Implement #16

Makefile

@@ -23,7 +23,7 @@ all: $(deltamp) $(module) $(steps) $(batch_spec) $(test_config)
 
 # rule to build deltamp, pipeline_master and check_prevuous_step
 $(deltamp): bin/% : %.main | lib/$(batch)/option_variables
-	SED=$$(sed 's/^/s\//;s/\t/\//;s/$$/\//' $| |  tr "\n" ";" | sed 's/^/sed "/;s/;$$/"/'); \
+	SED=$$(sed 's/^/s\//;s/\t/\//;s/$$/\/g/' $| |  tr "\n" ";" | sed 's/^/sed "/;s/;$$/"/'); \
 	eval $$SED $< | sed 's#^\(VERSION\[DELTAMP\]=\)$$#\1$(version)#;s#^\(DELTAMP_BUILD=\)$$#\1$(CURDIR)#' > $@ && chmod +x $@
 
 # rule to build the module file of the current version

lib/GridEngine/option_variables

@@ -1,6 +1,7 @@
 QUEUE_SUB	qsub
 QUEUE_OPTIONS	 -cwd -terse
 QUEUE_JOBNAME	-N
+QUEUE_ACCOUNT	-P
 QUEUE_HOLD	-hold_jid 
 QUEUE_SEP	,
 QUEUE_ARRAYS	-t

lib/Slurm/option_variables

@@ -1,6 +1,7 @@
 QUEUE_SUB	sbatch
 QUEUE_OPTIONS	 --parsable
 QUEUE_JOBNAME	-J
+QUEUE_ACCOUNT	-A
 QUEUE_HOLD	-d afterok:
 QUEUE_SEP	:
 QUEUE_ARRAYS	-a

src/deltamp.main

@@ -10,11 +10,13 @@ NAME
 	deltamp version ${VERSION[DELTAMP]} - amplicon pipeline for grid engine
 	
 SYNOPSIS
-	Usage: ${0##*/} [-cdhqs] [-m max_running_tasks] [-r SUBRPOJECT] [CONFIGURATION_FILE]
+	Usage: ${0##*/} [-a account_or_project_name] [-cdhqs] [-m max_running_tasks] [-r SUBRPOJECT] [CONFIGURATION_FILE]
 
 DESCRIPTION
 	-h	display this help and exit
 	
+	-a	account or project name for the job queueing system
+	
 	-c	at the end of a dry run (-d option), avoid the deletion of the SUBPROJECT and PROJECT (if empty) directories from output directory
 		
 	-d	avoid submission to queueing system and only display pipeline submission informations (aka. dry run)
@@ -93,11 +95,12 @@ BENCHM=yes
 REF_SUBPROJECT=no
 
 # get options
-while getopts ":cdfhm:nqsr:" opt
+while getopts ":a:cdfhm:nqsr:" opt
 do
 	case $opt in
 		h)	show_help | fmt -s -w $(tput cols)
 			exit 1;;
+		a)	DELTAMP_ACCOUNT=$OPTARG;;
 		c)	CLEAN=no;;
 		d)	DRY=yes;;
 		f)	show_default | fmt -s -w $(tput cols)
@@ -543,6 +546,12 @@ then
 	sed 's/QUEUE_SEP\${pair_end_jobid}//' $SUBPROJECT/config/steps.final > $SUBPROJECT/config/steps.final.tmp && mv $SUBPROJECT/config/steps.final.tmp $SUBPROJECT/config/steps.final
 fi
 
+# Add account/project name to queueing commands
+if [ ! -z $DELTAMP_ACCOUNT ]
+then
+	sed 's/QUEUE_SUB/QUEUE_SUB QUEUE_ACCOUNT $DELTAMP_ACCOUNT/' $SUBPROJECT/config/steps.final > $SUBPROJECT/config/steps.final.tmp && mv $SUBPROJECT/config/steps.final.tmp $SUBPROJECT/config/steps.final
+else
+
 # Save variables about previous SUBPROJECT
 comm -23 <(set -o posix; set | sort) <(sort /tmp/amp.$STIME.set) | tr "=" "\t" | grep -v "^[a-z]" | grep -P -v "^PWD\t" | sed "s/'//g" > $SUBPROJECT/config/prev.txt
 rm -f /tmp/amp.$STIME.set