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comparison FastQC/tool_dependencies.xml @ 4:928de8b704bc draft

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author fubar
date Mon, 03 Jun 2013 23:01:20 -0400
parents 0bec27668020
children ad21e380de48
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3:0bec27668020 4:928de8b704bc
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <set_environment version="1.0"> 3 <set_environment version="1.0">
4 <environment_variable name="FASTQC_INSTALL_PATH" action="set_to">$INSTALL_DIR/jars/FastQC</environment_variable> 4 <environment_variable name="FASTQC_INSTALL_PATH" action="set_to">$INSTALL_DIR/FastQC</environment_variable>
5 </set_environment> 5 </set_environment>
6 <package name="FastQC" version="0.10.1"> 6 <package name="FastQC" version="0.10.1">
7 <install version="1.0"> 7 <install version="1.0">
8 <actions> 8 <actions>
9 <action type="download_file">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action> 9 <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action>
10 <action type="shell_command">unzip fastqc_v0.10.1.zip -d $INSTALL_DIR/jars/</action> 10 <action type="move_directory_file">
11 <action type="shell_command">chmod ugo+x $INSTALL_DIR/jars/FastQC/fastqc</action> 11 <source>FastQC</source>
12 <destination>$INSTALL_DIR/FastQC</destination>
13 </action>
14 <action type="shell_command">chmod ugo+x $INSTALL_DIR/FastQC/fastqc</action>
12 </actions> 15 </actions>
13 </install> 16 </install>
14 <readme>You need a working unzip command line executable to install this tool and a suitable working Java run time environment 17 <readme>You need a working unzip command line executable to install this tool and a suitable working Java run time environment
15 available to all potential execution nodes for this tool to work. 18 available to all potential execution nodes for this tool to work.
16 Please see http://www.bioinformatics.babraham.ac.uk/projects/fastqc for all FastQC documentation</readme> 19 Please see http://www.bioinformatics.babraham.ac.uk/projects/fastqc for all FastQC documentation</readme>