Mercurial > repos > stef > falco
diff falco-call.sh @ 90:07c810e4061c draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 17 Jul 2015 06:53:45 -0400 |
| parents | b0a46916df02 |
| children |
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--- a/falco-call.sh Fri Jul 17 06:02:36 2015 -0400 +++ b/falco-call.sh Fri Jul 17 06:53:45 2015 -0400 @@ -40,6 +40,15 @@ #bam_base=`echo $bam_name | sed 's#.bam$##' - ` bam_base=$job_name +## in case of test run (re)set params +if [[ $test_run == 'true' ]] +then + MANIFEST_PARAM="" + FILTER_PARAM="" + bam_file=$TOOLDIR/tool-data/HCT116_test_ABL1.bam + #bam_base="GALAXY-FALCO-TEST" +fi + ## ---------- ## Status / debug ## ---------- @@ -47,11 +56,11 @@ if [ $DEBUG ] then DBS="[INFO] " - echo $DBS"FILTER: "$filter_file + echo $DBS"FILTER: "$filter_file echo $DBS"MANIFEST: "$manifest_file echo $DBS"REF FILE: "$REF_FILE - echo $DBS"DB KEY: "$DB_KEY - echo $DBS"REF SRC: "$REF_SOURCE + echo $DBS"DB KEY: "$DB_KEY + echo $DBS"REF SRC: "$REF_SOURCE echo $DBS"BAM FILE: "$bam_file echo $DBS"BAM NAME: "$bam_name echo $DBS"BAM BASE: "$bam_base @@ -89,7 +98,7 @@ echo "</head>" >> $html_out echo "<body>" >> $html_out echo " <h1>FALCO</h1>" >> $html_out -echo " <p>This page is way to get output files that are not implemented in galaxy history, it is not intended to be a user-friendly way of displaying anything ;)</p>" >> $html_out +echo " <p>This page is way to get output files that are not implemented in galaxy history, it is not intended to be a user-friendly way of displaying anything ;)</p><p>Also not all files might have been copied. To delete this files below from the galaxy installation delete the html page in your history.." >> $html_out #echo " <a href=\"index.html\">HTML</a>" >> $html_out echo " <table><tbody>" >> $html_out for file in *.vcf *.txt *stderr *stdout @@ -107,7 +116,7 @@ ## creating galaxy history outputs ## ---------- #cp 'index.html' $html_out # this is the overview of samples html -#cp $bam_base'.html' $out_path/'out.html' # this is the sample html +cp $bam_base'.html' $out_path/'out.html' # this is the sample html cp $bam_base'.falco.vcf' $vcf_out cp $bam_base'.qc.ann.qual.txt' $qc_ann_qual_out cp $bam_base'.qc2.ann.txt' $qc2_ann_txt_out @@ -118,7 +127,9 @@ ## ---------- #cp -r ./$bam_base/*png $out_path/$bam_base/ #cp -r ./* $out_path -cp *.vcf $out_path; cp *.txt $out_path; cp *_std* $out_path +cp *.vcf $out_path; +#cp *.txt $out_path; +cp *_std* $out_path ## ---------- echo "END falco sh"