hasta specific changes

emiliaol · web-flow · commit cd7eba539813 · 2019-04-02T09:02:33.000+02:00
* Remove seqtk directory
* Added sourcing of production conda env
diff --git a/scripts/downsample.sh b/scripts/downsample.sh
@@ -6,7 +6,12 @@ set -e
 # import logging/versioning
 source /mnt/hds/proj/bioinfo/SCRIPTS/log.bash
 
-VERSION=1.4.1
+#activate production conda env
+shopt -s expand_aliases
+source ${HOME}/.bashrc
+useprod
+
+VERSION=1.4.2
 log VERSION $VERSION
 
 ##################
@@ -62,8 +67,6 @@ TOTALREADS=$4
 
 [[ ! -e $OUTDIR ]] && mkdir $OUTDIR
 
-SEQTK_DIR=/mnt/hds/proj/bioinfo/SCRIPTS/git/downsampling/seqtk/
-
 ########
 # RUN! #
 ########
@@ -106,7 +109,7 @@ log 'Running:'
 PIDFILE=`mktemp`
 
 # create forward downsample file -- and put it in the background
-COMMAND1="${SEQTK_DIR}/seqtk sample -s $SEED $DOUBLEPASS"
+COMMAND1="seqtk sample -s $SEED $DOUBLEPASS"
 COMMAND2="gzip --to-stdout"
 log "$COMMAND1 <(zcat ${INDIR}/${FORWARD_PATTERN}) $SAMPLESIZE | $COMMAND2 > ${OUTDIR}/${FORWARD_OUTFILE} &"
 ( echo $BASHPID > $PIDFILE; exec $COMMAND1 <(zcat ${INDIR}/${FORWARD_PATTERN}) $SAMPLESIZE ) | $COMMAND2 > ${OUTDIR}/${FORWARD_OUTFILE} &
