Mercurial > repos > tduigou > sbol_converter
changeset 2:4ed045ebe449 draft
planemo upload for repository https://github.com/SynBioDex/SBOL-utilities commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
author | tduigou |
---|---|
date | Mon, 24 Apr 2023 13:35:33 +0000 |
parents | 529ee7dc1be9 |
children | 8d020045186c |
files | README.md |
diffstat | 1 files changed, 0 insertions(+), 36 deletions(-) [+] |
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--- a/README.md Tue Apr 18 07:51:41 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -# sbol-converter -- Convert between SBOL3 and other genetic design formats. - -The open-source software package sbol-converter is available here : https://github.com/SynBioDex/SBOL-utilities - -## How to run sbol-converter wrapper tests - -In order to execute tests on sbol-converter 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,bioconda --conda_debug tools/synbiocad-galaxy-wrappers/sbol-converter/wrap.xml - ``` - - You can also specify your data test directory with the following option: `--test_data DIRECTORY_DATA_TEST` - - 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