Mercurial > repos > iuc > package_gemini_0_9_1

comparison tool_dependencies.xml @ 4:a10ebb5a71bb draft

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Uploaded
author iuc
date Sun, 17 Aug 2014 07:44:39 -0400
parents 610ebefc0db1
children 9383ac88d426
comparison
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3:610ebefc0db1 4:a10ebb5a71bb
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="zlib" version="1.2.8"> 3 <package name="zlib" version="1.2.8">
4 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="grabix" version="0.1.3">
7 <repository changeset_revision="8a1184d30e64" name="package_grabix_0_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="tabix" version="0.2.6">
10 <repository changeset_revision="c1743e071a28" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="samtools" version="0.1.19">
13 <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="bedtools" version="2.19.1">
16 <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
17 </package>
6 <package name="gemini" version="0.9.1"> 18 <package name="gemini" version="0.9.1">
7 <install version="1.0"> 19 <install version="1.0">
8 <actions> 20 <actions>
9 <!-- first action is always downloading --> 21 <!-- first action is always downloading -->
10 <action type="download_by_url">https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py</action> 22 <action type="download_by_url">https://raw.github.com/bgruening/gemini-versioned-install/master/gemini_install_0.9.1.py</action>
11 23
12 <!-- populate the environment variables from the dependend repos --> 24 <!-- populate the environment variables from the dependend repos -->
13 <action type="set_environment_for_install"> 25 <action type="set_environment_for_install">
14 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 26 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
15 <package name="zlib" version="1.2.8" /> 27 <package name="zlib" version="1.2.8" />
16 </repository> 28 </repository>
29 <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
30 <package name="bedtools" version="2.19.1" />
31 </repository>
17 </action> 32 </action>
18 33
19 <action type="shell_command"> 34 <action type="shell_command">
20 python gemini_install.py $INSTALL_DIR $INSTALL_DIR --nosudo --nodata 35 python gemini_install.py $INSTALL_DIR $INSTALL_DIR --nosudo --nodata --notools
21 </action> 36 </action>
22 37
23 <action type="set_environment"> 38 <action type="set_environment">
24 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/anaconda/bin</environment_variable> 39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/anaconda/bin</environment_variable>
25 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/gemini/bin</environment_variable> 40 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/gemini/bin</environment_variable>