Mercurial > repos > jankanis > blast2html

comparison tool_dependencies.xml @ 82:3338571b44cd

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first attempt at running on python 2.6
author Jan Kanis <jan.code@jankanis.nl>
date Mon, 23 Jun 2014 17:11:58 +0200
parents c546e759bf2a
children 0b5819dc1478
comparison
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81:40ce2043006a 82:3338571b44cd
8 <package name="libxslt" version="1.1.28"> 8 <package name="libxslt" version="1.1.28">
9 <repository name="package_libxslt_1_1_28" owner="devteam" prior_installation_required="True" 9 <repository name="package_libxslt_1_1_28" owner="devteam" prior_installation_required="True"
10 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee" /> 10 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee" />
11 </package> 11 </package>
12 12
13 <package name="python3" version="3.4.1">
14 <repository name="package_python3_4" owner="jankanis" prior_installation_required="True"
15 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="d30e6a97dfbf" />
16 </package>
17
18 <package name="blast2html_venv" version="0.1"> 13 <package name="blast2html_venv" version="0.1">
19 <install version="1.0"> 14 <install version="1.0">
20 <actions> 15 <actions>
21 <action type="set_environment_for_install"> 16 <action type="set_environment_for_install">
22 <repository name="package_libxml2_2_9_1" owner="jankanis" 17 <repository name="package_libxml2_2_9_1" owner="jankanis"
25 </repository> 20 </repository>
26 <repository name="package_libxslt_1_1_28" owner="devteam" 21 <repository name="package_libxslt_1_1_28" owner="devteam"
27 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee"> 22 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee">
28 <package name="libxslt" version="1.1.28" /> 23 <package name="libxslt" version="1.1.28" />
29 </repository> 24 </repository>
30 <repository name="package_python3_4" owner="jankanis"
31 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="d30e6a97dfbf">
32 <package name="python3" version="3.4.1" />
33 </repository>
34 </action> 25 </action>
35 26
36 <action type="shell_command"> 27 <action type="setup_virtualenv">
37 # Unset any saved environment settings from parent virtual 28 lxml==2.9.1
38 # environments, e.g. for python 2 or if Galaxy itself is running 29 jinja2==2.7.3
39 # from within a virtual environment. 30 </action>
40 unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME
41 pyvenv blast2html_venv
42 blast2html_venv/bin/pip3 install lxml jinja2
43 </action>
44 31
45 <action type="set_environment"> 32 <action type="set_environment">
46 <!-- Remove any incoming PYTHONPATH elements from Galaxy's own environment -->
47 <environment_variable name="PYTHONPATH" action="set_to">$INSTALL_DIR/blast2html_venv/lib/python3.4/site-packages</environment_variable>
48 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/blast2html_venv/bin</environment_variable>
49 <environment_variable name="PYTHONHOME" action="set_to"></environment_variable>
50 <!-- To find shared libraries such as libssl or libxml2 --> 33 <!-- To find shared libraries such as libssl or libxml2 -->
51 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LD_LIBRARY_PATH]</environment_variable> 34 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LD_LIBRARY_PATH]</environment_variable>
52 <!-- libxml2 doesn't actually export its own LD_LIBRARY_PATH --> 35 <!-- libxml2 doesn't actually export its own LD_LIBRARY_PATH -->
53 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LIBXML_ROOT_PATH]/lib</environment_variable> 36 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LIBXML_ROOT_PATH]/lib</environment_variable>
54 </action> 37 </action>
55 </actions> 38 </actions>
56 </install> 39 </install>
57 <readme>A Python 3 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme> 40 <readme>A Python 2 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme>
58 </package> 41 </package>
59 42
60 </tool_dependency> 43 </tool_dependency>