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changeset 1:74391fc6e3f2 draft

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Add package requirement
author Jim Johnson <jj@umn.edu>
date Fri, 05 Oct 2012 13:08:43 -0500
parents 10e3476429b5
children f6ba0f12cca2
files gmap.xml gmap_build.xml gsnap.xml iit_store.xml snpindex.xml
diffstat 5 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/gmap.xml	Fri Oct 05 13:51:49 2012 -0400
+++ b/gmap.xml	Fri Oct 05 13:08:43 2012 -0500
@@ -1,7 +1,7 @@
 <tool id="gmap" name="GMAP" version="2.0.1">
   <description>Genomic Mapping and Alignment Program for mRNA and EST sequences</description>
   <requirements>
-    <requirement type="binary">gmap</requirement>
+    <requirement type="package" version="2011-11-30">gmap</requirement>
   </requirements>
   <version_string>gmap --version</version_string>
   <command>
--- a/gmap_build.xml	Fri Oct 05 13:51:49 2012 -0400
+++ b/gmap_build.xml	Fri Oct 05 13:08:43 2012 -0500
@@ -1,7 +1,7 @@
 <tool id="gmap_build" name="GMAP Build" version="2.0.0">
   <description>a database genome index for GMAP and GSNAP</description>
   <requirements>
-      <requirement type="binary">gmap_build</requirement>
+      <requirement type="package" version="2011-11-30">gmap</requirement>
   </requirements>
   <version_string>gmap --version</version_string>
   <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command>
--- a/gsnap.xml	Fri Oct 05 13:51:49 2012 -0400
+++ b/gsnap.xml	Fri Oct 05 13:08:43 2012 -0500
@@ -1,7 +1,7 @@
 <tool id="gsnap" name="GSNAP" version="2.0.1">
   <description>Genomic Short-read Nucleotide Alignment Program</description>
   <requirements>
-      <requirement type="binary">gsnap</requirement>
+      <requirement type="package" version="2011-11-30">gmap</requirement>
   </requirements>
   <version_string>gsnap --version</version_string>
   <command>
--- a/iit_store.xml	Fri Oct 05 13:51:49 2012 -0400
+++ b/iit_store.xml	Fri Oct 05 13:08:43 2012 -0500
@@ -1,7 +1,7 @@
 <tool id="gmap_iit_store" name="GMAP IIT" version="2.0.0">
   <description>Create a map store for known genes or SNPs</description>
   <requirements>
-      <requirement type="binary">iit_store</requirement>
+      <requirement type="package" version="2011-11-30">gmap</requirement>
   </requirements>
   <version_string>iit_store --version</version_string>
   <command interpreter="command"> /bin/bash $shscript 2> $log </command>
--- a/snpindex.xml	Fri Oct 05 13:51:49 2012 -0400
+++ b/snpindex.xml	Fri Oct 05 13:08:43 2012 -0500
@@ -1,7 +1,7 @@
 <tool id="gmap_snpindex" name="GMAP SNP Index" version="2.0.0">
   <description>build index files for known SNPs</description>
   <requirements>
-      <requirement type="binary">snpindex</requirement>
+      <requirement type="package" version="2011-11-30">gmap</requirement>
   </requirements>
   <version_string>snpindex --version</version_string>
   <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command>