Mercurial > repos > stef > falco
changeset 53:b4e2b4efae61 draft
Uploaded
| author | stef |
|---|---|
| date | Wed, 31 Dec 2014 06:53:48 -0500 |
| parents | 493bbb54ca1a |
| children | 036033e74757 |
| files | falco-call.sh |
| diffstat | 1 files changed, 19 insertions(+), 10 deletions(-) [+] |
line wrap: on
line diff
--- a/falco-call.sh Wed Dec 31 06:30:53 2014 -0500 +++ b/falco-call.sh Wed Dec 31 06:53:48 2014 -0500 @@ -11,7 +11,16 @@ bam_base=`echo $bam_name | sed 's#.bam$##' - ` ## ---------- -## Create extra init script +## make sure all is ok +## ---------- +if [ ! -f $REF_FILE".fai" ] +then + echo "No FAI index (fai) found for reference fasta [$REF_FILE]" + exit "No FAI index (fai) found for reference fasta [$REF_FILE]" +fi + +## ---------- +## set params ## ---------- if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default somehow is "None" then @@ -34,15 +43,15 @@ if [ $DEBUG ] then DBS="[INFO] " - echo $DBS"FILTER: "$filter_file - echo $DBS"MANIFES: "$manifest_file - echo $DBS"REFFILE: "$REF_FILE - echo $DBS"DB_KEY: "$DB_KEY - echo $DBS"REF_SRC: "$REF_SOURCE - echo $DBS"BAMFILE: "$bam_file - echo $DBS"BAMNAME: "$bam_name - echo $DBS"BAMBASE: "$bam_base - echo $DBS"OUTPATH: "$out_path + 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 $DBS"BAM FILE: "$bam_file + echo $DBS"BAM NAME: "$bam_name + echo $DBS"BAM BASE: "$bam_base + echo $DBS"OUT PATH: "$out_path fi ## ----------