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comparison FastQC/tool_dependencies.xml @ 4:d101029906cb draft

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new version with complex dependency on fastqc_dist_0_10_1
author fubar
date Wed, 05 Jun 2013 21:06:22 -0400
parents 40b80f54e1a7
children 5b1318a7c01f
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3:7e6db50c9d47 4:d101029906cb
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <set_environment version="1.0"> 3 <package name="FastQC_dist_0.10.1_dependency" version="0.10.1">
4 <environment_variable name="FASTQC_INSTALL_PATH" action="set_to">$INSTALL_DIR/FastQC/fastqc</environment_variable> 4 <repository changeset_revision="f868c5a825fa" name="fastqc_dist_0_10_1" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </set_environment> 5 <readme>This is a complex dependency on the FastQC java distribution. It will automagically install the required binary and set up the FastQC tool to use it
6 <package name="FastQC" version="0.10.1"> 6 Please see http://www.bioinformatics.babraham.ac.uk/projects/fastqc for all FastQC documentation
7 <install version="1.0"> 7 </readme>
8 <actions>
9 <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action>
10 <action type="move_directory_files">
11 <source_directory>../FastQC</source_directory>
12 <destination_directory>$INSTALL_DIR/FastQC</destination_directory>
13 </action>
14 <action type="shell_command">chmod ugo+x $INSTALL_DIR/FastQC/fastqc</action>
15 <action type="set_environment">
16 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/FastQC</environment_variable>
17 </action>
18 </actions>
19 </install>
20 <readme>You need a working unzip command line executable to install this tool and a suitable working Java run time environment
21 available to all potential execution nodes for this tool to work.
22 Please see http://www.bioinformatics.babraham.ac.uk/projects/fastqc for all FastQC documentation</readme>
23 </package> 8 </package>
24 </tool_dependency> 9 </tool_dependency>