Wrap some tools and make an example pipeline

1 files changed, 45 insertions, 0 deletions

diff --git a/lib/qsub.nix b/lib/qsub.nix
new file mode 100644
index 0000000..ba9456f
--- /dev/null
+++ b/lib/qsub.nix
@@ -0,0 +1,45 @@
+{lib}:
+
+
+{ ppn ? 1, mem ? 1, walltime ? "24:00:00" }: drv: lib.overrideDerivation drv ({ 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 ];
+})