Mercurial > repos > wolma > mimodd
annotate tool_dependencies.xml @ 22:24154c580718 draft
Uploaded
| author | wolma |
|---|---|
| date | Sun, 12 Jun 2016 07:39:46 -0400 |
| parents | c46406466625 |
| children | 5db0545b9004 |
| 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"> |
| 21 | 7 <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
| 13 | 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> |
| 18 | 12 <package name="python3" version="3.4"> |
| 21 | 13 <repository changeset_revision="83407422ec16" name="package_python_3_4_x_lean" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
| 0 | 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 | 21 <repository changeset_revision="83407422ec16" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu"> |
| 18 | 22 <package name="python3" version="3.4" /> |
| 0 | 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 $INSTALL_DIR/MiModD_venv/bin/python</action> | |
| 18 | 29 |
| 30 <!-- download and install setuptools (required to install rpy2) --> | |
| 20 | 31 <action type="change_directory">$TMP_WORK_DIR</action> |
| 32 <action sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25" type="download_file">https://depot.galaxyproject.org/software/setuptools/setuptools_18.2_src_all.tar.bz2</action> | |
| 18 | 33 <action type="shell_command">tar -xjf setuptools_18.2_src_all.tar.bz2</action> |
| 34 <action type="change_directory">pypa-setuptools-1a981f2e5031</action> | |
| 19 | 35 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action> |
| 18 | 36 |
| 37 <!-- download and install six (required by rpy2) --> | |
| 20 | 38 <action type="change_directory">$TMP_WORK_DIR</action> |
| 39 <action sha256sum="e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5" type="download_file">https://depot.galaxyproject.org/software/six/six_1.9.0_src_all.tar.gz</action> | |
| 18 | 40 <action type="shell_command">tar -xzf six_1.9.0_src_all.tar.gz</action> |
| 41 <action type="change_directory">six-1.9.0</action> | |
| 19 | 42 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action> |
| 18 | 43 |
| 13 | 44 <!-- download and install rpy2 --> |
| 20 | 45 <action type="change_directory">$TMP_WORK_DIR</action> |
| 46 <action sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441" type="download_file">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action> | |
| 17 | 47 <action type="shell_command">tar -xzf rpy2_2.7.5_src_all.tar.gz</action> |
| 48 <action type="change_directory">rpy2-2.7.5</action> | |
| 13 | 49 <action type="set_environment_for_install"> |
| 15 | 50 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
| 16 | 51 <package name="readline" version="6.3" /> |
| 13 | 52 </repository> |
| 21 | 53 <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
| 13 | 54 <package name="R" version="3.2.1" /> |
| 55 </repository> | |
| 56 </action> | |
| 57 <action type="shell_command"> | |
| 58 export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" && | |
| 59 export CPPFLAGS="-I$READLINE_INCLUDE_PATH" && | |
| 19 | 60 $INSTALL_DIR/MiModD_venv/bin/python3 setup.py install |
| 13 | 61 </action> |
| 62 | |
| 63 <!-- download and install MiModD --> | |
| 20 | 64 <action type="change_directory">$TMP_WORK_DIR</action> |
| 17 | 65 <action type="download_file">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action> |
| 66 <action type="shell_command">tar -xzf MiModD-0.1.7.2.tar.gz</action> | |
| 67 <action type="change_directory">MiModD-0.1.7.2</action> | |
| 0 | 68 <action type="set_environment_for_install"> |
| 16 | 69 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
| 0 | 70 <package name="zlib" version="1.2.8" /> |
| 71 </repository> | |
| 72 </action> | |
| 20 | 73 <!-- install MiModD placing the entry script mimodd into the venv's bin directory --> |
| 19 | 74 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action> |
| 20 | 75 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself --> |
| 19 | 76 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action> |
| 20 | 77 |
| 78 <!-- configure environment --> | |
| 0 | 79 <action type="set_environment"> |
| 22 | 80 <!-- since the iuc R package does not export the path to R's libR.so, |
| 81 any venv using rpy2, needs to record this path --> | |
| 82 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[R_HOME]/lib</environment_variable> | |
| 21 | 83 <!-- to make MiModD accessible it is sufficient to simply add the |
| 84 venvs site-packages directory to PYTHONPATH; | |
| 85 SITE_PACKAGES_RELPATH will be made available by the python3 | |
| 86 package, which all MiModD toolwrappers require --> | |
| 87 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/MiModD_venv/$SITE_PACKAGES_RELPATH</environment_variable> | |
| 0 | 88 </action> |
| 89 </actions> | |
| 90 </install> | |
| 20 | 91 |
| 0 | 92 <readme> |
| 93 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs | |
| 94 Home-page: http://sourceforge.net/projects/mimodd/ | |
| 95 Author: Wolfgang Maier | |
| 96 Author-email: wolfgang.maier@biologie.uni-freiburg.de | |
| 97 License: GPL | |
| 98 Download-URL: http://sourceforge.net/projects/mimodd/ | |
| 99 | |
| 100 MiModD - Identify Mutations from Whole-Genome Sequencing Data | |
| 101 ************************************************************* | |
| 102 | |
| 103 MiModD is an integrated solution for efficient and user-friendly analysis of | |
| 104 whole-genome sequencing (WGS) data from laboratory model organisms. | |
| 105 It enables geneticists to identify the genetic mutations present in an organism | |
| 106 starting from just raw WGS read data and a reference genome without the help of | |
| 107 a trained bioinformatician. | |
| 108 | |
| 109 MiModD is designed for good performance on standard hardware and enables WGS | |
| 110 data analysis for most model organisms on regular desktop PCs. | |
| 111 | |
| 20 | 112 Detailed documentation of the software can be found at: |
| 113 | |
| 114 http://mimodd.readthedocs.io | |
| 115 | |
| 0 | 116 </readme> |
| 117 </package> | |
| 118 </tool_dependency> |