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comparison tool_dependencies.xml @ 0:e9407b729a69 draft

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author jankanis
date Thu, 22 May 2014 05:58:18 -0400
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children 09faf0ae581b
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-1:000000000000 0:e9407b729a69
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="openssl" version="1.0.1g">
4 <repository changeset_revision="e459a9ce3fce" name="package_openssl" owner="jankanis" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package>
6
7 <package name="python3" version="3.4.1">
8 <install version="1.0">
9 <actions>
10 <action type="download_by_url">https://www.python.org/ftp/python/3.4.1/Python-3.4.1.tgz</action>
11 <action type="set_environment_for_install">
12 <repository changeset_revision="e459a9ce3fce" name="package_openssl" owner="jankanis" toolshed="http://toolshed.g2.bx.psu.edu">
13 <package name="openssl" version="1.0.1g" />
14 </repository>
15 </action>
16 <action type="autoconf">--prefix=$INSTALL_DIR</action>
17 <action type="set_environment">
18 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
19 <!-- empty PYTHONPATH, otherwise we will get Galaxy's Python 2 libraries in the Python 3 path-->
20 <environment_variable action="set_to" name="PYTHONPATH" />
21 <environment_variable action="set_to" name="PYTHONHOME">$INSTALL_DIR</environment_variable>
22 </action>
23 </actions>
24 </install>
25
26 <readme>
27 Python 3.4.1. Configured with the default settings, using --prefix=$INSTALL_DIR.
28
29 Python as of version 3.3 includes a built-in virtual environment manager. To create a python 3 virtual env, include the following actions in your tool_dependencies.xml:
30
31 &lt;action type="set_environment_for_install"&gt;
32 &lt;repository name="python3" owner="jankanis"&gt;
33 &lt;package name="python3" version="3.4.1" /&gt;
34 &lt;/repository&gt;
35 &lt;/action&gt;
36 &lt;action type="shell_command"&gt;
37 # Unset any saved environment settings from parent virtual
38 # environments, e.g. for python 2 or if Galaxy itself is running
39 # from within a virtual environment.
40 unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME
41 pyvenv {{$MY_PACKAGE_NAME}}
42 . {{$MY_PACKAGE_NAME}}/bin/activate
43 pip install {{$PYTHON-PACKAGE}}
44 &lt;/action&gt;
45 &lt;action type="set_environment"&gt;
46 &lt;environment_variable name="PYTHONPATH" action="prepend_to"&gt;$INSTALL_DIR/lib/python3.4/site-packages:$INSTALL_DIR/lib64/python3.4/iste-packages&lt;/environment_variable&gt;
47 &lt;/action&gt;
48
49 </readme>
50
51 </package>
52 </tool_dependency>