Fully implements #3 and due to 5f950f5 closes #14, closes #59 and closes

 #66.

Makefile

@@ -23,7 +23,7 @@ vpath %.config src
 .PHONY: all clean
 all: $(deltamp) $(module) $(steps) $(batch_spec) $(test_config)
 
-# rule to build deltamp, pipeline_master and check_previous_step
+# rule to build deltamp, pipeline_master, restart_from_step, delete_subproject and check_previous_step
 $(deltamp): bin/% : %.main | lib/$(batch)/option_variables
 	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 $@

bin/check_subproject.sh

@@ -0,0 +1,52 @@
+#!/bin/bash
+
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
+if [ ! -d $PROUT ]
+then
+	echo "project directory $PROUT does not exist."
+	exit 1
+else
+	MD5CONFIG=$(md5sum $METAD)
+	SUB_LIST=($(for i in $PROUT/${PROJECT}_${TECH}_${TARG}_*/config/conf*; do echo "${MD5CONFIG% *} $i" | md5sum -c | sed -n '/: OK$/s/\/[^\/]*\/[^\/]*: OK$//p' ; done))
+	if [ -z $SUB_LIST ]
+	then
+		echo "project directory $PROUT does not contain any subproject ${PROJECT}_${TECH}_${TARG}_xxx with a configuration file identical to $METAD."
+		exit 1
+	elif [ ${#SUB_LIST[@]} -eq 1 ]
+	then
+		echo $SUB_LIST
+	else
+		LAST_SUB=$(for i in ${SUB_LIST[@]} ; do tree=$i/config/tree.summary; if [ -f $tree ] ; then stat -c "%s %n" $tree ; fi ; done | sort -k 1,1nr | cut -f 2 -d " ")
+		echo -e "# The same configuration file was found in ${#SUB_LIST[@]} subproject with the following checkpointing relationship:\n" >&2
+		column -t -s $'\t' $LAST_SUB >&2
+		echo -e "\nPlease select the subproject you want to use:\n$(echo ${SUB_LIST[@]##*/} | awk '{printf "1) %s",$1;for(i=2;i<=NF;i++){printf "\\n%s) %s",i,$i}}')" >&2
+		n=""
+		while true
+		do
+		    read -p 'Select option: ' n
+		    if [ "$n" -eq "$n" ] && [ "$n" -gt 0 ] && [ "$n" -le "${#SUB_LIST[@]}" ]
+			then
+				echo ${SUB_LIST[$((n-1))]##*/} ; break
+			else
+				echo "Please give a number between 1 and ${#SUB_LIST[@]} or type 'no' to cancel" >&2
+			fi
+		done
+	fi
+fi

lib/GridEngine/option_variables

@@ -7,3 +7,5 @@ QUEUE_HOLD	-hold_jid
 QUEUE_SEP	,
 QUEUE_ARRAYS	-t
 QUEUE_THREADMAX	 -tc 
+QUEUE_DEL	qdel
+QUEUE_STAT	qstat

lib/Slurm/option_variables

@@ -7,3 +7,5 @@ QUEUE_HOLD	-d afterok:
 QUEUE_SEP	:
 QUEUE_ARRAYS	-a
 QUEUE_THREADMAX	%
+QUEUE_DEL	scancel
+QUEUE_STAT	squeue