Mercurial > repos > stef > falco
diff falco-call.sh @ 38:f1b32c09deaf draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 10 Oct 2014 11:28:57 -0400 |
| parents | 12f7ce7de71f |
| children | a793ffd0cd04 |
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--- a/falco-call.sh Fri Oct 10 11:07:36 2014 -0400 +++ b/falco-call.sh Fri Oct 10 11:28:57 2014 -0400 @@ -62,16 +62,17 @@ echo "VCFOUT : "$vcf_out echo "INIT : "$init_file +echo "------ sourcing init_file" source $init_file -echo "------ --- ------" -echo "------ sam ------" -echo "------ --- ------" -$samtools -echo "------ --- ------" -echo "------ bcf ------" -echo "------ --- ------" -$bcftools +#echo "------ --- ------" +#echo "------ sam ------" +#echo "------ --- ------" +#$samtools +#echo "------ --- ------" +#echo "------ bcf ------" +#echo "------ --- ------" +#$bcftools #echo "--- snpsift ---" #java -jar $snpSift/SnpSift.jar #echo "--- snpeff ---" @@ -85,17 +86,16 @@ ## ---------- ## create output files dir ## ---------- -#mkdir $out_path -#mkdir $out_path/$bam_base +mkdir $out_path +mkdir $out_path/$bam_base ## ---------- ## running analysis ## ---------- -echo "Starting VcAn" ## DEBUG #exit 0 - +echo "Starting VcAn" $TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base echo "...done with VcAn" #$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more @@ -117,29 +117,29 @@ ## ---------- ## create index html for main galaxy output ## ---------- -# echo "<!DOCTYPE html>" >> $html_out -# echo "<html>" >> $html_out -# echo "<head>" >> $html_out -# echo "<style>" >> $html_out -# echo " body{ padding: 0px 20px; }" >> $html_out -# echo " h1{ color: red; }" >> $html_out -# echo " table{ border: 1px solid black; padding: 5px }" >> $html_out -# echo "</style>" >> $html_out -# echo "</head>" >> $html_out -# echo "<body>" >> $html_out -# echo " <h1>FALCO</h1>" >> $html_out -# echo " <a href=\"index.html\">HTML</a>" >> $html_out -# echo " <table><tbody>" >> $html_out -# #for file in *.vcf *.txt *.tsv -# for file in * -# do -# lineCount=`wc -l $file | cut -f 1 -d " "` -# echo " <tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out -# #echo " <tr><td> HEAD: " `head $file` "</td></tr>" >> $html_out -# done -# echo " </tbody></table>" >> $html_out -# echo "</body>" >> $html_out -# echo "</html>" >> $html_out +echo "<!DOCTYPE html>" >> $html_out +echo "<html>" >> $html_out +echo "<head>" >> $html_out +echo "<style>" >> $html_out +echo " body{ padding: 0px 20px; }" >> $html_out +echo " h1{ color: red; }" >> $html_out +echo " table{ border: 1px solid black; padding: 5px }" >> $html_out +echo "</style>" >> $html_out +echo "</head>" >> $html_out +echo "<body>" >> $html_out +echo " <h1>FALCO</h1>" >> $html_out +echo " <a href=\"index.html\">HTML</a>" >> $html_out +echo " <table><tbody>" >> $html_out +#for file in *.vcf *.txt *.tsv +for file in * +do + lineCount=`wc -l $file | cut -f 1 -d " "` + echo " <tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out + #echo " <tr><td> HEAD: " `head $file` "</td></tr>" >> $html_out +done +echo " </tbody></table>" >> $html_out +echo "</body>" >> $html_out +echo "</html>" >> $html_out ## ---------- ## creating galaxy history outputs