Mercurial > repos > fubar > genomic_association_tester

changeset 8:7d4725d78cbc draft

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Uploaded
author fubar
date Wed, 28 Aug 2013 23:48:32 -0400
parents 453d54adbc51
children de02c8db9da6
files rlGAT/rlGAT.xml rlGAT/tool_dependencies.xml
diffstat 2 files changed, 12 insertions(+), 11 deletions(-) [+]
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line diff
--- a/rlGAT/rlGAT.xml	Wed Aug 28 02:53:26 2013 -0400
+++ b/rlGAT/rlGAT.xml	Wed Aug 28 23:48:32 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="rlGAT" name="Genomic association tests" version="0.1">
+<tool id="rlGAT" name="Genomic association tests" version="0.1.1">
   <description>using the GAT package</description>
   <stdio>
    <regex match=".*" source="both" level="warning" description="stdout/err chatter from gat-run.py"/>
@@ -126,18 +126,18 @@
 Within a bed formatted file, different tracks can be separated using a UCSC formatted track line, such as this::
 
     track name="segmentset1"
-	chr1  23     100
-	chr3  50     2000
-	track name="segmentset2"
-	chr1  1000   2000
-	chr3  4000   5000
+    chr1  23     100
+    chr3  50     2000
+    track name="segmentset2"
+    chr1  1000   2000
+    chr3  4000   5000
 
 or alternatively, using the fourth column in a bed formatted file::
 
-	chr1 23      100     segmentset1
-	chr3 50      2000    segmentset1
-	chr1 1000    2000    segmentset2
-	chr3 4000    5000    segmentset2
+    chr1 23      100     segmentset1
+    chr3 50      2000    segmentset1
+    chr1 1000    2000    segmentset2
+    chr3 4000    5000    segmentset2
 
 The latter takes precedence. The option –ignore-segment-tracks forces gat to ignore the fourth column and consider all intervals to be from a single interval set.
 
--- a/rlGAT/tool_dependencies.xml	Wed Aug 28 02:53:26 2013 -0400
+++ b/rlGAT/tool_dependencies.xml	Wed Aug 28 23:48:32 2013 -0400
@@ -12,7 +12,8 @@
     <package name="gat" version="0.1">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">https://genomic-association-tester.googlecode.com/files/genomic-association-tester-0.1.tar.gz</action>
+                <!--<action type="download_by_url">https://genomic-association-tester.googlecode.com/files/genomic-association-tester-0.1.tar.gz</action> -->
+                <action type="download_by_url">https://dl.dropboxusercontent.com/u/7144491/gat_galaxysetup_tar.gz</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
                 <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
                 <action type="set_environment_for_install">