Mercurial > repos > rnateam > package_gemini_0_10_0_1

comparison tool_dependencies.xml @ 0:816cb6c1a983 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_gemini_0_10_0_1 commit 0568344062d931c58be6a017998cfb22e702a94e-dirty
author rnateam
date Tue, 08 Dec 2015 10:54:35 -0500
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children e532cf8a27ba
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-1:000000000000 0:816cb6c1a983
1 <?xml version="1.0"?>
2 <tool_dependency>
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" />
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="54f8b9bf9b6c" 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="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" 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>
18 <package name="gemini" version="0.10.0.1">
19 <install version="1.0">
20 <actions>
21 <!-- first action is always downloading -->
22 <action type="download_file">https://raw.githubusercontent.com/arq5x/gemini/adf750301f9766c95654d1189381ca370df66bcd/gemini/scripts/gemini_install.py</action>
23
24 <!-- populate the environment variables from the dependend repos -->
25 <action type="set_environment_for_install">
26 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
27 <package name="zlib" version="1.2.8" />
28 </repository>
29 </action>
30
31 <action type="shell_command">
32 export HOME=$INSTALL_DIR &amp;&amp; python gemini_install.py $INSTALL_DIR $INSTALL_DIR --nosudo --nodata --notools --gemini-version 0.10.0
33 </action>
34
35 <action type="set_environment">
36 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/anaconda/bin</environment_variable>
37 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/gemini/bin</environment_variable>
38 <environment_variable action="set_to" name="GEMINI_ROOT_DIR">$INSTALL_DIR</environment_variable>
39 <environment_variable action="set_to" name="HOME">.</environment_variable>
40 </action>
41 </actions>
42 </install>
43 <readme>Compiling GEMINI requires a recent c++ compiler, usually gcc.</readme>
44 </package>
45 </tool_dependency>