicore = true;
}
diff --git a/tools/samtools-flagstat.nix b/tools/samtools-flagstat.nix
index 57d8bb6..d733f2f 100644
--- a/tools/samtools-flagstat.nix
+++ b/tools/samtools-flagstat.nix
@@ -10,4 +10,5 @@ stage {
name = "samtools-index";
buildInputs = with pkgs; [ samtools ];
buildCommand = "samtools flagstat -@ $NIX_BUILD_CORES ${input} > $out";
+ passthru.multicore = true;
}
diff --git a/tools/samtools-index.nix b/tools/samtools-index.nix
index 84ebbe1..d0f8d7a 100644
--- a/tools/samtools-index.nix
+++ b/tools/samtools-index.nix
@@ -19,4 +19,5 @@ stage {
samtools index -@ $NIX_BUILD_CORES ${optionalString (flags != null) flags} input.bam
cp input.bam.bai $out
'';
+ passthru.multicore = true;
}
diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix
index d01c83f..e3fbff8 100644
--- a/tools/samtools-sort.nix
+++ b/tools/samtools-sort.nix
@@ -34,4 +34,5 @@ in stage {
${input} > $out
'';
passthru.filetype = if nameSort then bionix.types.nameSort outfmtR else coordSort outfmtR;
+ passthru.multicore = true;
}
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index 1162558..4471d7d 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -40,4 +40,5 @@ stage {
cp -r results $out
'';
+ passthru.multicore = true;
}
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix
index 5be4c0e..ed5626b 100644
--- a/tools/strelka-callSomatic.nix
+++ b/tools/strelka-callSomatic.nix
@@ -42,4 +42,5 @@ stage {
cp -r results $out
'';
+ passthru.multicore = true;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-26 18:28:18 +0000