Mercurial > repos > wolma > mimodd
annotate tool_dependencies.xml @ 9:93db2f9bca12
upgrade to v0.1.7.2
| author | Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de |
|---|---|
| date | Thu, 28 Jan 2016 17:26:58 +0100 |
| parents | d79fe626c6fd |
| children | ac3eac581b83 |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 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" /> | |
| 5 </package> | |
| 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" /> | |
| 8 </package> | |
| 9 | |
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9
93db2f9bca12
upgrade to v0.1.7.2
Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
parents:
8
diff
changeset
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10 <package name="mimodd" version="0.1.7.2"> |
| 0 | 11 <install version="1.0"> |
| 12 <actions> | |
| 8 | 13 <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.1.tar.gz</action> |
| 0 | 14 <action type="set_environment_for_install"> |
| 15 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu"> | |
| 16 <package name="python3" version="3.4.1" /> | |
| 17 </repository> | |
| 18 </action> | |
| 19 <action type="set_environment_for_install"> | |
| 20 <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu"> | |
| 21 <package name="zlib" version="1.2.8" /> | |
| 22 </repository> | |
| 23 </action> | |
| 24 <action type="shell_command">pyvenv --without-pip $INSTALL_DIR/MiModD_venv</action> | |
| 25 <!-- remove the plain python symlink from the venv to avoid its | |
| 26 accidental use by Galaxy, MiModD uses python3 explicitly --> | |
| 27 <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action> | |
| 28 <!-- install MiModD placing the entry script mimodd into the venv's bin directory --> | |
| 29 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action> | |
| 30 <!-- make MiModD's wrapped binaries executable --> | |
| 31 <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action> | |
| 7 | 32 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself --> |
| 33 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action> | |
| 34 | |
| 0 | 35 <action type="set_environment"> |
| 36 <!-- make the mimodd entry script discoverable --> | |
| 37 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable> | |
| 38 <!-- clear $PYTHONPATH and $PYTHONHOME --> | |
| 39 <environment_variable action="set_to" name="PYTHONPATH" /> | |
| 40 <environment_variable action="set_to" name="PYTHONHOME" /> | |
| 41 <!-- propagate $LD_LIBRARY_PATH --> | |
| 42 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable> | |
| 43 </action> | |
| 44 | |
| 45 | |
| 46 </actions> | |
| 47 </install> | |
| 48 <readme> | |
| 49 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs | |
| 50 Home-page: http://sourceforge.net/projects/mimodd/ | |
| 51 Author: Wolfgang Maier | |
| 52 Author-email: wolfgang.maier@biologie.uni-freiburg.de | |
| 53 License: GPL | |
| 54 Download-URL: http://sourceforge.net/projects/mimodd/ | |
| 55 | |
| 56 MiModD - Identify Mutations from Whole-Genome Sequencing Data | |
| 57 ************************************************************* | |
| 58 | |
| 59 MiModD is an integrated solution for efficient and user-friendly analysis of | |
| 60 whole-genome sequencing (WGS) data from laboratory model organisms. | |
| 61 It enables geneticists to identify the genetic mutations present in an organism | |
| 62 starting from just raw WGS read data and a reference genome without the help of | |
| 63 a trained bioinformatician. | |
| 64 | |
| 65 MiModD is designed for good performance on standard hardware and enables WGS | |
| 66 data analysis for most model organisms on regular desktop PCs. | |
| 67 | |
| 68 MiModD can be installed under Linux and Mac OS with minimal software | |
| 69 requirements and a simple setup procedure. As a standalone package it can be | |
| 70 used from the command line, but can also be integrated seamlessly and easily | |
| 71 into any local installation of a Galaxy bioinformatics server providing a | |
| 72 graphical user interface, database management of results and simple composition | |
| 73 of analysis steps into workflows. | |
| 74 </readme> | |
| 75 </package> | |
| 76 </tool_dependency> |