Mercurial > repos > yating-l > jbrowsearchivecreator

annotate tool_dependencies.xml @ 17:315a40b0b694 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 891eca7a697643c9b5365781bbab5b655972ffdc
author yating-l
date Mon, 25 Jun 2018 16:05:01 -0400
parents 7cb67cbbd8e5
children 62dee5369e80
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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="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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5 </package>
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7 <package name="tabix" version="0.2.6">
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8 <repository changeset_revision="389d2376b60b" name="package_tabix_0_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
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9 </package>
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11 <package name="ucsc_hac" version="340">
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12 <repository changeset_revision="1a15120c22c8" name="package_ucsc_hac_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" />
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13 </package>
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14
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15 <package name="numpy" version="1.9">
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16 <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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17 </package>
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19 <package name="biopython" version="1.68">
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20 <readme>
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21 This package is based on package_biopython_1_67 owned by biopython.
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22 https://toolshed.g2.bx.psu.edu/repository?user_id=fd5c6d0f82f315d8
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23
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24 This Galaxy Tool Shed package installs Biopython from source, having
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25 first installed NumPy which is a build time depencency. This requires
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26 and assumes a standard C compiler is already installed, along with
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27 the Python header files.
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28
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29 Development of this dependency definition is being done here on GitHub:
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30 https://github.com/biopython/galaxy_packages
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31
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32 The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.
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33 </readme>
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34 <install version="1.0">
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35 <actions>
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36 <action type="download_by_url">http://biopython.org/DIST/biopython-1.68.tar.gz</action>
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37 <action type="set_environment_for_install">
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38 <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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39 <package name="numpy" version="1.9" />
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40 </repository>
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41 </action>
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42 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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43 <action type="shell_command">
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44 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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45 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
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46 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
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47 python setup.py install --install-lib $INSTALL_DIR/lib/python
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48 </action>
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49 <action type="set_environment">
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50 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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51 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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52 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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53 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
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54 </action>
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55 </actions>
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56 </install>
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57 </package>
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59 <package name="jbrowse_tools" version="1.13.1">
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60 <install version="1.0">
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61 <actions_group>
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62 <actions architecture="x86_64" os="linux">
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63 <action type="download_by_url">https://github.com/GMOD/jbrowse/releases/download/1.13.1-release/JBrowse-1.13.1.zip</action>
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64 <action type="make_directory">$INSTALL_DIR/jbrowse</action>
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65 <action type="shell_command">
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66 export HOME=$INSTALL_DIR/jbrowse &amp;&amp; ./setup.sh
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67 </action>
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68 <action type="move_directory_files">
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69 <source_directory>.</source_directory>
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70 <destination_directory>$INSTALL_DIR/jbrowse</destination_directory>
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71 </action>
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72 <action type="set_environment">
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73 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse</environment_variable>
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74 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/bin</environment_variable>
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75 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/src</environment_variable>
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76 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/extlib</environment_variable>
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77 </action>
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78 </actions>
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79 </actions_group>
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80 </install>
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81 <readme>The perl scripts for converting flat files to json.</readme>
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82 </package>
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83
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84 <package name="gff3sort" version="1.0">
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85 <install version="1.0">
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86 <actions_group>
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87 <actions architecture="x86_64" os="linux">
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88 <action type="download_by_url">https://github.com/billzt/gff3sort/archive/v0.1-alpha.zip</action>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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89 <action type="make_directory">$INSTALL_DIR/gff3sort</action>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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90 <action type="move_directory_files">
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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91 <source_directory>.</source_directory>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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92 <destination_directory>$INSTALL_DIR/gff3sort</destination_directory>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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93 </action>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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94 <action type="set_environment">
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95 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/gff3sort</environment_variable>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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96 </action>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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97 </actions>
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98 </actions_group>
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99 </install>
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100 <readme>A Perl Script to sort gff3 files and produce suitable results for tabix tools. </readme>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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101 </package>
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102
0
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103 </tool_dependency>