Mercurial > repos > lparsons > rseqc_dev3

changeset 1:5eef4ef0ab25 draft

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Update R dependency version
author lparsons
date Mon, 07 Oct 2013 14:41:52 -0400
parents f85fac5a4dce
children 39a3a6b086b1
files RPKM_saturation.xml bam2wig.xml clipping_profile.xml geneBody_coverage.xml geneBody_coverage2.xml inner_distance.xml junction_annotation.xml junction_saturation.xml read_GC.xml read_NVC.xml read_duplication.xml read_quality.xml
diffstat 12 files changed, 12 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/RPKM_saturation.xml	Mon Oct 07 14:36:38 2013 -0400
+++ b/RPKM_saturation.xml	Mon Oct 07 14:41:52 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="1.1">
     <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description>
     <requirements>
-        <requirement type="package" version="2.11.0">R</requirement>
+        <requirement type="package" version="3.0.1">R</requirement>
         <requirement type="package" version="1.7.1">numpy</requirement>
         <requirement type="package" version="2.3.7">rseqc</requirement>
     </requirements>
--- a/bam2wig.xml	Mon Oct 07 14:36:38 2013 -0400
+++ b/bam2wig.xml	Mon Oct 07 14:41:52 2013 -0400
@@ -3,7 +3,7 @@
         converts all types of RNA-seq data from .bam to .wig 
     </description>
     <requirements>
-        <requirement type="package" version="2.11.0">R</requirement>
+        <requirement type="package" version="3.0.1">R</requirement>
         <requirement type="package" version="1.7.1">numpy</requirement>
         <requirement type="package" version="2.3.7">rseqc</requirement>
     </requirements>
--- a/clipping_profile.xml	Mon Oct 07 14:36:38 2013 -0400
+++ b/clipping_profile.xml	Mon Oct 07 14:41:52 2013 -0400
@@ -3,7 +3,7 @@
      estimates clipping profile of RNA-seq reads from BAM or SAM file
     </description>
     <requirements>
-        <requirement type="package" version="2.11.0">R</requirement>
+        <requirement type="package" version="3.0.1">R</requirement>
         <requirement type="package" version="1.7.1">numpy</requirement>
         <requirement type="package" version="2.3.7">rseqc</requirement>
     </requirements>
--- a/geneBody_coverage.xml	Mon Oct 07 14:36:38 2013 -0400
+++ b/geneBody_coverage.xml	Mon Oct 07 14:41:52 2013 -0400
@@ -3,7 +3,7 @@
         Read coverage over gene body.
     </description>
     <requirements>
-        <requirement type="package" version="2.11.0">R</requirement>
+        <requirement type="package" version="3.0.1">R</requirement>
         <requirement type="package" version="1.7.1">numpy</requirement>
         <requirement type="package" version="2.3.7">rseqc</requirement>
     </requirements>
--- a/geneBody_coverage2.xml	Mon Oct 07 14:36:38 2013 -0400
+++ b/geneBody_coverage2.xml	Mon Oct 07 14:41:52 2013 -0400
@@ -3,7 +3,7 @@
         Read coverage over gene body
     </description>
     <requirements>
-        <requirement type="package" version="2.11.0">R</requirement>
+        <requirement type="package" version="3.0.1">R</requirement>
         <requirement type="package" version="1.7.1">numpy</requirement>
         <requirement type="package" version="2.3.7">rseqc</requirement>
     </requirements>
--- a/inner_distance.xml	Mon Oct 07 14:36:38 2013 -0400
+++ b/inner_distance.xml	Mon Oct 07 14:41:52 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="rseqc_inner_distance" name="Inner Distance" version="1.1">
     <description>calculate the inner distance (or insert size) between two paired RNA reads</description>
     <requirements>
-        <requirement type="package" version="2.11.0">R</requirement>
+        <requirement type="package" version="3.0.1">R</requirement>
         <requirement type="package" version="1.7.1">numpy</requirement>
         <requirement type="package" version="2.3.7">rseqc</requirement>
     </requirements>
--- a/junction_annotation.xml	Mon Oct 07 14:36:38 2013 -0400
+++ b/junction_annotation.xml	Mon Oct 07 14:41:52 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="1.1">
     <description>compares detected splice junctions to reference gene model</description>
     <requirements>
-        <requirement type="package" version="2.11.0">R</requirement>
+        <requirement type="package" version="3.0.1">R</requirement>
         <requirement type="package" version="1.7.1">numpy</requirement>
         <requirement type="package" version="2.3.7">rseqc</requirement>
     </requirements>
--- a/junction_saturation.xml	Mon Oct 07 14:36:38 2013 -0400
+++ b/junction_saturation.xml	Mon Oct 07 14:41:52 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="rseqc_junction_saturation" name="Junction Saturation" version="1.1">
     <description>detects splice junctions from each subset and compares them to reference gene model</description>
     <requirements>
-        <requirement type="package" version="2.11.0">R</requirement>
+        <requirement type="package" version="3.0.1">R</requirement>
         <requirement type="package" version="1.7.1">numpy</requirement>
         <requirement type="package" version="2.3.7">rseqc</requirement>
     </requirements>
--- a/read_GC.xml	Mon Oct 07 14:36:38 2013 -0400
+++ b/read_GC.xml	Mon Oct 07 14:41:52 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="rseqc_read_GC" name="Read GC" version="1.1">
     <description>determines GC% and read count</description>
     <requirements>
-        <requirement type="package" version="2.11.0">R</requirement>
+        <requirement type="package" version="3.0.1">R</requirement>
         <requirement type="package" version="1.7.1">numpy</requirement>
         <requirement type="package" version="2.3.7">rseqc</requirement>
     </requirements>
--- a/read_NVC.xml	Mon Oct 07 14:36:38 2013 -0400
+++ b/read_NVC.xml	Mon Oct 07 14:41:52 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="rseqc_read_NVC" name="Read NVC" version="1.1">
     <description>to check the nucleotide composition bias</description>
     <requirements>
-        <requirement type="package" version="2.11.0">R</requirement>
+        <requirement type="package" version="3.0.1">R</requirement>
         <requirement type="package" version="1.7.1">numpy</requirement>
         <requirement type="package" version="2.3.7">rseqc</requirement>
     </requirements>
--- a/read_duplication.xml	Mon Oct 07 14:36:38 2013 -0400
+++ b/read_duplication.xml	Mon Oct 07 14:41:52 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="rseqc_read_duplication" name="Read Duplication" version="1.1">
     <description>determines reads duplication rate with sequence-based and mapping-based strategies</description>
     <requirements>
-        <requirement type="package" version="2.11.0">R</requirement>
+        <requirement type="package" version="3.0.1">R</requirement>
         <requirement type="package" version="1.7.1">numpy</requirement>
         <requirement type="package" version="2.3.7">rseqc</requirement>
     </requirements>
--- a/read_quality.xml	Mon Oct 07 14:36:38 2013 -0400
+++ b/read_quality.xml	Mon Oct 07 14:41:52 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="rseqc_read_quality" name="Read Quality" version="1.1">
     <description>determines Phred quality score</description>
     <requirements>
-        <requirement type="package" version="2.11.0">R</requirement>
+        <requirement type="package" version="3.0.1">R</requirement>
         <requirement type="package" version="1.7.1">numpy</requirement>
         <requirement type="package" version="2.3.7">rseqc</requirement>
     </requirements>