Mercurial > repos > yating-l > jbrowsearchivecreator

annotate tool_dependencies.xml @ 7:5d5fdcb798da draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
author yating-l
date Fri, 20 Apr 2018 13:51:23 -0400
parents 237707a6b74d
children 7cb67cbbd8e5
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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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6
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7 <package name="ucsc_hac" version="340">
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8 <repository changeset_revision="1a15120c22c8" name="package_ucsc_hac_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" />
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9 </package>
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10
0
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11 <package name="numpy" version="1.9">
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12 <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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13 </package>
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15 <package name="biopython" version="1.68">
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16 <readme>
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17 This package is based on package_biopython_1_67 owned by biopython.
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18 https://toolshed.g2.bx.psu.edu/repository?user_id=fd5c6d0f82f315d8
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20 This Galaxy Tool Shed package installs Biopython from source, having
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21 first installed NumPy which is a build time depencency. This requires
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22 and assumes a standard C compiler is already installed, along with
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23 the Python header files.
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24
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25 Development of this dependency definition is being done here on GitHub:
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26 https://github.com/biopython/galaxy_packages
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27
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28 The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.
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29 </readme>
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30 <install version="1.0">
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31 <actions>
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32 <action type="download_by_url">http://biopython.org/DIST/biopython-1.68.tar.gz</action>
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33 <action type="set_environment_for_install">
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34 <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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35 <package name="numpy" version="1.9" />
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36 </repository>
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37 </action>
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38 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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39 <action type="shell_command">
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40 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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41 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
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42 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
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43 python setup.py install --install-lib $INSTALL_DIR/lib/python
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44 </action>
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45 <action type="set_environment">
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46 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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47 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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48 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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49 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
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50 </action>
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51 </actions>
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52 </install>
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53 </package>
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54
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55 <package name="jbrowse_tools" version="1.13.1">
0
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56 <install version="1.0">
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57 <actions_group>
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58 <actions architecture="x86_64" os="linux">
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59 <action type="download_by_url">https://github.com/GMOD/jbrowse/releases/download/1.13.1-release/JBrowse-1.13.1.zip</action>
0
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60 <action type="make_directory">$INSTALL_DIR/jbrowse</action>
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61 <action type="shell_command">
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62 export HOME=$INSTALL_DIR/jbrowse &amp;&amp; ./setup.sh
0
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63 </action>
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64 <action type="move_directory_files">
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65 <source_directory>.</source_directory>
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66 <destination_directory>$INSTALL_DIR/jbrowse</destination_directory>
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67 </action>
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68 <action type="set_environment">
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69 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse</environment_variable>
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70 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/bin</environment_variable>
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71 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/src</environment_variable>
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72 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/extlib</environment_variable>
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73 </action>
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74 </actions>
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75 </actions_group>
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76 </install>
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77 <readme>The perl scripts for converting flat files to json.</readme>
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78 </package>
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79
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80 <package name="gff3sort" version="1.0">
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81 <install version="1.0">
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82 <actions_group>
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83 <actions architecture="x86_64" os="linux">
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84 <action type="download_by_url">https://github.com/billzt/gff3sort/archive/v0.1-alpha.zip</action>
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85 <action type="make_directory">$INSTALL_DIR/gff3sort</action>
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86 <action type="move_directory_files">
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87 <source_directory>.</source_directory>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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88 <destination_directory>$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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89 </action>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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90 <action type="set_environment">
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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91 <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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92 </action>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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93 </actions>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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94 </actions_group>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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95 </install>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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96 <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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97 </package>
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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98
0
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99 </tool_dependency>