diff deseq-hts_1.0/src/deseq-hts.sh @ 9:e27b4f7811c2 draft

Updated DESeq version 1.12

--- a/deseq-hts_1.0/src/deseq-hts.sh	Wed Jun 27 15:38:39 2012 -0400
+++ b/deseq-hts_1.0/src/deseq-hts.sh	Tue Oct 08 08:09:28 2013 -0400
@@ -5,7 +5,7 @@
 # the Free Software Foundation; either version 3 of the License, or
 # (at your option) any later version.
 #
-# Copyright (C) 2009-2012 Max Planck Society
+# Copyright (C) 2009-2013 Max Planck Society & Memorial Sloan-Kettering Cancer Center 
 #
 
 set -e 
@@ -16,7 +16,7 @@
 . ${DIR}/../bin/deseq_config.sh
 
 echo
-echo ${PROG}: FML http://galaxy.fml.mpg.de Galaxy wrapper for the DESeq version $DESEQ_VERSION.
+echo ${PROG}: Oqtans http://galaxy.cbio.mskcc.org Galaxy wrapper for the DESeq version $DESEQ_VERSION.
 echo
 echo DESeq performs differential expression testing from RNA-Seq measurements.
 echo 
@@ -35,14 +35,12 @@
 echo %%%%%%%%%%%%%%%%%%%%%%%
 echo
 echo load the genome annotation in GFF3 format and create an annotation object
-echo
 export PYTHONPATH=$PYTHONPATH:${SCIPY_PATH}
 ${PYTHON_PATH} ${DIR}/../tools/ParseGFF.py ${ANNO_INPUT} ${GENES_FN}
-${DIR}/../bin/genes_cell2struct ${GENES_FN} 2>&1
+${DIR}/../bin/genes_cell2struct ${GENES_FN} 
 echo 
 echo genome annotation stored in $GENES_FN
 
-echo
 echo %%%%%%%%%%%%%%%%%%%%
 echo % 2. Read counting %
 echo %%%%%%%%%%%%%%%%%%%%
@@ -68,22 +66,18 @@
 tmpfile=`mktemp --tmpdir=/tmp`
 
 echo "${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile $@"
-${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile "$@" 2>&1
+${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile "$@" 
 
-echo
 echo %%%%%%%%%%%%%%%%%%%%%%%%%%%
 echo % 3. Differential testing %
 echo %%%%%%%%%%%%%%%%%%%%%%%%%%%
 echo
-
 echo testing genes for differential expression using given alignments
 
 echo "cat ${DIR}/../src/difftest_deseq.R | $R_PATH --slave --args $tmpfile ${DESEQ_RES_FILE} $#"
-cat ${DIR}/../src/difftest_deseq.R | $R_PATH --slave --args $tmpfile ${DESEQ_RES_FILE} $# 2> /dev/null
+cat ${DIR}/../src/difftest_deseq.R | $R_PATH --slave --args $tmpfile ${DESEQ_RES_FILE} $# 
 
 rm $tmpfile ${tmpfile}_COUNTS.tab ${tmpfile}_CONDITIONS.tab
-echo
 echo %%%%%%%%
 echo % Done %
 echo %%%%%%%%
-echo