Mercurial > repos > peterjc > mira_assembler
changeset 5:216bf640baaf draft
Uploaded v0.0.4 which fixes a problem in v0.0.3 with the backbone arguments.
| author | peterjc |
|---|---|
| date | Wed, 09 May 2012 12:40:06 -0400 |
| parents | 117cce3296af |
| children | 3e7eca1f5d04 |
| files | tools/sr_assembly/mira.txt tools/sr_assembly/mira.xml |
| diffstat | 2 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/tools/sr_assembly/mira.txt Wed Dec 21 11:33:19 2011 -0500 +++ b/tools/sr_assembly/mira.txt Wed May 09 12:40:06 2012 -0400 @@ -36,10 +36,11 @@ v0.0.1 - Initial version (working prototype, using MIRA 3.2.1) v0.0.2 - Improve capture of stdout/stderr (should see it as it runs) v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later - (some other switched changed, e.g. -OUT rrol to rrot, which + (some other switches changed, e.g. -OUT rrol to rrot, which means the wrapper no longer works with MIRA 3.2.x) - The contig summary file (TCS file) was removed in MIRA 3.4 - Report all missing output files (not just first missing one) +v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3 Developers
--- a/tools/sr_assembly/mira.xml Wed Dec 21 11:33:19 2011 -0500 +++ b/tools/sr_assembly/mira.xml Wed May 09 12:40:06 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.3"> +<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.4"> <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description> <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log ##Give the wrapper script list of output filenames, then the mira command... @@ -7,7 +7,7 @@ ##Input files #if $condBackbone.use == "true": ## Can this be linked to job_method as well? If mapping we need the backbone... - -SB:lb=1:bft=1 -FN:bbin=${condBackbone.filename} + -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename} #end if #if $condSanger.use == "true": SANGER_SETTINGS