# HG changeset patch
# User mytest
# Date 1438327528 14400
# Node ID fbafdad29706bb9f85ec65db18422d17fcb765ba
Uploaded
diff -r 000000000000 -r fbafdad29706 testing6/README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/README.rst Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,18 @@
+Introduction
+============
+
+Welcome to the Home of Next Generation Sequence Analysis Pipelines (NGSAP). Our mission is to provide a user friendly platform for NGS analysis to support Indian researchers working on myriad aspects of life sciences with post processing of the next generation sequencing data. Present portal introduces readers to the transcriptomics tools available through Galaxy for data analysis which can be translated into meaningful scientific publications. NGSAP is an initiative of NGSAP team working in School of Computational and Integrative Sciences at Jawaharlal Nehru University, Delhi
+
+Two workflows in NGSAP
+
+
+Denovo Assembly and differential gene analysis workflow
+========================================================
+
+details of the workflow
+
+
+Reference based assembly and differential gene analysis workflow
+=================================================================
+details of the workflow
+
diff -r 000000000000 -r fbafdad29706 testing6/README.rst~
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/README.rst~ Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,18 @@
+Introduction
+============
+
+Welcome to the Home of Next Generation Sequence Analysis Pipelines (NGSAP). Our mission is to provide a user friendly platform for NGS analysis to support Indian researchers working on myriad aspects of life sciences with post processing of the next generation sequencing data. Present portal introduces readers to the transcriptomics tools available through Galaxy for data analysis which can be translated into meaningful scientific publications. NGSAP is an initiative of NGSAP team working in School of Computational and Integrative Sciences at Jawaharlal Nehru University, Delhi
+
+Two workflows in NGSAP
+
+
+Denovo Assembly and differential gene analysis workflow
+========================================================
+
+details of the workflow
+
+
+Reference based assembly and differential gene analysis workflow
+=================================================================
+details of the workflow
+
diff -r 000000000000 -r fbafdad29706 testing6/abundance_estimates_to_matrix.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/abundance_estimates_to_matrix.xml Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,39 @@
+
+ Generates combined Matrix for abundance estimates
+
+
+ trinityrnaseq
+ edgeR
+ TRINITY_HOME
+
+
+\$TRINITY_HOME/util/abundance_estimates_to_matrix.pl
+ --est_method $est_method
+ #for $i in $isoform_sample:
+ $i.isoform_sample_matrix
+ #end for
+ > $output_log 2>&1;
+
+
+
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diff -r 000000000000 -r fbafdad29706 testing6/align_and_estimate_abundance.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/align_and_estimate_abundance.xml Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,150 @@
+
+
+align_and_estimate_abundance
+
+
+ trinityrnaseq
+ rsem
+ eXpress
+ bowtie2
+ bowtie
+ samtools
+ TRINITY_HOME
+
+
+perl \$TRINITY_HOME/util/align_and_estimate_abundance.pl
+ --transcripts $transcripts
+ --est_method $est_method
+ --aln_method $aln_method
+ --prep_reference
+
+ ## Inputs.
+ #if str($reads.paired_or_single) == "paired":
+
+ --left $reads.left_input --right $reads.right_input
+
+ #if $reads.left_input.ext == 'fa':
+ --seqType fa
+ #else:
+ --seqType fq
+ #end if
+
+ ## Additional parameters.
+ #if str($reads.optional.use_options) == "yes":
+
+ #if str($reads.optional.library_type) != "None":
+ --SS_lib_type $reads.optional.library_type
+ #end if
+
+
+
+ #end if
+
+ #else:
+ --single $reads.input
+
+ #if str($reads.input.ext) == 'fa':
+ --seqType fa
+ #else:
+ --seqType fq
+ #end if
+
+ ## Additional parameters.
+ #if str($reads.optional.use_option) == "yes":
+
+ #if str($reads.additional_params.library_type) != "None":
+ --SS_lib_type $reads.optional.library_type
+ #end if
+
+ #end if
+ #end if
+
+## direct to output
+> $align_and_estimate_abundance_log 2>&1
+
+
+
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diff -r 000000000000 -r fbafdad29706 testing6/all_de_steps.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/all_de_steps.xml Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,94 @@
+
+Generates results for DE
+
+
+ trinityrnaseq
+ TRINITY_HOME
+
+
+
+
+echo -e "Differential Expression Log File" > $output_log 2>&1;
+
+## Step 0: preprocess input_file preparaton
+
+ #for $i in $isoform_sample:
+ cp -s $i.isoform_sample_matrix $i.sample_name;
+ #end for;
+
+
+## Step 1: abundance_estimates_to_matrix
+echo -e "" >> $output_log 2>&1;
+echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" >> $output_log 2>&1;
+echo -e "\#\# Step 1: abundance_estimates_to_matrix" >> $output_log 2>&1;
+echo -e "" >> $output_log 2>&1;
+
+
+perl \$TRINITY_HOME/util/abundance_estimates_to_matrix.pl
+ --est_method $est_method
+ #for $i in $isoform_sample:
+ $i.sample_name
+ #end for
+ >> $output_log 2>&1;
+
+
+## Step 2: run_DE_analysis
+echo -e "" >> $output_log 2>&1;
+echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" >> $output_log 2>&1;
+echo -e "\#\# Step 2: run_DE_analysis" >> $output_log 2>&1;
+echo -e "" >> $output_log 2>&1;
+
+perl \$TRINITY_HOME/Analysis/DifferentialExpression/run_DE_analysis.pl
+ --matrix matrix.counts.matrix
+ --method $method
+ --output result_dir
+ >> $output_log 2>&1;
+
+## Step 3: analyze_diff_expr
+echo -e "" >> $output_log 2>&1;
+echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" >> $output_log 2>&1;
+echo -e "\#\# Step 3: analyze_diff_expr" >> $output_log 2>&1;
+echo -e "" >> $output_log 2>&1;
+
+cd result_dir && perl \$TRINITY_HOME/Analysis/DifferentialExpression/analyze_diff_expr.pl
+
+ --matrix ../matrix.TMM.fpkm.matrix
+
+ >> $output_log 2>&1;
+
+pwd;
+cd .. && zip -r results.zip result_dir;
+
+
+
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diff -r 000000000000 -r fbafdad29706 testing6/blast_parser.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/blast_parser.xml Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,59 @@
+
+
+
+parses Blast Output File
+
+
+ /bin/awk
+ 'BEGIN {FS="\t"} {if($11 <= $evalue && $13 >= $qcovs) print $0 }'
+ $blastoutfile
+ > $parsed_blastfile_above_cutoff;
+
+ /bin/awk
+ '{FS="\t"} {if($11 > $evalue || $13 < $qcovs) print $0 }'
+ $blastoutfile
+ > $parsed_blastfile_below_cutoff;
+
+ /bin/sed -e '/^>/s/$/@@@@/' -e 's/^>/#/' $trinityassembledfile
+ | tr -d '\n'
+ | tr "#" '\n'
+ | sed -e 's/^/>/' -e 's/@@@@/\n/'
+ | sed -e "1d"
+ > $oneline_file;
+
+ /bin/awk
+ 'BEGIN {FS="|"} {print "grep -w -A 1 \""$1"\" $oneline_file >> $blastfile_below_cutoff"}'
+ $parsed_blastfile_below_cutoff
+ > pick_below_sh;
+
+ /bin/sh pick_below_sh;
+
+ /bin/awk
+ 'BEGIN {FS="|"} {print "grep -w -A 1 \""$1"\" $oneline_file >> $blastfile_above_cutoff"}'
+ $parsed_blastfile_above_cutoff
+ > pick_above_sh;
+
+ /bin/sh pick_above_sh;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+blast output parser tool
+
+
+
diff -r 000000000000 -r fbafdad29706 testing6/gtf2fasta.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/gtf2fasta.xml Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,30 @@
+
+
+
+ Converts gtf to fasta
+
+
+ tophat2
+
+
+gtf_to_fasta $gtf $genome $fasta
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+ Converts gtf file to fasta using reference genome
+
+
+
+
+
diff -r 000000000000 -r fbafdad29706 testing6/gtf2fasta.xml~
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/gtf2fasta.xml~ Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,30 @@
+
+
+
+ Converts gtf to fasta
+
+
+ tophat2
+
+
+gtf_to_fasta $gtf $genome $fasta
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+ Converts gtf file to fasta using reference genome
+
+
+
+
+
diff -r 000000000000 -r fbafdad29706 testing6/insilico_read_normalization.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/insilico_read_normalization.xml Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,152 @@
+
+
+
+Read Normalization
+
+ trinityrnaseq
+ TRINITY_HOME
+
+
+ \$TRINITY_HOME/util/insilico_read_normalization.pl
+--JM $JM
+--max_cov $maximum_coverage
+
+## Inputs.
+#if str($inputs.paired_or_single) == "paired":
+
+ --left $inputs.left_input --right $inputs.right_input
+
+ #if $inputs.left_input.ext == 'fa':
+ --seqType fa
+ #else:
+ --seqType fq
+ #end if
+
+ ## Additional parameters.
+ #if str($inputs.additional_params.use_additional) == "yes":
+
+ #if str($inputs.additional_params.library_type) != "None":
+ --SS_lib_type $inputs.additional_params.library_type
+ #end if
+
+ $inputs.additional_params.pairs_together
+ --CPU $inputs.additional_params.CPU
+ $inputs.additional_params.PARALLEL_STATS
+ --KMER_SIZE $inputs.additional_params.KMER_SIZE
+ --max_pct_stdev $inputs.additional_params.max_pct_stdev
+
+ #end if
+
+
+#else:
+
+ --single $inputs.input
+
+ #if str($inputs.input.ext) == 'fa':
+ --seqType fa
+ #else:
+ --seqType fq
+ #end if
+
+ ## Additional parameters.
+ #if str($inputs.additional_params.use_additional) == "yes":
+
+ #if str($inputs.additional_params.library_type) != "None":
+ --SS_lib_type $inputs.additional_params.library_type
+ #end if
+
+ ##$inputs.additional_params.pairs_together
+ --CPU $inputs.additional_params.CPU
+ ##$inputs.additional_params.PARALLEL_STATS
+ --KMER_SIZE $inputs.additional_params.KMER_SIZE
+ --max_pct_stdev $inputs.additional_params.max_pct_stdev
+
+ #end if
+
+#end if
+
+
+
+## direct to output
+> $insilico_read_normalization_log 2>&1
+
+
+
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+Insilico Read Normalization
+
+
diff -r 000000000000 -r fbafdad29706 testing6/pfam_db.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/pfam_db.loc.sample Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,3 @@
+
+###1_name ###2_date ###2_path_to_db
+pfam_db.hmm july 2014 /home/username/galaxy-dist/tool-data/pfam_db.hmm
diff -r 000000000000 -r fbafdad29706 testing6/repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/repository_dependencies.xml Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,13 @@
+
+
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+
diff -r 000000000000 -r fbafdad29706 testing6/repository_dependencies.xml~
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/repository_dependencies.xml~ Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,13 @@
+
+
+
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+
diff -r 000000000000 -r fbafdad29706 testing6/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/tool_dependencies.xml Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,324 @@
+
+
+
+
+
+ http://tools.osdd.jnu.ac.in/ngsap/trinityrnaseq_r20140717.tar.gz
+ make
+
+ .
+ $INSTALL_DIR
+
+
+ $INSTALL_DIR
+
+
+ $INSTALL_DIR
+
+
+
+
+
+
+
+
+
+
+ http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.tar.bz2
+ sed -i.bak 's/-lcurses/-lncurses/' Makefile
+ make
+
+ samtools
+ $INSTALL_DIR/bin
+
+
+ libbam.a
+ $INSTALL_DIR/lib
+
+
+ .
+ $INSTALL_DIR/include/bam
+
+
+
+ $INSTALL_DIR/bin
+ $INSTALL_DIR/lib
+ $INSTALL_DIR
+
+
+
+
+
+
+
+
+
+ http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.1.17.tar.gz
+ make
+ $INSTALL_DIR/bin/sam
+
+ sam/samtools
+ $INSTALL_DIR/bin/sam
+
+
+ convert-sam-for-rsem
+ $INSTALL_DIR/bin
+
+
+ extract-transcript-to-gene-map-from-trinity
+ $INSTALL_DIR/bin
+
+
+ rsem-bam2readdepth
+ $INSTALL_DIR/bin
+
+
+ rsem-bam2wig
+ $INSTALL_DIR/bin
+
+
+ rsem-build-read-index
+ $INSTALL_DIR/bin
+
+
+ rsem-calculate-credibility-intervals
+ $INSTALL_DIR/bin
+
+
+ rsem-calculate-expression
+ $INSTALL_DIR/bin
+
+
+ rsem-extract-reference-transcripts
+ $INSTALL_DIR/bin
+
+
+ rsem-gen-transcript-plots
+ $INSTALL_DIR/bin
+
+
+ rsem-get-unique
+ $INSTALL_DIR/bin
+
+
+ rsem-parse-alignments
+ $INSTALL_DIR/bin
+
+
+ rsem-plot-model
+ $INSTALL_DIR/bin
+
+
+ rsem-plot-transcript-wiggles
+ $INSTALL_DIR/bin
+
+
+ rsem-prepare-reference
+ $INSTALL_DIR/bin
+
+
+ rsem-preref
+ $INSTALL_DIR/bin
+
+
+ rsem-run-em
+ $INSTALL_DIR/bin
+
+
+ rsem-run-gibbs
+ $INSTALL_DIR/bin
+
+
+ rsem-simulate-reads
+ $INSTALL_DIR/bin
+
+
+ rsem-synthesis-reference-transcripts
+ $INSTALL_DIR/bin
+
+
+ rsem-tbam2gbam
+ $INSTALL_DIR/bin
+
+
+ $INSTALL_DIR/bin
+
+
+
+
+
+
+
+
+
+
+ http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-linux_x86_64.tgz
+
+ .
+ $INSTALL_DIR/bin
+
+
+
+ http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-macosx_x86_64.tgz
+
+ .
+ $INSTALL_DIR/bin
+
+
+
+ http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-src.tgz
+ cmake src -DCMAKE_INSTALL_PREFIX:PATH=$INSTALL_DIR
+ make && make install
+
+
+ $INSTALL_DIR/bin
+
+
+
+
+
+
+
+
+
+ http://depot.galaxyproject.org/package/linux/x86_64/bowtie/bowtie-0.12.7-linux-x86_64.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/darwin/x86_64/bowtie/bowtie-0.12.7-macos-10.5-x86_64.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/linux/i386/bowtie/bowtie-0.12.7-linux-i386.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/darwin/i386/bowtie/bowtie-0.12.7-macos-10.5-i386.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip
+ make
+
+ bowtie
+ $INSTALL_DIR
+
+
+ bowtie-build
+ $INSTALL_DIR
+
+
+ bowtie-inspect
+ $INSTALL_DIR
+
+
+
+ $INSTALL_DIR
+
+
+
+
+
+
+
+
+
+ http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.1.0-linux-x86_64.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/darwin/x86_64/bowtie2/bowtie2-2.1.0-macos-x86_64.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/linux/i386/bowtie2/bowtie2-2.1.0-linux-i386.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/darwin/i386/bowtie2/bowtie2-2.1.0-macos-i386.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip
+ make
+
+ bowtie2
+ $INSTALL_DIR
+
+
+ bowtie2-align
+ $INSTALL_DIR
+
+
+ bowtie2-build
+ $INSTALL_DIR
+
+
+ bowtie2-inspect
+ $INSTALL_DIR
+
+
+
+ $INSTALL_DIR
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r fbafdad29706 testing6/tool_dependencies.xml~
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/tool_dependencies.xml~ Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,324 @@
+
+
+
+
+
+ http://tools.osdd.jnu.ac.in/ngsap/trinityrnaseq_r20140717.tar.gz
+ make
+
+ .
+ $INSTALL_DIR
+
+
+ $INSTALL_DIR
+
+
+ $INSTALL_DIR
+
+
+
+
+
+
+
+
+
+
+ http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.tar.bz2
+ sed -i.bak 's/-lcurses/-lncurses/' Makefile
+ make
+
+ samtools
+ $INSTALL_DIR/bin
+
+
+ libbam.a
+ $INSTALL_DIR/lib
+
+
+ .
+ $INSTALL_DIR/include/bam
+
+
+
+ $INSTALL_DIR/bin
+ $INSTALL_DIR/lib
+ $INSTALL_DIR
+
+
+
+
+
+
+
+
+
+ http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.1.17.tar.gz
+ make
+ $INSTALL_DIR/bin/sam
+
+ sam/samtools
+ $INSTALL_DIR/bin/sam
+
+
+ convert-sam-for-rsem
+ $INSTALL_DIR/bin
+
+
+ extract-transcript-to-gene-map-from-trinity
+ $INSTALL_DIR/bin
+
+
+ rsem-bam2readdepth
+ $INSTALL_DIR/bin
+
+
+ rsem-bam2wig
+ $INSTALL_DIR/bin
+
+
+ rsem-build-read-index
+ $INSTALL_DIR/bin
+
+
+ rsem-calculate-credibility-intervals
+ $INSTALL_DIR/bin
+
+
+ rsem-calculate-expression
+ $INSTALL_DIR/bin
+
+
+ rsem-extract-reference-transcripts
+ $INSTALL_DIR/bin
+
+
+ rsem-gen-transcript-plots
+ $INSTALL_DIR/bin
+
+
+ rsem-get-unique
+ $INSTALL_DIR/bin
+
+
+ rsem-parse-alignments
+ $INSTALL_DIR/bin
+
+
+ rsem-plot-model
+ $INSTALL_DIR/bin
+
+
+ rsem-plot-transcript-wiggles
+ $INSTALL_DIR/bin
+
+
+ rsem-prepare-reference
+ $INSTALL_DIR/bin
+
+
+ rsem-preref
+ $INSTALL_DIR/bin
+
+
+ rsem-run-em
+ $INSTALL_DIR/bin
+
+
+ rsem-run-gibbs
+ $INSTALL_DIR/bin
+
+
+ rsem-simulate-reads
+ $INSTALL_DIR/bin
+
+
+ rsem-synthesis-reference-transcripts
+ $INSTALL_DIR/bin
+
+
+ rsem-tbam2gbam
+ $INSTALL_DIR/bin
+
+
+ $INSTALL_DIR/bin
+
+
+
+
+
+
+
+
+
+
+ http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-linux_x86_64.tgz
+
+ .
+ $INSTALL_DIR/bin
+
+
+
+ http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-macosx_x86_64.tgz
+
+ .
+ $INSTALL_DIR/bin
+
+
+
+ http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-src.tgz
+ cmake src -DCMAKE_INSTALL_PREFIX:PATH=$INSTALL_DIR
+ make && make install
+
+
+ $INSTALL_DIR/bin
+
+
+
+
+
+
+
+
+
+ http://depot.galaxyproject.org/package/linux/x86_64/bowtie/bowtie-0.12.7-linux-x86_64.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/darwin/x86_64/bowtie/bowtie-0.12.7-macos-10.5-x86_64.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/linux/i386/bowtie/bowtie-0.12.7-linux-i386.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/darwin/i386/bowtie/bowtie-0.12.7-macos-10.5-i386.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip
+ make
+
+ bowtie
+ $INSTALL_DIR
+
+
+ bowtie-build
+ $INSTALL_DIR
+
+
+ bowtie-inspect
+ $INSTALL_DIR
+
+
+
+ $INSTALL_DIR
+
+
+
+
+
+
+
+
+
+ http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.1.0-linux-x86_64.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/darwin/x86_64/bowtie2/bowtie2-2.1.0-macos-x86_64.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/linux/i386/bowtie2/bowtie2-2.1.0-linux-i386.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://depot.galaxyproject.org/package/darwin/i386/bowtie2/bowtie2-2.1.0-macos-i386.tgz
+
+ .
+ $INSTALL_DIR
+
+
+
+ http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip
+ make
+
+ bowtie2
+ $INSTALL_DIR
+
+
+ bowtie2-align
+ $INSTALL_DIR
+
+
+ bowtie2-build
+ $INSTALL_DIR
+
+
+ bowtie2-inspect
+ $INSTALL_DIR
+
+
+
+ $INSTALL_DIR
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r fbafdad29706 testing6/transDecoder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/transDecoder.xml Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,120 @@
+
+ coding region
+
+
+ trinityrnaseq
+ TRINITY_HOME
+
+
+ \$TRINITY_HOME/trinity-plugins/transdecoder/TransDecoder
+
+ -t $transcript
+
+ #if str($optional.parameters) == 'yes':
+ #if ($train):
+ --train $train
+ #end if
+
+ #if ($min_protein_length):
+ -m $min_protein_length
+ #end if
+
+ #if ($genetic_code):
+ -G $genetic_code
+ #end if
+
+ #if ($strand-specific):
+ $strand-specific
+ #end if
+
+ #if ($lottmn):
+ -T $lottmm
+ #end if
+
+ #if ($retain_long_orfs):
+ --retain_long_orfs $retain_long_orfs
+ #end if
+ #end if
+
+ #if str($pfam.options) == 'yes':
+ #if ($pfam_db):
+ --search_pfam $pfam_db
+ #end if
+
+ #if ($CPU):
+ --CPU $CPU
+ #end if
+ #end if
+
+ ##log file
+ > $transdecoder_log 2>&1;
+
+
+ ## output renaming
+
+ cp -s dataset_*.dat.transdecoder.pep transcript.transdecoder.pep;
+ cp -s dataset_*.dat.transdecoder.cds transcript.transdecoder.cds;
+ cp -s dataset_*.dat.transdecoder.bed transcript.transdecoder.bed;
+ cp -s dataset_*.dat.transdecoder.gff3 transcript.transdecoder.gff3;
+ cp -s dataset_*.dat.transdecoder.mRNA transcript.transdecoder.mRNA;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
diff -r 000000000000 -r fbafdad29706 testing6/trinityStats.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/trinityStats.xml Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,25 @@
+
+ check stats...
+
+
+ trinityrnaseq
+ TRINITY_HOME
+
+
+perl \$TRINITY_HOME/util/TrinityStats.pl $fastafile
+> $statsfile 2>&1;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r fbafdad29706 testing6/trinityrnaseq.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/trinityrnaseq.xml Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,129 @@
+
+
+
+ De novo assembly of RNA-Seq data Using Trinity
+
+ trinityrnaseq
+ TRINITY_HOME
+
+
+
+ \$TRINITY_HOME/Trinity --JM $JM --CPU $CPU
+
+ ## Inputs.
+ #if str($inputs.paired_or_single) == "paired":
+ --left $inputs.left_input --right $inputs.right_input
+ #if $inputs.left_input.ext == 'fa':
+ --seqType fa
+ #else:
+ --seqType fq
+ #end if
+ #if str($inputs.library_type) != "None":
+ --SS_lib_type $inputs.library_type
+ #end if
+ --group_pairs_distance $inputs.group_pairs_distance
+ #else:
+ --single $inputs.input
+ #if str($inputs.input.ext) == 'fa':
+ --seqType fa
+ #else:
+ --seqType fq
+ #end if
+ #if str($inputs.library_type) != "None":
+ --SS_lib_type $inputs.library_type
+ #end if
+ #end if
+
+ ## Additional parameters.
+ #if str($additional_params.use_additional) == "yes":
+ --min_kmer_cov $inputs.min_kmer_cov --max_reads_per_graph $inputs.max_reads_per_graph --bflyHeapSpaceMax $input.bflyHeapSpaceMax
+ #if $inputs.bfly_opts != 'None':
+ --bfly_opts " $inputs.bfly_opts "
+ #end if
+ #end if
+
+
+ ## direct to output
+ > $trinity_log 2>&1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Trinity is a de novo transcript assembler that uses RNA-seq data as input. This tool runs all Trinity_ commands--Inchworm, Chrysalis, and Butterfly--in a single pass.
+
+ .. _Trinity: http://trinityrnaseq.sourceforge.net
+
+