From 1c64d66d2b4be66b365b1e2ff116c83cbc7f54f8 Mon Sep 17 00:00:00 2001
From: Sam Brightman <s.brightman@hartwigmedicalfoundation.nl>
Date: Fri, 13 Jan 2017 14:53:56 +0100
Subject: [PATCH] Avoid breaking command line length limit when there is a
 large hold_jid dependency list

---
 inc/qsub                | 11 +++++++++--
 lib/HMF/Pipeline/Job.pm |  8 +++++++-
 2 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/inc/qsub b/inc/qsub
index fedf4b6..f6bb387 100755
--- a/inc/qsub
+++ b/inc/qsub
@@ -1,13 +1,20 @@
 #!/usr/bin/env bash
 
-function main() {
+function parse_options() {
     local i
     for ((i = 1; i <= $#; i++)); do
         if [[ "${@:$i:1}" == "-N" ]]; then
-            local name="${*:$i+1:1}"
+            echo "${*:$i+1:1}"
+            return
+        fi
+        if [[ "${@:$i:1}" == "-@" ]]; then
+            parse_options $(cat "${*:$i+1:1}")
         fi
     done
+}
 
+function main() {
+    local name=$(parse_options "$@")
     echo "Your job $$ (\"${name}\") has been submitted"
 
     local me=$(basename "$0")
diff --git a/lib/HMF/Pipeline/Job.pm b/lib/HMF/Pipeline/Job.pm
index c940c62..60492c9 100644
--- a/lib/HMF/Pipeline/Job.pm
+++ b/lib/HMF/Pipeline/Job.pm
@@ -59,7 +59,13 @@ sub submit {
     my $stdout = catfile($dirs->{log}, "${job_name}.out");
     my $stderr = catfile($dirs->{log}, "${job_name}.err");
     my $hold_jid = hold_jid($hold_jids);
-    system "$qsub -o $stdout -e $stderr -N $job_id $hold_jid $bash_file";
+
+    my $option_file = File::Temp->new();
+    open my $fh, ">", $option_file;
+    say $fh "-o $stdout -e $stderr -N $job_id $hold_jid";
+    close $fh;
+    system "$qsub -@ $option_file $bash_file";
+
     return;
 }