Mercurial > repos > tduigou > rp2paths
changeset 3:9c11cb2b1a71 draft
planemo upload for repository https://github.com/brsynth/rp2paths commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
| author | tduigou |
|---|---|
| date | Mon, 01 May 2023 01:21:17 +0000 |
| parents | 2452952f7bc2 |
| children | aed346f2e254 |
| files | LICENSE.txt README.md rp2paths.xml |
| diffstat | 3 files changed, 1 insertions(+), 58 deletions(-) [+] |
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--- a/LICENSE.txt Mon Apr 03 08:15:46 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -MIT License - -Copyright (c) 2020 Jean-Loup Faulon's group & INRA -Copyright (c) 2020 University of Evry / Paris-Saclay - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE.
--- a/README.md Mon Apr 03 08:15:46 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -# rp2paths -- Enumerate and seperate the different pathways generated by RetroPath2.0 - -The open-source software package rp2paths is available here : https://github.com/brsynth/rp2paths - -## How to run rp2paths wrapper tests - -In order to execute tests on rp2paths wrapper, you need to: - - - Connect to your galaxy instance in interactive mode: - - ```bash - docker exec -it -u root galaxy_galaxy_1 bash - ``` - - Copy all the contents of `test-data` folder into your own test-data directory which is located in your local galaxy instance : `/galaxy/test-data`. It contains all the input files and expected output files needed for the tests. - - - Install Planemo: - You can see here the documentation for Planemo Installation : https://planemo.readthedocs.io/en/latest/installation.html - Note that they recommand to install Planemo by setting up a virtual environment: - - ```bash - python3 -m venv planemo - . planemo/bin/activate - pip install -U planemo - ``` - - - run the tests: - - ```bash - planemo test --conda_channels conda-forge,brsynth --conda_debug tools/BRSynthTools/rp2paths/wrap.xml - ``` - - IMPORTANT: Maybe you will need to remove CONDA from your PATH for the command `planemo test` to run correctly. To do that, you can edit this file `~/.bashrc`, comment this line `PATH="/root/anaconda3/bin:$PATH"` and save changes. - - Planemo will output an html test summary `tool_test_output.html`. \ No newline at end of file
--- a/rp2paths.xml Mon Apr 03 08:15:46 2023 +0000 +++ b/rp2paths.xml Mon May 01 01:21:17 2023 +0000 @@ -1,8 +1,7 @@ -<tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" licence="@LICENSE@"> +<tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT"> <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description> <macros> <token name="@TOOL_VERSION@">1.5.0</token> - <token name="@LICENSE@">MIT</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>