Mercurial > repos > tduigou > sbol_converter
changeset 1:529ee7dc1be9 draft
planemo upload commit a452ea11b96167cb1a683a1e9eea01a62840e547
author | tduigou |
---|---|
date | Tue, 18 Apr 2023 07:51:41 +0000 |
parents | 38a0feb2e79d |
children | 4ed045ebe449 |
files | README.md |
diffstat | 1 files changed, 36 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Apr 18 07:51:41 2023 +0000 @@ -0,0 +1,36 @@ +# 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