Mercurial > repos > wolma > mimodd
annotate tool_dependencies.xml @ 16:e676aa6997cc draft
Uploaded
| author | wolma |
|---|---|
| date | Mon, 25 Apr 2016 18:00:02 -0400 |
| parents | 92bd325c70da |
| children | b658c34ee3fd |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 3 <package name="zlib" version="1.2.8"> | |
| 16 | 4 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
| 0 | 5 </package> |
| 13 | 6 <package name="R" version="3.2.1"> |
| 7 <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
| 8 </package> | |
| 14 | 9 <package name="readline" version="6.3"> |
| 10 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
| 13 | 11 </package> |
| 0 | 12 <package name="python3" version="3.4.1"> |
| 13 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
| 14 </package> | |
| 15 | |
|
9
93db2f9bca12
upgrade to v0.1.7.2
Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
parents:
8
diff
changeset
|
16 <package name="mimodd" version="0.1.7.2"> |
| 0 | 17 <install version="1.0"> |
| 18 <actions> | |
| 13 | 19 <!-- prepare a python3 venv to install into --> |
| 0 | 20 <action type="set_environment_for_install"> |
| 21 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu"> | |
| 22 <package name="python3" version="3.4.1" /> | |
| 23 </repository> | |
| 24 </action> | |
| 13 | 25 <action type="shell_command">python3 -m venv --without-pip $INSTALL_DIR/MiModD_venv</action> |
| 26 <!-- remove the plain python symlink from the venv to avoid its | |
| 27 accidental use by Galaxy, MiModD uses python3 explicitly --> | |
| 28 <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action> | |
| 29 <action type="shell_command">. $INSTALL_DIR/MiModD_venv/bin/activate</action> | |
| 30 | |
| 31 <!-- download and install rpy2 --> | |
| 32 <action sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441" type="download_by_url"> | |
| 33 https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz | |
| 34 </action> | |
| 35 <action type="set_environment_for_install"> | |
| 15 | 36 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
| 16 | 37 <package name="readline" version="6.3" /> |
| 13 | 38 </repository> |
| 39 <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | |
| 40 <package name="R" version="3.2.1" /> | |
| 41 </repository> | |
| 42 </action> | |
| 43 <action type="shell_command"> | |
| 44 export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" && | |
| 45 export CPPFLAGS="-I$READLINE_INCLUDE_PATH" && | |
| 46 python3 setup.py install | |
| 47 </action> | |
| 48 <action type="change_directory">$TMP_WORK_DIR</action> | |
| 49 | |
| 50 <!-- download and install MiModD --> | |
| 51 <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action> | |
| 0 | 52 <action type="set_environment_for_install"> |
| 16 | 53 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
| 0 | 54 <package name="zlib" version="1.2.8" /> |
| 55 </repository> | |
| 56 </action> | |
| 57 <!-- install MiModD placing the entry script mimodd into the venv's bin directory --> | |
| 13 | 58 <action type="shell_command">python3 setup.py install</action> |
| 0 | 59 <!-- make MiModD's wrapped binaries executable --> |
| 13 | 60 <action type="chmod"><file mode="755">$INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</file></action> |
| 7 | 61 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself --> |
| 13 | 62 <action type="shell_command">python3 -m MiModD.__first_run__</action> |
| 7 | 63 |
| 0 | 64 <action type="set_environment"> |
| 65 <!-- make the mimodd entry script discoverable --> | |
| 66 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable> | |
| 67 <!-- clear $PYTHONPATH and $PYTHONHOME --> | |
| 68 <environment_variable action="set_to" name="PYTHONPATH" /> | |
| 69 <environment_variable action="set_to" name="PYTHONHOME" /> | |
| 70 <!-- propagate $LD_LIBRARY_PATH --> | |
| 71 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable> | |
| 72 </action> | |
| 73 | |
| 74 </actions> | |
| 75 </install> | |
| 76 <readme> | |
| 77 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs | |
| 78 Home-page: http://sourceforge.net/projects/mimodd/ | |
| 79 Author: Wolfgang Maier | |
| 80 Author-email: wolfgang.maier@biologie.uni-freiburg.de | |
| 81 License: GPL | |
| 82 Download-URL: http://sourceforge.net/projects/mimodd/ | |
| 83 | |
| 84 MiModD - Identify Mutations from Whole-Genome Sequencing Data | |
| 85 ************************************************************* | |
| 86 | |
| 87 MiModD is an integrated solution for efficient and user-friendly analysis of | |
| 88 whole-genome sequencing (WGS) data from laboratory model organisms. | |
| 89 It enables geneticists to identify the genetic mutations present in an organism | |
| 90 starting from just raw WGS read data and a reference genome without the help of | |
| 91 a trained bioinformatician. | |
| 92 | |
| 93 MiModD is designed for good performance on standard hardware and enables WGS | |
| 94 data analysis for most model organisms on regular desktop PCs. | |
| 95 | |
| 96 MiModD can be installed under Linux and Mac OS with minimal software | |
| 97 requirements and a simple setup procedure. As a standalone package it can be | |
| 98 used from the command line, but can also be integrated seamlessly and easily | |
| 99 into any local installation of a Galaxy bioinformatics server providing a | |
| 100 graphical user interface, database management of results and simple composition | |
| 101 of analysis steps into workflows. | |
| 102 </readme> | |
| 103 </package> | |
| 104 </tool_dependency> |