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annotate tool_dependencies.xml @ 58:39df29f647e8

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set other environment variables as well
author Jan Kanis <jan.code@jankanis.nl>
date Tue, 27 May 2014 12:45:50 +0200
parents 159989f6bfa6
children cd31e2fb5f22
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="libxml2" version="2.9.1">
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4 <repository name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True"
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5 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="3af7ad13a6fb" />
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6 </package>
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7
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8 <package name="libxslt" version="1.1.28">
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9 <repository name="package_libxslt_1_1_28" owner="devteam" prior_installation_required="True"
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10 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee" />
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11 </package>
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12
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13 <package name="python3" version="3.4.1">
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14 <repository name="package_python3_4" owner="jankanis" prior_installation_required="True"
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15 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="59b33d253163" />
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16 </package>
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18 <package name="blast2html_venv" version="0.1">
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19 <install version="1.0">
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20 <actions>
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21 <action type="set_environment_for_install">
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22 <repository name="package_libxml2_2_9_1" owner="devteam"
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23 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="3af7ad13a6fb">
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24 <package name="libxml2" version="2.9.1" />
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25 </repository>
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26 <repository name="package_libxslt_1_1_28" owner="devteam"
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27 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee">
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28 <package name="libxslt" version="1.1.28" />
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29 </repository>
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30 <repository name="package_python3_4" owner="jankanis"
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31 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="59b33d253163">
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32 <package name="python3" version="3.4.1" />
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33 </repository>
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34 </action>
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36 <action type="shell_command">
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37 # Unset any saved environment settings from parent virtual
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38 # environments, e.g. for python 2 or if Galaxy itself is running
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39 # from within a virtual environment.
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40 unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME
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41 pyvenv blast2html_venv
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42 blast2html_venv/bin/pip3 install lxml jinja2
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43 </action>
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45 <action type="set_environment">
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46 <!-- Remove any incoming PYTHONPATH elements from Galaxy's own environment -->
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47 <environment_variable name="PYTHONPATH" action="set_to">$INSTALL_DIR/blast2html_venv/lib/python3.4/site-packages</environment_variable>
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48 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/blast2html_venv/bin</environment_variable>
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49 <environment_variable name="PYTHONHOME" action="set_to"></environment_variable>
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50 <!-- To find shared libraries such as libssl or libxml2 -->
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51 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LD_LIBRARY_PATH]</environment_variable>
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52 </action>
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53 </actions>
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54 </install>
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55 <readme>A Python 3 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme>
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56 </package>
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58 </tool_dependency>