Mercurial > repos > fubar > weblogo3

changeset 15:01ec43556e16 draft

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use iuc dependendencies
author fubar
date Mon, 18 Nov 2013 02:19:03 -0500
parents a75696764683
children 21bcfe99f623
files rgweblogo/README rgweblogo/tool_dependencies.xml
diffstat 2 files changed, 9 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/rgweblogo/README	Wed Sep 25 23:31:04 2013 -0400
+++ b/rgweblogo/README	Mon Nov 18 02:19:03 2013 -0500
@@ -1,6 +1,7 @@
 This is a Galaxy tool wrapper for weblogo3 already available as a web app at the site below but neat as a Galaxy tool
+Last updated by Ross to install iuc ghostscript and numpy dependencies.
 
-It generates sequence logos from fasta files such as the alignments generated by clustalw
+Weblogo generates sequence logos from fasta files such as the alignments generated by clustalw
 
 Note that the image for the help must be in static/images for it to show up on the tool form - it's the same image as goes in test-data
 
@@ -10,6 +11,9 @@
 
 ** Manual Installation**
 
+Don't.
+
+If you insist, 
 Make sure weblogo3 is installed in your system python and is available on the path for all your nodes
 
 Move the test data files to your galaxy root test-data
@@ -25,7 +29,7 @@
 
 Source for the weblogo3 python executable is at http://weblogo.berkeley.edu
 
-Written by Ross Lazarus for the Rgenetics project
+Galaxy tool wrapper written by Ross Lazarus for the Rgenetics project
 
 Copyright Ross Lazarus at gmail com 2011
 
--- a/rgweblogo/tool_dependencies.xml	Wed Sep 25 23:31:04 2013 -0400
+++ b/rgweblogo/tool_dependencies.xml	Mon Nov 18 02:19:03 2013 -0500
@@ -6,6 +6,7 @@
     <package name="ghostscript" version="9.07">
         <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
+
     <package name="package_weblogo" version="3.3">
         <install version="1.0">
             <actions>
@@ -14,10 +15,10 @@
                 <action type="shell_command">echo `ls -lt` &amp;&amp; echo `pwd`</action>
                 
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                    <repository changeset_revision="c842299349c0" name="package_ghostscript_9_07" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                         <package name="ghostscript" version="9.07" />
                     </repository>
-                    <repository changeset_revision="af9633757cf0" name="package_numpy_1_7" owner="blankenberg" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                    <repository changeset_revision="af9633757cf0" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                         <package name="numpy" version="1.7.1" />
                     </repository>
                 </action>