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annotate tool_dependencies.xml @ 10:e76638b1532c draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
author yating-l
date Tue, 14 Mar 2017 13:11:22 -0400
parents 83202aa58873
children 22efe9f6e8a8
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1 <?xml version="1.0"?>
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2 <tool_dependency>
2
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3 <package name="numpy" version="1.9">
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4 <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="biopython" version="1.68">
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7 <readme>
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8 This Galaxy Tool Shed package installs Biopython from source, having
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9 first installed NumPy which is a build time depencency. This requires
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10 and assumes a standard C compiler is already installed, along with
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11 the Python header files.
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12
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13 Development of this dependency definition is being done here on GitHub:
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14 https://github.com/biopython/galaxy_packages
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16 The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.
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17 </readme>
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18 <install version="1.0">
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19 <actions>
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20 <action type="download_by_url">http://biopython.org/DIST/biopython-1.68.tar.gz</action>
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21 <action type="set_environment_for_install">
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22 <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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23 <package name="numpy" version="1.9" />
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24 </repository>
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25 </action>
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26 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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27 <action type="shell_command">
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28 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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29 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
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30 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
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31 python setup.py install --install-lib $INSTALL_DIR/lib/python
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32 </action>
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33 <action type="set_environment">
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34 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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35 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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36 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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37 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
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38 </action>
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39 </actions>
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40 </install>
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41 </package>
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42 <package name="ucsc_tools_340" version="1.0">
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43 <install version="1.0">
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44 <actions_group>
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45 <actions architecture="x86_64" os="linux">
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46 <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action>
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47 <action type="move_directory_files">
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48 <source_directory>.</source_directory>
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49 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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50 </action>
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51 </actions>
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52 <action type="set_environment">
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53 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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54 </action>
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55 </actions_group>
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56 </install>
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57 <readme>The well known UCSC tools from Jim Kent.</readme>
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58 </package>
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59 <package name="jbrowse_tools" version="1.12.1">
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60 <install version="1.0">
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61 <actions_group>
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62 <actions architecture="x86_64" os="linux">
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63 <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/jbrowse_tools.tar.gz</action>
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64 <action type="make_directory">$INSTALL_DIR/jbrowse</action>
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65 <action type="move_directory_files">
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66 <source_directory>.</source_directory>
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67 <destination_directory>$INSTALL_DIR/jbrowse</destination_directory>
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68 </action>
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69 </actions>
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70 <action type="set_environment">
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71 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse</environment_variable>
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72 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/bin</environment_variable>
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73 </action>
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74 </actions_group>
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75 </install>
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76 <readme>The perl scripts for converting flat files to json.</readme>
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77 </package>
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78
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80 </tool_dependency>