# HG changeset patch
# User fubar
# Date 1376098486 14400
# Node ID 94e775b410410d3f0e2a11da7a7a5a40401a1396
# Parent 00ab5d9c061f4f431b2bb7b035cf43c37151f121
fixed
diff -r 00ab5d9c061f -r 94e775b41041 prepStar.sh
--- a/prepStar.sh Fri Aug 09 05:13:04 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-# 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 00ab5d9c061f -r 94e775b41041 rg_rnaStar.xml
--- a/rg_rnaStar.xml Fri Aug 09 05:13:04 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,219 +0,0 @@
-
- Gapped-read mapper for RNA-seq data
-
- rnastar
- 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 $params.chim_segment_min > 0:
- ; samtools view -Shb Chimeric.out.sam | samtools sort - Chimeric.out
- #end if
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-**Attributions**
-
-Note that each component has its own license. Good luck with figuring out your obligations.
-
-rna_star - see the web site at rna_star_
-
-For details, please see the rna_starMS_
-"STAR: ultrafast universal RNA-seq aligner"
-A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635
-
-Galaxy_ (that's what you are using right now!) for gluing everything together
-
-Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper
-
-Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies
-and odds and ends of other code and documentation comprising this tool was
-written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts
-
-.. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml
-.. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
-.. _rna_star: http://code.google.com/p/rna-star/
-.. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full
-.. _Galaxy: http://getgalaxy.org
-
-
-
diff -r 00ab5d9c061f -r 94e775b41041 rgrnastar/prepStar.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rgrnastar/prepStar.sh Fri Aug 09 21:34:46 2013 -0400
@@ -0,0 +1,12 @@
+# automate their generation f
+# from existing fasta genomes
+INDEXROOT=/data/ucsc
+# fix that
+for genome in hg19 hg18 mm9 mm10 rn4 rn5
+do
+ TARGET=${INDEXROOT}/${genome}/rnastar
+ mkdir -p $TARGET
+ cd $TARGET
+ STAR --runMode genomeGenerate --genomeDir $TARGET --genomeFastaFiles ${TARGET}/$genome.fa --runThreadN 4
+done
+
diff -r 00ab5d9c061f -r 94e775b41041 rgrnastar/rg_rnaStar.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rgrnastar/rg_rnaStar.xml Fri Aug 09 21:34:46 2013 -0400
@@ -0,0 +1,219 @@
+
+ Gapped-read mapper for RNA-seq data
+
+ rnastar
+ 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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+
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+
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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 00ab5d9c061f -r 94e775b41041 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 21:34:46 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 00ab5d9c061f -r 94e775b41041 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 21:34:46 2013 -0400
@@ -0,0 +1,7 @@
+
+
+
+ value, dbkey, name, path
+
+
+
diff -r 00ab5d9c061f -r 94e775b41041 rgrnastar/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rgrnastar/tool_dependencies.xml Fri Aug 09 21:34:46 2013 -0400
@@ -0,0 +1,26 @@
+
+
+
+
+
+ $INSTALL_DIR
+ $INSTALL_DIR/bin
+ http://rna-star.googlecode.com/files/STAR_2.3.0e.tgz
+ cp -r ./* /tmp/test
+ echo `ls -lt` > /tmp/lslt
+ make
+
+ STAR
+ $INSTALL_DIR/bin
+
+
+ $INSTALL_DIR/bin
+
+
+
+
+Installs the STAR binary for rnastar - see https://code.google.com/p/rna-star/
+
+
+
+
diff -r 00ab5d9c061f -r 94e775b41041 tool-data/rnastar_indices.loc.sample
--- a/tool-data/rnastar_indices.loc.sample Fri Aug 09 05:13:04 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-#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 00ab5d9c061f -r 94e775b41041 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Fri Aug 09 05:13:04 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-
-
-
- value, dbkey, name, path
-
-
-
diff -r 00ab5d9c061f -r 94e775b41041 tool_dependencies.xml
--- a/tool_dependencies.xml Fri Aug 09 05:13:04 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-
-
-
-
-
- $INSTALL_DIR
- $INSTALL_DIR/bin
- https://rna-star.googlecode.com/files/STAR_2.3.0e.tgz
- make
-
- STAR
- $INSTALL_DIR/bin
-
-
- $INSTALL_DIR/bin
-
-
-
-
-Installs the STAR binary for rnastar - see https://code.google.com/p/rna-star/
-
-
-
-