Mercurial > repos > jankanis > blast2html
annotate tool_dependencies.xml @ 62:b90441d0fe7d
Undo including $ENV[PYTHONPATH] in PYTHONPATH
If $ENV[PYTHONPATH] is empty, Galaxy replaces it with $PYTHONPATH instead of an empty string, which introduces
python 2 code in the python 3 path.
| author | Jan Kanis <jan.code@jankanis.nl> |
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| date | Wed, 28 May 2014 14:02:38 +0200 |
| parents | cd31e2fb5f22 |
| children | fb823a59918f |
| rev | line source |
|---|---|
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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="7719329e5b98" /> |
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16 </package> |
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17 |
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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="7719329e5b98"> |
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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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35 |
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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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44 |
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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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58
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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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57 |
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58 </tool_dependency> |