Mercurial > repos > greg > multigps
changeset 31:71b0f24e12f6 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 14 Dec 2016 08:31:55 -0500 |
| parents | 9aca70ab05c2 |
| children | 7a5a2e70b588 |
| files | multigps.xml |
| diffstat | 1 files changed, 15 insertions(+), 14 deletions(-) [+] |
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--- a/multigps.xml Wed Dec 14 08:21:48 2016 -0500 +++ b/multigps.xml Wed Dec 14 08:31:55 2016 -0500 @@ -32,6 +32,21 @@ #set rloc = $aoc.reads_limits_options_cond #set sdc = $aoc.scale_data_cond #set umc = $aoc.use_motif_cond + #if str($umc.use_motif) == "yes": + #set rgc = $umc.reference_genome_cond + #if str($rgc.reference_genome_source) == "cached": + #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0] + #else: + ## MultiGPS requires a directory containing reference files, so symlink the history dataset. + #import os + #import tempfile + #set seq_dir = tempfile.mkdtemp(prefix="tmp-multigps-seq-dir") + #set seq_file = str($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 $seq_file && + #end if + #end if ############################ ## Limits on how many reads ############################ @@ -105,20 +120,6 @@ ############################ #if str($umc.use_motif) == 'yes': #set mpc = $umc.multigps_priors_cond - #set rgc = $umc.reference_genome_cond - #if str($rgc.reference_genome_source) == "cached": - #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0] - #else: - ## MultiGPS requires a directory containing reference files, so symlink the history dataset. - #import os - #import tempfile - #set seq_dir = tempfile.mkdtemp(prefix="tmp-multigps-seq-dir") - #set seq_file = str($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 && - #end if - --seq $seq_dir #if str($mpc.multigps_priors) == 'yes': #set bmc = $mpc.both_motifs_cond #if str($mpc.noposprior) == 'no':