# HG changeset patch
# User fubar
# Date 1376037015 14400
# Node ID 2700820cbec16f8e9731f971a4f471f434519ecb
# Parent 17ca51ddd516f7ce616e865581c58c6e41c840f4
Uploaded
diff -r 17ca51ddd516 -r 2700820cbec1 prepStar.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/prepStar.sh Fri Aug 09 04:30:15 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 17ca51ddd516 -r 2700820cbec1 rg_rnaStar.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rg_rnaStar.xml Fri Aug 09 04:30:15 2013 -0400
@@ -0,0 +1,217 @@
+
+ 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 17ca51ddd516 -r 2700820cbec1 tool-data/rnastar_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rnastar_indices.loc.sample Fri Aug 09 04:30:15 2013 -0400
@@ -0,0 +1,16 @@
+#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 17ca51ddd516 -r 2700820cbec1 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Aug 09 04:30:15 2013 -0400
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+
+
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+ value, dbkey, name, path
+
+
+
diff -r 17ca51ddd516 -r 2700820cbec1 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Aug 09 04:30:15 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
+
+
+ $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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+