Mercurial > repos > iuc > package_gemini_0_10_0
comparison tool_dependencies.xml @ 0:42c72725f879 draft
Imported from capsule None
author | iuc |
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date | Mon, 25 Aug 2014 17:15:52 -0400 |
parents | |
children | 0a450b7b5bc3 |
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-1:000000000000 | 0:42c72725f879 |
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1 <?xml version="1.0"?> | |
2 <tool_dependency> | |
3 <package name="zlib" version="1.2.8"> | |
4 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
5 </package> | |
6 <package name="grabix" version="0.1.3"> | |
7 <repository changeset_revision="0714d88bd854" name="package_grabix_0_1_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
8 </package> | |
9 <package name="tabix" version="0.2.6"> | |
10 <repository changeset_revision="3d6beba7393e" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
11 </package> | |
12 <package name="samtools" version="0.1.19"> | |
13 <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
14 </package> | |
15 <package name="bedtools" version="2.19.1"> | |
16 <repository changeset_revision="fb3a854c7104" name="package_bedtools_2_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
17 </package> | |
18 <package name="gemini" version="0.10.0"> | |
19 <install version="1.0"> | |
20 <actions> | |
21 <!-- first action is always downloading --> | |
22 <action type="download_file">https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py</action> | |
23 <!-- populate the environment variables from the dependend repos --> | |
24 <action type="set_environment_for_install"> | |
25 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | |
26 <package name="zlib" version="1.2.8" /> | |
27 </repository> | |
28 </action> | |
29 <action type="shell_command"> | |
30 python gemini_install.py $INSTALL_DIR $INSTALL_DIR --nosudo --nodata --notools --gemini-version 0.10.0 | |
31 </action> | |
32 <action type="set_environment"> | |
33 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/anaconda/bin</environment_variable> | |
34 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/gemini/bin</environment_variable> | |
35 <environment_variable action="set_to" name="GEMINI_ROOT_DIR">$INSTALL_DIR</environment_variable> | |
36 </action> | |
37 </actions> | |
38 </install> | |
39 <readme>Compiling GEMINI requires a recent c++ compiler, usually gcc.</readme> | |
40 </package> | |
41 </tool_dependency> |