diff TEdenovo.sh @ 0:baea09e6722b draft default tip

1st Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEdenovo.sh	Mon Feb 06 13:31:53 2017 -0500
@@ -0,0 +1,44 @@
+#!/bin/bash 
+set -e
+
+fasta=$1
+outputfasta=$2
+classif=$3
+outputlog=$4
+outputclassif=$7
+outputconfig=$5
+outputstats=$6
+
+projectname=$(date "+%Y%m%d")
+
+
+add=''
+
+if [ $classif == yes ]
+then
+  add='-c'
+fi
+`dirname $0`'/'TEdenovo_lite.py -i $fasta -o $outputfasta $add > $outputlog
+projectname_complete=$(ls $(pwd)|grep $projectname)
+working_dir=$(pwd)/$projectname_complete
+sed -i 's@'"$working_dir"'@'$projectname'@g' $outputlog 
+mv $outputfasta-$projectname-denovoLibTEs_filtered.fa $outputfasta
+mv $outputfasta-$projectname-classif_stats.txt $outputstats
+if [ $classif == yes ]
+then
+  mv $outputfasta-$projectname.classif $outputclassif
+fi
+
+
+workingconfigfile=$working_dir/TEdenovo_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
+