# HG changeset patch
# User fubar
# Date 1376036033 14400
# Node ID 52c43185e3f33e195001f902be2ca1f48a2b7e42
initial commit
diff -r 000000000000 -r 52c43185e3f3 rgrnastar/prepStar.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rgrnastar/prepStar.sh Fri Aug 09 04:13:53 2013 -0400
@@ -0,0 +1,12 @@
+# automate their generation f
+# from existing fasta genomes
+INDEXROOT=/data/ucsc
+# fix that
+for genome in hg19 hg18 mm9 mm10 rn4 rn5
+do
+ TARGET=${INDEXROOT}/${genome}/rnastar
+ mkdir -p $TARGET
+ cd $TARGET
+ STAR --runMode genomeGenerate --genomeDir $TARGET --genomeFastaFiles ${TARGET}/$genome.fa --runThreadN 4
+done
+
diff -r 000000000000 -r 52c43185e3f3 rgrnastar/rg_rnaStar.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rgrnastar/rg_rnaStar.xml Fri Aug 09 04:13:53 2013 -0400
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+
+ Gapped-read mapper for RNA-seq data
+
+ star
+ samtools
+
+
+ ##
+ ## Run STAR.
+ ##
+
+ STAR
+ ## Can adjust this as appropriate for the system.
+ --genomeLoad NoSharedMemory
+
+ --genomeDir ${refGenomeSource.index.fields.path}
+ --readFilesIn $input1
+ #if $singlePaired.sPaired == "paired"
+ $singlePaired.input2
+ #end if
+
+ --runThreadN 4
+
+ ## Parameters.
+ #if $params.settingsType == "full":
+ --chimSegmentMin $params.chim_segment_min
+ --chimScoreMin $params.chim_score_min
+ #end if
+
+ ## Needed to generate SAM tags for Cufflinks tools.
+ --outSAMstrandField intronMotif
+
+ ;
+
+ ##
+ ## BAM conversion.
+ ##
+
+ ## Convert aligned reads.
+ samtools view -Shb Aligned.out.sam | samtools sort - Aligned.out
+
+ ## Convert chimeric reads.
+ #if $params.settingsType == "full" and $params.chim_segment_min > 0:
+ ; samtools view -Shb Chimeric.out.sam | samtools sort - Chimeric.out
+ #end if
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+ (params['settingsType'] == 'full' and params['chim_segment_min'] > 0)
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+ (params['settingsType'] == 'full' and params['chim_segment_min'] > 0)
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+**Attributions**
+Note that each component has its own license. Good luck with figuring out your obligations.
+
+rna_star - see the web site at rna_star_
+
+For details, please see the rna_starMS_
+"STAR: ultrafast universal RNA-seq aligner"
+A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635
+
+Galaxy_ (that's what you are using right now!) for gluing everything together
+
+Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper
+
+Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies and odds and ends of other code and documentation comprising this tool was written by Ross Lazarus and
+that part is licensed_ the same way as other rgenetics artefacts
+
+.. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml
+.. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
+.. _rna_star: http://code.google.com/p/rna-star/
+.. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full
+.. _Galaxy: http://getgalaxy.org
+
+
+
diff -r 000000000000 -r 52c43185e3f3 rgrnastar/rnastar_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rgrnastar/rnastar_macros.xml Fri Aug 09 04:13:53 2013 -0400
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diff -r 000000000000 -r 52c43185e3f3 rgrnastar/tool-data/rnastar_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rgrnastar/tool-data/rnastar_indices.loc.sample Fri Aug 09 04:13:53 2013 -0400
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+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of rna-star indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie2_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+hg19 hg19 hg19 full /data/ucsc/hg19/rnastar
+hg18 hg18 hg18 full /data/ucsc/hg18/rnastar
+mm9 mm9 mm9 full /data/ucsc/mm9/rnastar
+mm10 mm10 mm10 full /data/ucsc/mm10/rnastar
+rn4 rn4 rn4 full /data/ucsc/rn4/rnastar
+rn5 rn5 rn5 full /data/ucsc/rn5/rnastar
+
diff -r 000000000000 -r 52c43185e3f3 rgrnastar/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rgrnastar/tool_data_table_conf.xml.sample Fri Aug 09 04:13:53 2013 -0400
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+ value, dbkey, name, path
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diff -r 000000000000 -r 52c43185e3f3 rgrnastar/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rgrnastar/tool_dependencies.xml Fri Aug 09 04:13:53 2013 -0400
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+
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+ $INSTALL_DIR
+ $INSTALL_DIR/bin
+ https://rna-star.googlecode.com/files/STAR_2.3.0e.tgz
+ make
+
+ STAR
+ $INSTALL_DIR/bin
+
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+ $INSTALL_DIR/bin
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+Installs the STAR binary for rnastar - see https://code.google.com/p/rna-star/
+
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+