Merge branch 'chrisgulvik-master' for stampy fixes

Author: lskatz

Makefile

@@ -148,8 +148,6 @@ scripts/raxmlHPC-PTHREADS: scripts/raxmlHPC
 # been installed and so it shouldn't depend on a file existing and
 # should run no matter what. CPAN will know if the module will be
 # there.
-# TODO I should probably have an individual install command per 
-# module so that Make can do its job.
 install-perlModules: lib/lib/perl5/Config/Simple.pm lib/lib/perl5/File/Slurp.pm lib/lib/perl5/Math/Round.pm lib/lib/perl5/Number/Range.pm lib/lib/perl5/Statistics/Distributions.pm lib/lib/perl5/Statistics/Basic.pm lib/lib/perl5/Graph/Centrality/Pagerank.pm lib/lib/perl5/String/Escape.pm lib/lib/perl5/Statistics/LineFit.pm
 	@echo "Done with Perl modules"
 lib/lib/perl5/Config/Simple.pm:

README.md

@@ -85,7 +85,7 @@ See: [examples.md](docs/EXAMPLES.md) for more details.
 
 The script `set_manage.pl` sets up the project directory and adds reads, and you should use the following syntax. Note that paired end reads should be in interleaved format. Scripts that interleave reads include `run_assembly_shuffleReads.pl` in the CG-Pipeline package (included with `make install`) and also `shuffleSequences_fastq.pl` in the Velvet package.
 
-    # Shuffle your reads if they are not already.
+    # Shuffle your reads if they are not shuffled already.
     $ shuffleSplitReads.pl some/directory/*.fastq.gz -o interleaved # interleaved directory will be created for you
     # Create the project directory `setTest`
     $ set_manage.pl --create setTest

scripts/launch_stampy.sh

@@ -1,10 +1,11 @@
 #!/bin/bash
 
 
-SCRIPT=$(basename $0);
+set -e
+
 function usage() { 
 	echo "
-	Usage: $SCRIPT -f file.fastq[.gz] -b file.bam -t tmp/ -r reference.fasta [-s '']
+	Usage: `basename $0` -f file.fastq[.gz] -b file.bam -t tmp/ -r reference.fasta [-s '']
 		
 		-t [default: ./tmp] Path to temporary directory
 		-n [default: 1] Number of threads to use
@@ -118,30 +119,22 @@ else
 	exit 1
 fi
 
+
 # Add onto xopts so that files can be overwritten 
 # and so that we don't worry whether XOPTS is an empty variable.
-XOPTS="$XOPTS --overwrite "; 
+XOPTS="$XOPTS --overwrite "
 # Map with stampy
 COMMAND="stampy.py -g $REFERENCE -h $REFERENCE -t $CPUS --substitutionrate=0.01 --minposterior=20 --sensitive --inputformat=fastq -f sam -o $TMP/$OUT_PREFIX.sam --insertsize=500 --insertsd=250 -M $STAMPY_READS $XOPTS"
 eval $COMMAND
-if [ $? -gt 0 ]; then 
-  echo "ERROR running command: $COMMAND";
-  exit 1; 
-fi;
-
 
 
 # Post-processing of mapped sequences
 if [ -s "$TMP"/"$OUT_PREFIX".sam ]; then
 	# Convert output to binary, sort according to reference position/coordinate, and index
 	samtools view -@ "$CPUS" -bSh "$TMP"/"$OUT_PREFIX".sam -o "$TMP"/"$OUT_PREFIX".unsorted.bam -T "$REFERENCE"
-  if [ $? -gt 0 ]; then exit 1; fi;
 	samtools sort -@ "$CPUS" "$TMP"/"$OUT_PREFIX".unsorted.bam -O bam -o "$TMP"/"$OUT_PREFIX".sorted.bam -T "$BAM"
-  if [ $? -gt 0 ]; then exit 1; fi;
 	mv -v "$TMP"/"$OUT_PREFIX".sorted.bam "$BAM"
-  if [ $? -gt 0 ]; then exit 1; fi;
 	samtools index -b "$BAM"
-  if [ $? -gt 0 ]; then exit 1; fi;
 
 	# Cleanup
 	rm -fv "$TMP"/"$OUT_PREFIX".sam "$TMP"/"$OUT_PREFIX".unsorted.bam "$TMP"/"$OUT_PREFIX".[12].fastq