Mercurial > repos > yating-l > jbrowse_hub

annotate tool_dependencies.xml @ 32:f45a253f7c6a draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
author yating-l
date Fri, 17 Mar 2017 12:37:08 -0400
parents d8049deb0c97
children 66db979c21f0
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1 <?xml version="1.0"?>
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2 <tool_dependency>
30
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3 <package name="samtools" version="1.2">
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4 <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" 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="numpy" version="1.9">
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7 <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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8 </package>
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9 <package name="biopython" version="1.68">
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10 <readme>
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11 This package is based on package_biopython_1_67 owned by biopython.
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12 https://toolshed.g2.bx.psu.edu/repository?user_id=fd5c6d0f82f315d8
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13
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14 This Galaxy Tool Shed package installs Biopython from source, having
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15 first installed NumPy which is a build time depencency. This requires
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16 and assumes a standard C compiler is already installed, along with
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17 the Python header files.
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18
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19 Development of this dependency definition is being done here on GitHub:
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20 https://github.com/biopython/galaxy_packages
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21
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22 The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.
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23 </readme>
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24 <install version="1.0">
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25 <actions>
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26 <action type="download_by_url">http://biopython.org/DIST/biopython-1.68.tar.gz</action>
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27 <action type="set_environment_for_install">
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28 <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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29 <package name="numpy" version="1.9" />
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30 </repository>
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31 </action>
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32 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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33 <action type="shell_command">
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34 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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35 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
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36 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
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37 python setup.py install --install-lib $INSTALL_DIR/lib/python
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38 </action>
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39 <action type="set_environment">
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40 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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41 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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42 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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43 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
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44 </action>
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45 </actions>
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46 </install>
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47 </package>
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48 <package name="ucsc_tools_340" version="1.0">
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49 <install version="1.0">
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50 <actions_group>
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51 <actions architecture="x86_64" os="linux">
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52 <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action>
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53 <action type="move_directory_files">
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54 <source_directory>.</source_directory>
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55 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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56 </action>
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57 </actions>
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58 <action type="set_environment">
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59 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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60 </action>
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61 </actions_group>
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62 </install>
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63 <readme>The well known UCSC tools from Jim Kent.</readme>
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64 </package>
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65 <package name="jbrowse_tools" version="1.12.1">
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66 <install version="1.0">
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67 <actions_group>
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68 <actions architecture="x86_64" os="linux">
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69 <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/jbrowse_tools.tar.gz</action>
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70 <action type="make_directory">$INSTALL_DIR/jbrowse</action>
7
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71 <action type="move_directory_files">
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72 <source_directory>.</source_directory>
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73 <destination_directory>$INSTALL_DIR/jbrowse</destination_directory>
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74 </action>
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75 </actions>
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76 <action type="set_environment">
10
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77 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse</environment_variable>
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78 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/bin</environment_variable>
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79 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/src</environment_variable>
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80 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/extlib</environment_variable>
7
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81 </action>
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82 </actions_group>
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83 </install>
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84 <readme>The perl scripts for converting flat files to json.</readme>
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85 </package>
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86
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87
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88 </tool_dependency>