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|
{pkgs ? import <nixpkgs> {}}:
with pkgs;
let
qsub = drv: lib.overrideDerivation drv ({ ppn ? 1, mem ? 1, walltime ? "24:00:00", args, builder, ... }: {
builder = "/bin/bash";
args = let
script = writeScript "qsub-script" ''
#!${stdenv.shell}
while [ ! -e /stornext/HPCScratch/$PBS_JOBID ] ; do
sleep 5
done
set -a
. /stornext/HPCScratch/$PBS_JOBID
set +a
TMPDIR=/tmp/$PBS_JOBID
TEMP=$TMPDIR
TMP=$TMPDIR
NIX_BUILD_TOP=$TMPDIR
mkdir $TMPDIR
cd $TMPDIR
rm /stornext/HPCScratch/$PBS_JOBID
${builder} ${lib.escapeShellArgs args} && touch /stornext/HPCScratch/$PBS_JOBID
cd /
rm -rf $TMPDIR
'';
qsub = writeScript "qsub" ''
#!/bin/bash
PATH=/usr/bin:/bin:/usr/sbin:/sbin
SHELL=/bin/sh
NIX_BUILD_CORES=${toString ppn}
id=$(qsub -l nodes=1:ppn=${toString ppn},mem=${toString mem}gb,walltime=${walltime} ${script})
set > /stornext/HPCScratch/$id
while qstat ''${id%%.} 2> /dev/null > /dev/null ; do
sleep 5
done
if [[ -e /stornext/HPCScratch/$id ]] ; then
rm /stornext/HPCScratch/$id
exit 0
fi
exit 1
'';
in [ "-c" qsub ];
});
qstat = stdenv.mkDerivation rec {
name = "qstat";
buildCommand = "/usr/bin/qstat > $out";
};
grep = x: stdenv.mkDerivation rec {
name = "grep";
buildInputs = [ bwa ];
buildCommand = "/usr/bin/grep distefano.l ${x} > $out";
};
dummy = x: stdenv.mkDerivation rec {
name = "dummy";
buildCommand = "sleep 5 && echo ${toString x} > $out";
};
in stdenv.mkDerivation rec {
name = "dummies";
dummies = map dummy [1 2 3 4 5];
buildCommand = "for f in ${toString dummies} ; cat $f >> $out";
}
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