Mercurial > repos > bgruening > bismark

comparison tool_dependencies.xml @ 1:9d02cd7883ad draft

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Uploaded
author bgruening
date Sat, 06 Jul 2013 10:04:23 -0400
parents 62c6da72dd4a
children 82814a8a2395
comparison
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0:62c6da72dd4a 1:9d02cd7883ad
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <package name="samtools" version="0.1.18">
3 <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_samtools_0_1_18" owner="devteam " changeset_revision="a7936f4ea405" />
4 </package>
5 <tool_dependency> 2 <tool_dependency>
3 <package name="samtools" version="0.1.18">
4 <repository changeset_revision="a7936f4ea405" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package>
6 <set_environment version="1.0"> 6 <set_environment version="1.0">
7 <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> 7 <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
8 </set_environment> 8 </set_environment>
9 <package name="bowtie2" version="2.1.0"> 9 <package name="bowtie2" version="2.1.0">
10 <install version="1.0"> 10 <install version="1.0">
11 <actions> 11 <actions>
12 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action> 12 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
23 <source>bowtie2-build</source> 23 <source>bowtie2-build</source>
24 <destination>$INSTALL_DIR/bin</destination> 24 <destination>$INSTALL_DIR/bin</destination>
25 </action> 25 </action>
26 <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action> 26 <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action>
27 <action type="set_environment"> 27 <action type="set_environment">
28 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 28 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
29 </action> 29 </action>
30 </actions> 30 </actions>
31 </install> 31 </install>
32 <readme> 32 <readme>
33 Compiling bowtie2 requires zlib and libpthread to be present on your system. 33 Compiling bowtie2 requires zlib and libpthread to be present on your system.
49 <action type="move_file"> 49 <action type="move_file">
50 <source>bowtie-build</source> 50 <source>bowtie-build</source>
51 <destination>$INSTALL_DIR/bin</destination> 51 <destination>$INSTALL_DIR/bin</destination>
52 </action> 52 </action>
53 <action type="set_environment"> 53 <action type="set_environment">
54 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 54 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
55 </action> 55 </action>
56 </actions> 56 </actions>
57 </install> 57 </install>
58 <readme> 58 <readme>
59 </readme> 59 </readme>
60 </package> 60 </package>
61 </tool_dependency> 61 </tool_dependency>
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