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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-# 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`.
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