Mercurial > repos > wolma > package_mimodd_0_1_5

comparison tool_dependencies.xml @ 1:46fd9b9b753f draft

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upgrade to v0.1.5.1
author wolma
date Fri, 16 Jan 2015 10:34:59 -0500
parents fbac402764d6
children a1ed24182b03
comparison
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0:fbac402764d6 1:46fd9b9b753f
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="zlib" version="1.2.8"> 3 <package name="zlib" version="1.2.8">
4 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="python3" version="3.4.1"> 6 <package name="python3" version="3.4.1">
7 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="mimodd" version="0.1.5"> 9
10 <install version="1.0"> 10 <package name="mimodd" version="0.1.5">
11 <actions> 11 <install version="1.0">
12 <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.5.tar.gz</action> 12 <actions>
13 <action type="set_environment_for_install"> 13 <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.5.1.tar.gz</action>
14 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu"> 14 <action type="set_environment_for_install">
15 <package name="python3" version="3.4.1" /> 15 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu">
16 </repository> 16 <package name="python3" version="3.4.1" />
17 </action> 17 </repository>
18 <action type="set_environment_for_install"> 18 </action>
19 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu"> 19 <action type="set_environment_for_install">
20 <package name="zlib" version="1.2.8" /> 20 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu">
21 </repository> 21 <package name="zlib" version="1.2.8" />
22 </action> 22 </repository>
23 <action type="shell_command">pyvenv --without-pip $INSTALL_DIR/MiModD_venv</action> 23 </action>
24 <!-- install MiModD placing the entry script mimodd into the venv's bin directory --> 24 <action type="shell_command">pyvenv --without-pip $INSTALL_DIR/MiModD_venv</action>
25 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action> 25 <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
26 <!-- make MiModD's wrapped binaries executable --> 26 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
27 <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action> 27 <!-- make MiModD's wrapped binaries executable -->
28 <action type="set_environment"> 28 <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action>
29 <!-- make the mimodd entry script discoverable --> 29
30 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable> 30
31 <!-- clear $PYTHONPATH and $PYTHONHOME --> 31 <action type="set_environment">
32 <environment_variable action="set_to" name="PYTHONPATH" /> 32 <!-- make the mimodd entry script discoverable -->
33 <environment_variable action="set_to" name="PYTHONHOME" /> 33 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
34 <!-- propagate $LD_LIBRARY_PATH --> 34 <!-- clear $PYTHONPATH and $PYTHONHOME -->
35 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable> 35 <environment_variable action="set_to" name="PYTHONPATH" />
36 </action> 36 <environment_variable action="set_to" name="PYTHONHOME" />
37 </actions> 37 <!-- propagate $LD_LIBRARY_PATH -->
38 </install> 38 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
39 <readme> 39 </action>
40
41
42 </actions>
43 </install>
44 <readme>
40 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs 45 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
41 Home-page: http://sourceforge.net/projects/mimodd/ 46 Home-page: http://sourceforge.net/projects/mimodd/
42 Author: Wolfgang Maier 47 Author: Wolfgang Maier
43 Author-email: wolfgang.maier@biologie.uni-freiburg.de 48 Author-email: wolfgang.maier@biologie.uni-freiburg.de
44 License: GPL 49 License: GPL
61 used from the command line, but can also be integrated seamlessly and easily 66 used from the command line, but can also be integrated seamlessly and easily
62 into any local installation of a Galaxy bioinformatics server providing a 67 into any local installation of a Galaxy bioinformatics server providing a
63 graphical user interface, database management of results and simple composition 68 graphical user interface, database management of results and simple composition
64 of analysis steps into workflows. 69 of analysis steps into workflows.
65 </readme> 70 </readme>
66 </package> 71 </package>
67 </tool_dependency> 72 </tool_dependency>