Mercurial > repos > yating-l > jbrowsearchivecreator

annotate tool_dependencies.xml @ 0:8d1cf7ce65cd draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
author yating-l
date Thu, 18 May 2017 17:25:33 -0400
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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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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7 <package name="numpy" version="1.9">
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8 <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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9 </package>
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11 <package name="biopython" version="1.68">
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12 <readme>
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13 This package is based on package_biopython_1_67 owned by biopython.
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14 https://toolshed.g2.bx.psu.edu/repository?user_id=fd5c6d0f82f315d8
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16 This Galaxy Tool Shed package installs Biopython from source, having
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17 first installed NumPy which is a build time depencency. This requires
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18 and assumes a standard C compiler is already installed, along with
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19 the Python header files.
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21 Development of this dependency definition is being done here on GitHub:
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22 https://github.com/biopython/galaxy_packages
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23
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24 The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.
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25 </readme>
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26 <install version="1.0">
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27 <actions>
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28 <action type="download_by_url">http://biopython.org/DIST/biopython-1.68.tar.gz</action>
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29 <action type="set_environment_for_install">
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30 <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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31 <package name="numpy" version="1.9" />
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32 </repository>
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33 </action>
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34 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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35 <action type="shell_command">
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36 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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37 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
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38 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
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39 python setup.py install --install-lib $INSTALL_DIR/lib/python
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40 </action>
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41 <action type="set_environment">
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42 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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43 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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44 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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45 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
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46 </action>
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47 </actions>
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48 </install>
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49 </package>
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50
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51 <package name="ucsc_tools_340" version="1.0">
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52 <install version="1.0">
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53 <actions_group>
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54 <actions architecture="x86_64" os="linux">
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55 <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action>
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56 <action type="move_directory_files">
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57 <source_directory>.</source_directory>
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58 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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59 </action>
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60 </actions>
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61 <action type="set_environment">
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62 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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63 </action>
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64 </actions_group>
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65 </install>
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66 <readme>The well known UCSC tools from Jim Kent.</readme>
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67 </package>
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68 <package name="jbrowse_tools" version="1.12.1">
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69 <install version="1.0">
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70 <actions_group>
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71 <action type="setup_perl_environment">
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72 <repository name="package_perl_5_18" owner="iuc">
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73 <package name="perl" version="5.18.1" />
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74 </repository>
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75 <package>XML::Parser</package>
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76 <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package>
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77 </action>
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78 <actions architecture="x86_64" os="linux">
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79 <action type="download_by_url">http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=105</action>
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80 <action type="make_directory">$INSTALL_DIR/jbrowse</action>
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81 <action type="shell_command">
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82 ./setup.sh
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83 </action>
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84 <action type="move_directory_files">
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85 <source_directory>.</source_directory>
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86 <destination_directory>$INSTALL_DIR/jbrowse</destination_directory>
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87 </action>
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88 <action type="set_environment">
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89 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse</environment_variable>
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90 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/bin</environment_variable>
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91 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/src</environment_variable>
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92 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/extlib</environment_variable>
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93 </action>
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94 </actions>
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95 </actions_group>
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96 </install>
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97 <readme>The perl scripts for converting flat files to json.</readme>
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98 </package>
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99
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100
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101 </tool_dependency>