diff TEannot.sh @ 0:b126ea31824f draft default tip

1st Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEannot.sh	Mon Feb 06 13:37:49 2017 -0500
@@ -0,0 +1,50 @@
+#!/bin/bash 
+set -e
+
+fasta=$1
+library=$2
+outputfile=$3
+outputmaskedfile=$4
+outputlog=$5
+outputconfig=$6
+outputStats=$7
+classif=$8
+outputmasked_SSRmaskfile=$9
+
+projectname=$(date "+%Y%m%d")
+
+add=''
+
+if [ -f $classif ]
+then
+  add='-c '$classif
+fi
+
+if [ -f $outputStats ]
+then
+  add=$add' -s'
+fi
+
+`dirname $0`'/'TEannot_lite.py -i $fasta -l $library -o $outputfile $add > $outputlog 
+projectname_complete=$(ls $(pwd)|grep $projectname)
+working_dir=$(pwd)/$projectname_complete
+sed -i 's@'"$working_dir"'@'$projectname'@g' $outputlog
+mv $outputfile-$projectname.gff3 $outputfile
+mv $outputfile-$projectname.mask $outputmaskedfile
+mv $outputfile-$projectname.mask_SSRmask.fa $outputmasked_SSRmaskfile
+if [ -f $outputStats ]
+then
+  mv $outputfile-$projectname-TEstats.txt $outputStats
+fi
+
+workingconfigfile=$working_dir/TEannot_Galaxy_config_$projectname_complete
+sed -i 's|repet_host:.*|repet_host:|g' $workingconfigfile
+sed -i 's|repet_user:.*|repet_user:|g' $workingconfigfile
+sed -i 's|repet_pw:.*|repet_pw:|g' $workingconfigfile
+sed -i 's|repet_db:.*|repet_db:|g' $workingconfigfile
+sed -i 's|repet_port:.*|repet_port:|g' $workingconfigfile
+sed -i 's|repet_job_manager:.*|repet_job_manager:|g' $workingconfigfile
+sed -i 's|project_name:.*|project_name: '$projectname'|g' $workingconfigfile
+sed -i 's|project_dir:.*|project_dir:|g' $workingconfigfile
+sed -i 's|tmpDir:.*|tmpDir:|g' $workingconfigfile
+mv $workingconfigfile $outputconfig