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annotate tool_dependencies.xml @ 9:d3ea5f1b4d79 draft

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Another attempt at getting the environment settings right.
author jankanis
date Sat, 24 May 2014 17:54:04 -0400
parents a468d4d76af3
children 30e2c5ac5550
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="openssl" version="1.0.1g">
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4 <repository changeset_revision="23ebff671a20" name="package_openssl" owner="jankanis" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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6
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7 <package name="sqlite" version="3.8.3">
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8 <repository changeset_revision="706b1f3b1fc0" name="package_sqlite_3_8_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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9 </package>
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11 <package name="gdbm" version="1.11">
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12 <repository changeset_revision="15e7435c2663" name="package_gdbm_1_11" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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13 </package>
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16 <package name="python3" version="3.4.1">
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17 <install version="1.0">
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18 <actions>
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19 <action type="download_by_url">https://www.python.org/ftp/python/3.4.1/Python-3.4.1.tgz</action>
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21 <action type="set_environment_for_install">
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22 <repository changeset_revision="23ebff671a20" name="package_openssl" owner="jankanis" toolshed="http://toolshed.g2.bx.psu.edu">
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23 <package name="openssl" version="1.0.1g" />
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24 </repository>
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25 <repository changeset_revision="706b1f3b1fc0" name="package_sqlite_3_8_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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26 <package name="sqlite" version="3.8.3" />
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27 </repository>
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28 <repository changeset_revision="15e7435c2663" name="package_gdbm_1_11" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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29 <package name="gdbm" version="1.11" />
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30 </repository>
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31 </action>
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32
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33 <action type="shell_command">
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34 # The python build system doesn't check C_INCLUDE_PATH which is set by the depended-upon tool
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35 # definitions for these sources, but it does check CFLAGS.
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36 export CFLAGS="$CFLAGS -I$SQLITE_ROOT_DIR/lib -I$GDBM_ROOT_PATH/lib -I$OPENSSL_ROOT_DIR/lib"
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37 export LDFLAGS="$LDFLAGS -L$SQLITE_ROOT_DIR/include -L$GDBM_ROOT_PATH/include -L$OPENSSL_ROOT_DIR/include"
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38 # Clear variables that may be used in Galaxy's extenal python 2 environment
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39 unset PYTHONPATH
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40 unset PYTHONHOME
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41 ./configure --prefix=$INSTALL_DIR --with-ensurepip --enable-loadable-sqlite-extensions \
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42 &amp;&amp; make \
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43 &amp;&amp; make instal
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44 </action>
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45 <action type="make_install" />
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47 <action type="set_environment">
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48 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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49 <!-- empty PYTHONPATH, otherwise we will get Galaxy's Python 2 libraries in the Python 3 path -->
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50 <environment_variable action="set_to" name="PYTHONPATH" />
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51 <environment_variable action="set_to" name="PYTHONHOME">$INSTALL_DIR</environment_variable>
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52 <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable>
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53 </action>
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54 </actions>
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55 </install>
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56
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57 <readme>
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58 Python 3.4.1. Configured with the default settings, using --prefix=$INSTALL_DIR.
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59
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60 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:
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61
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62 &lt;action type="set_environment_for_install"&gt;
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63 &lt;repository name="python3" owner="jankanis"&gt;
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64 &lt;package name="python3" version="3.4.1" /&gt;
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65 &lt;/repository&gt;
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66 &lt;/action&gt;
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67 &lt;action type="shell_command"&gt;
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68 # Unset any saved environment settings from parent virtual
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69 # environments, e.g. for python 2 or if Galaxy itself is running
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70 # from within a virtual environment.
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71 unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME
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72 pyvenv {{\$MY_PACKAGE_NAME}}
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73 . {{\$MY_PACKAGE_NAME}}/bin/activate
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74 pip3 install {{\$PYTHON-PACKAGE}}
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75 &lt;/action&gt;
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76 &lt;action type="set_environment"&gt;
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77 &lt;environment_variable name="PYTHONPATH" action="prepend_to"&gt;\$INSTALL_DIR/lib/python3.4/site-packages&lt;/environment_variable&gt;
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78 &lt;/action&gt;
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79
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80 </readme>
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81
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82 </package>
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83 </tool_dependency>