Mercurial > repos > fubar > rgrnastar_203e
changeset 14:1e40b977aa58 draft
Uploaded
| author | fubar |
|---|---|
| date | Sat, 31 Aug 2013 03:06:03 -0400 |
| parents | 9f65a7b3abeb |
| children | 9d72d0221c7f |
| files | rgrnastar/prepStar.sh rgrnastar/rg_rnaStar.xml |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/rgrnastar/prepStar.sh Tue Aug 20 22:39:23 2013 -0400 +++ b/rgrnastar/prepStar.sh Sat Aug 31 03:06:03 2013 -0400 @@ -9,7 +9,7 @@ TARGET=${INDEXROOT}/${genome}/rnastar mkdir -p $TARGET cd $TARGET -/mnt/galaxy/tools/rnastar/2.3.0e/fubar/rgrnastar_203e/9425706f4e97/bin/STAR --runMode genomeGenerate --genomeDir $TARGET --genomeFastaFiles ${SOURCE}/${genome}.fa --runThreadN 2 genomeLoad=NoSharedMemory --genomeChrBinNbits 13 genomeSAindexNbases 12 genomeSAsparseD 1 + /mnt/galaxy/tools/rnastar/2.3.0e/fubar/rgrnastar_203e/9425706f4e97/bin/STAR --runMode genomeGenerate --genomeDir $TARGET --genomeFastaFiles ${SOURCE}/${genome}.fa --runThreadN 2 genomeLoad=NoSharedMemory done echo "#add these lines TABS not spaces please to rnastar_indexes.loc in tool-data" > rnastar_indexes.loc
--- a/rgrnastar/rg_rnaStar.xml Tue Aug 20 22:39:23 2013 -0400 +++ b/rgrnastar/rg_rnaStar.xml Sat Aug 31 03:06:03 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="rna_star" name="RNA-STAR" version="0.22"> +<tool id="rna_star" name="RNA-STAR" version="0.23"> <description>Gapped-read mapper for RNA-seq data</description> <requirements> <requirement type="package" version="2.3.0e">rnastar</requirement> @@ -116,8 +116,8 @@ </inputs> <outputs> - <data format="txt" name="output_log" label="${on_string}_{jobName}.log" from_work_dir="Log.final.out"/> - <data format="interval" name="chimeric_junctions" label="${on_string}_{jobName}_starchimjunc.bed" from_work_dir="Chimeric.out.junction"> + <data format="txt" name="output_log" label="${on_string}_${jobName}.log" from_work_dir="Log.final.out"/> + <data format="interval" name="chimeric_junctions" label="${on_string}_${jobName}_starchimjunc.bed" from_work_dir="Chimeric.out.junction"> <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter> <actions> <conditional name="refGenomeSource.genomeSource">