Mercurial > repos > stemcellcommons > rnaseq_workflows

changeset 1:ba1b76257fa5 draft

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Update workflows and add dependency info
author stemcellcommons
date Thu, 21 Jul 2016 11:55:13 -0400
parents cbd6667ca478
children 324f32e70ea4
files RNA-seq_paired_end_with_TopHat_-_hg19.ga RNA-seq_paired_end_with_TopHat_-_mm10.ga RNA-seq_single_end_with_TopHat_-_hg19.ga RNA-seq_single_end_with_TopHat_-_mm10.ga repository_dependencies.xml
diffstat 5 files changed, 133 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/RNA-seq_paired_end_with_TopHat_-_hg19.ga	Wed Jul 20 16:58:05 2016 -0400
+++ b/RNA-seq_paired_end_with_TopHat_-_hg19.ga	Thu Jul 21 11:55:13 2016 -0400
@@ -82,7 +82,13 @@
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+                "name": "fastq_groomer_parallel", 
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@@ -114,7 +120,13 @@
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+            "tool_shed_repository": {
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+                "name": "fastq_groomer_parallel", 
+                "owner": "kevyin", 
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@@ -174,7 +186,13 @@
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@@ -234,7 +252,13 @@
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--- a/RNA-seq_paired_end_with_TopHat_-_mm10.ga	Wed Jul 20 16:58:05 2016 -0400
+++ b/RNA-seq_paired_end_with_TopHat_-_mm10.ga	Thu Jul 21 11:55:13 2016 -0400
@@ -82,7 +82,13 @@
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+            "tool_shed_repository": {
+                "changeset_revision": "66ca0d174cf2", 
+                "name": "fastq_groomer_parallel", 
+                "owner": "kevyin", 
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--- a/RNA-seq_single_end_with_TopHat_-_hg19.ga	Wed Jul 20 16:58:05 2016 -0400
+++ b/RNA-seq_single_end_with_TopHat_-_hg19.ga	Thu Jul 21 11:55:13 2016 -0400
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+                "name": "fastq_groomer_parallel", 
+                "owner": "kevyin", 
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+            "tool_shed_repository": {
+                "changeset_revision": "f8a9a5eaca8a", 
+                "name": "trimmomatic", 
+                "owner": "pjbriggs", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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--- a/RNA-seq_single_end_with_TopHat_-_mm10.ga	Wed Jul 20 16:58:05 2016 -0400
+++ b/RNA-seq_single_end_with_TopHat_-_mm10.ga	Thu Jul 21 11:55:13 2016 -0400
@@ -56,7 +56,13 @@
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+            "tool_shed_repository": {
+                "changeset_revision": "66ca0d174cf2", 
+                "name": "fastq_groomer_parallel", 
+                "owner": "kevyin", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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+                "tool_shed": "toolshed.g2.bx.psu.edu"
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Thu Jul 21 11:55:13 2016 -0400
@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
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+  <repository toolshed="toolshed.g2.bx.psu.edu" name="tophat2_with_gene_annotations" owner="scottx611x" changeset_revision="015a0cc3c012" />
+  <repository toolshed="toolshed.g2.bx.psu.edu" name="featurecounts" owner="yhoogstrate" changeset_revision="e04fbcc4e91a" />
+</repositories>