| Previous changeset 6:3e7eca1f5d04 (2013-02-01) Next changeset 8:4266cccbb45a (2013-04-24) |
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Commit message:
Uploaded v0.0.6, tell MIRA to use /tmp for temporary files, and ignore long read names (to prevent it aborting). |
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modified:
tools/sr_assembly/mira.txt tools/sr_assembly/mira.xml |
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| diff -r 3e7eca1f5d04 -r 4d3f94dfb857 tools/sr_assembly/mira.txt --- a/tools/sr_assembly/mira.txt Fri Feb 01 10:34:21 2013 -0500 +++ b/tools/sr_assembly/mira.txt Thu Feb 14 06:26:32 2013 -0500 |
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| @@ -44,6 +44,8 @@ v0.0.5 - Implement the <version_command> tag to record the wrapper version and the MIRA version being used. - Check using MIRA 3.4 (later versions have a different API) +v0.0.6 - Tell MIRA to use /tmp for temporary files + - Tell MIRA to ignore long read names (otherwise it aborts) Developers |
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| diff -r 3e7eca1f5d04 -r 4d3f94dfb857 tools/sr_assembly/mira.xml --- a/tools/sr_assembly/mira.xml Fri Feb 01 10:34:21 2013 -0500 +++ b/tools/sr_assembly/mira.xml Thu Feb 14 06:26:32 2013 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.5"> +<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.6"> <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description> <version_command interpreter="python">mira.py -v</version_command> <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log @@ -37,12 +37,20 @@ ##Output files COMMON_SETTINGS + +##ignore warnings about long read names +-MI:somrnl=0 + ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output ##Explicitly disable formats we won't use like MAF (reduce IO) -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 + ##remove_rollover_tmps, remove_tmp_directory -OUT:rrot=1:rtd=1 +##put mira temp directory on local storage +-DI:trt=/tmp + </command> <inputs> <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)"> @@ -124,11 +132,12 @@ <data name="out_ace" format="txt" label="MIRA contigs (ACE)" /> <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> <data name="out_log" format="txt" label="MIRA log" /> - </outputs> + </outputs> <tests> </tests> <requirements> <requirement type="python-module">Bio</requirement> + <requirement type="binary">mira</requirement> </requirements> <help> |