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comparison tool_dependencies.xml @ 1:09faf0ae581b draft

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Fix some whitespace
author jankanis
date Thu, 22 May 2014 06:00:27 -0400
parents e9407b729a69
children ab42c5133d1c
comparison
equal deleted inserted replaced
0:e9407b729a69 1:09faf0ae581b
5 </package> 5 </package>
6 6
7 <package name="python3" version="3.4.1"> 7 <package name="python3" version="3.4.1">
8 <install version="1.0"> 8 <install version="1.0">
9 <actions> 9 <actions>
10 <action type="download_by_url">https://www.python.org/ftp/python/3.4.1/Python-3.4.1.tgz</action> 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"> 11 <action type="set_environment_for_install">
12 <repository changeset_revision="e459a9ce3fce" name="package_openssl" owner="jankanis" toolshed="http://toolshed.g2.bx.psu.edu"> 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" /> 13 <package name="openssl" version="1.0.1g" />
14 </repository> 14 </repository>
15 </action> 15 </action>
16 <action type="autoconf">--prefix=$INSTALL_DIR</action> 16 <action type="autoconf">--prefix=$INSTALL_DIR</action>
17 <action type="set_environment"> 17 <action type="set_environment">
18 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 18 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
19 <!-- empty PYTHONPATH, otherwise we will get Galaxy's Python 2 libraries in the Python 3 path--> 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" /> 20 <environment_variable action="set_to" name="PYTHONPATH" />
21 <environment_variable action="set_to" name="PYTHONHOME">$INSTALL_DIR</environment_variable> 21 <environment_variable action="set_to" name="PYTHONHOME">$INSTALL_DIR</environment_variable>
22 </action> 22 </action>
23 </actions> 23 </actions>
24 </install> 24 </install>
25 25
26 <readme> 26 <readme>
27 Python 3.4.1. Configured with the default settings, using --prefix=$INSTALL_DIR. 27 Python 3.4.1. Configured with the default settings, using --prefix=$INSTALL_DIR.
28 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: 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 30
31 &lt;action type="set_environment_for_install"&gt; 31 &lt;action type="set_environment_for_install"&gt;
32 &lt;repository name="python3" owner="jankanis"&gt; 32 &lt;repository name="python3" owner="jankanis"&gt;
33 &lt;package name="python3" version="3.4.1" /&gt; 33 &lt;package name="python3" version="3.4.1" /&gt;
34 &lt;/repository&gt; 34 &lt;/repository&gt;
35 &lt;/action&gt; 35 &lt;/action&gt;
36 &lt;action type="shell_command"&gt; 36 &lt;action type="shell_command"&gt;
37 # Unset any saved environment settings from parent virtual 37 # Unset any saved environment settings from parent virtual
38 # environments, e.g. for python 2 or if Galaxy itself is running 38 # environments, e.g. for python 2 or if Galaxy itself is running
39 # from within a virtual environment. 39 # from within a virtual environment.
40 unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME 40 unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME
41 pyvenv {{$MY_PACKAGE_NAME}} 41 pyvenv {{$MY_PACKAGE_NAME}}
42 . {{$MY_PACKAGE_NAME}}/bin/activate 42 . {{$MY_PACKAGE_NAME}}/bin/activate
43 pip install {{$PYTHON-PACKAGE}} 43 pip install {{$PYTHON-PACKAGE}}
44 &lt;/action&gt; 44 &lt;/action&gt;
45 &lt;action type="set_environment"&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; 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; 47 &lt;/action&gt;
48 48
49 </readme> 49 </readme>
50 50
51 </package> 51 </package>