Mercurial > repos > wolma > mimodd
annotate tool_dependencies.xml @ 20:aba6d9b1c1f1 draft
Uploaded
| author | wolma |
|---|---|
| date | Fri, 29 Apr 2016 06:01:46 -0400 |
| parents | 8f108b41a149 |
| children | c46406466625 |
| 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> |
| 18 | 12 <package name="python3" version="3.4"> |
| 20 | 13 <repository changeset_revision="5e5653b689ca" 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"> |
| 20 | 21 <repository changeset_revision="5e5653b689ca" 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> |
| 53 <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | |
| 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"> |
| 20 | 80 <!-- make the mimodd entry script discoverable --> |
| 0 | 81 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable> |
| 82 </action> | |
| 83 </actions> | |
| 84 </install> | |
| 20 | 85 |
| 0 | 86 <readme> |
| 87 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs | |
| 88 Home-page: http://sourceforge.net/projects/mimodd/ | |
| 89 Author: Wolfgang Maier | |
| 90 Author-email: wolfgang.maier@biologie.uni-freiburg.de | |
| 91 License: GPL | |
| 92 Download-URL: http://sourceforge.net/projects/mimodd/ | |
| 93 | |
| 94 MiModD - Identify Mutations from Whole-Genome Sequencing Data | |
| 95 ************************************************************* | |
| 96 | |
| 97 MiModD is an integrated solution for efficient and user-friendly analysis of | |
| 98 whole-genome sequencing (WGS) data from laboratory model organisms. | |
| 99 It enables geneticists to identify the genetic mutations present in an organism | |
| 100 starting from just raw WGS read data and a reference genome without the help of | |
| 101 a trained bioinformatician. | |
| 102 | |
| 103 MiModD is designed for good performance on standard hardware and enables WGS | |
| 104 data analysis for most model organisms on regular desktop PCs. | |
| 105 | |
| 20 | 106 Detailed documentation of the software can be found at: |
| 107 | |
| 108 http://mimodd.readthedocs.io | |
| 109 | |
| 0 | 110 </readme> |
| 111 </package> | |
| 112 </tool_dependency> |