Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam

changeset 75:c09dd61c0239 draft

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Uploaded
author yhoogstrate
date Tue, 10 Jun 2014 09:48:26 -0400
parents f04ca3ca089f
children 344f5b5ddfd3
files tool_dependencies.xml varscan_mpileup2snp_from_bam.xml
diffstat 2 files changed, 13 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed May 21 04:10:41 2014 -0400
+++ b/tool_dependencies.xml	Tue Jun 10 09:48:26 2014 -0400
@@ -40,9 +40,19 @@
 		</readme>
 	</package>
 	
+	<!--
 	<package name="package_samtools_0_1_19" version="0.1.19">
 		<repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 	</package>
+	-->
+	
+	<package name="ncurses" version="5.9">
+		<repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+	</package>
+		
+	<package name="samtools" version="0.1.19">
+		<repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+	</package>
 	
 	<package name="varscan" version="2.3.6">
 		<repository changeset_revision="f82940004c84" name="varscan_version_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
--- a/varscan_mpileup2snp_from_bam.xml	Wed May 21 04:10:41 2014 -0400
+++ b/varscan_mpileup2snp_from_bam.xml	Tue Jun 10 09:48:26 2014 -0400
@@ -5,7 +5,9 @@
 		<requirement type="package" version="5.9">ncurses</requirement>
 		<requirement type="package" version="0.1.19a">samtools_parallel_mpileup_0_1_19a</requirement>
 		<requirement type="package" version="2.3.6">varscan</requirement>
-		<requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement>
+		<!-- <requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement> -->
+		<requirement type="package" version="5.9">ncurses</requirement>
+		<requirement type="package" version="0.1.19">samtools</requirement>
 	</requirements>
 	<command>
 		#if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1