Mercurial > repos > greg > multigps
changeset 43:181076e82999 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 09 Feb 2017 13:29:45 -0500 |
| parents | 8d30aeacb52a |
| children | d1a381f360f6 |
| files | multigps.xml |
| diffstat | 1 files changed, 7 insertions(+), 10 deletions(-) [+] |
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--- a/multigps.xml Wed Feb 08 12:57:32 2017 -0500 +++ b/multigps.xml Thu Feb 09 13:29:45 2017 -0500 @@ -14,6 +14,10 @@ ############################ ## General options ############################ + ## Append .txt extensions to events hrefs + ## in output dataset so files will render + ## in the browser. + --eventsaretxt --expt '$expt' --format $expt.ext #if str($ctrl) != 'None': @@ -38,18 +42,11 @@ #if str($umc.use_motif) == 'yes': #set rgc = $umc.reference_genome_cond #if str($rgc.reference_genome_source) == 'cached': - #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0] + #set seq = '$rgc.reference_genome.fields.path' #else: - ## MultiGPS requires a directory containing reference files, so symlink the history dataset. - #import os - #import tempfile - #set seq_dir = tempfile.mkdtemp(prefix='tmp-multigps-seq-dir') - #set seq_file = str($rgc.reference_genome) - #set tmp_filename = '%s.fa' % str($rgc.reference_genome.dbkey) - #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename) - ln -f -s $tmp_seq_file $seq_file && + #set seq = '$rgc.reference_genome' #end if - --seq $seq_dir + --seq $seq #end if ############################ ## Limits on how many reads