Mercurial > repos > fubar > fastqc

changeset 4:d101029906cb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
new version with complex dependency on fastqc_dist_0_10_1
author fubar
date Wed, 05 Jun 2013 21:06:22 -0400
parents 7e6db50c9d47
children 6480aba750fc
files FastQC/tool_dependencies.xml
diffstat 1 files changed, 5 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/FastQC/tool_dependencies.xml	Tue Jun 04 22:42:51 2013 -0400
+++ b/FastQC/tool_dependencies.xml	Wed Jun 05 21:06:22 2013 -0400
@@ -1,24 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="FASTQC_INSTALL_PATH" action="set_to">$INSTALL_DIR/FastQC/fastqc</environment_variable>   
-    </set_environment>
-    <package name="FastQC" version="0.10.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action>
-                <action type="move_directory_files">
-                    <source_directory>../FastQC</source_directory>
-                    <destination_directory>$INSTALL_DIR/FastQC</destination_directory>
-                </action>                
-                <action type="shell_command">chmod ugo+x $INSTALL_DIR/FastQC/fastqc</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/FastQC</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>You need a working unzip command line executable to install this tool and a suitable working Java run time environment 
-                available to all potential execution nodes for this tool to work.
-                Please see http://www.bioinformatics.babraham.ac.uk/projects/fastqc for all FastQC documentation</readme>
+    <package name="FastQC_dist_0.10.1_dependency" version="0.10.1">
+        <repository changeset_revision="f868c5a825fa" name="fastqc_dist_0_10_1" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <readme>This is a complex dependency on the FastQC java distribution. It will automagically install the required binary and set up the FastQC tool to use it
+                    Please see http://www.bioinformatics.babraham.ac.uk/projects/fastqc for all FastQC documentation
+        </readme>
     </package>
 </tool_dependency>