Mercurial > repos > iuc > trinity

diff tool_dependencies.xml @ 7:1b7800489efb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 6dad4ca6483946af64f484feaff78ac9d1d87352
author iuc
date Mon, 20 Jun 2016 11:44:50 -0400
parents f7564c3f9dc0
children 8bd817614cc8
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--- a/tool_dependencies.xml	Wed Jun 08 06:49:31 2016 -0400
+++ b/tool_dependencies.xml	Mon Jun 20 11:44:50 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="trinity" version="2.1.1">
-        <repository changeset_revision="7a745f45e753" name="package_trinity_2_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="cec8b7f159c5" name="package_trinity_2_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="bowtie" version="1.1.2">
         <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
@@ -12,22 +12,22 @@
     <package name="samtools" version="1.2">
         <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="edger" version="3.12.0">
-        <repository changeset_revision="bb14bf1e4535" name="package_r_edger_3_12_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="bioconductor-edger" version="3.14.0">
+        <repository changeset_revision="8ed6cfd2b21f" name="package_bioconductor_edger_3_14_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="rsem" version="1.2.28">
         <repository changeset_revision="4567331d510a" name="package_rsem_1_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="express" version="1.5.1">
+    <package name="eXpress" version="1.5.1">
         <repository changeset_revision="93017e8743e5" name="package_express_1_5_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="limma" version="3.28.2">
-        <repository changeset_revision="4fa8ed0ffea1" name="package_r_limma_3_28_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="bioconductor-limma" version="3.28.10">
+        <repository changeset_revision="fc78b4bbe0ab" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="deseq2" version="1.10.0">
        <repository changeset_revision="e4a11a7d33d6" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <set_environment version="1.0">
-        <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">--max_memory 30G --bflyHeapSpaceMax 30G</environment_variable>
+        <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">'--max_memory 30G --bflyHeapSpaceMax 30G'</environment_variable>
     </set_environment>
 </tool_dependency>