Mercurial > repos > tduigou > retropath2
changeset 7:0a25e8aaad7c draft
planemo upload commit 250fc47bd655aa7d952fb13f0b8e481443465b8f
| author | tduigou |
|---|---|
| date | Thu, 20 Apr 2023 12:38:17 +0000 |
| parents | 8d76e8616839 |
| children | c49002305b53 |
| files | README.md config/job_conf.xml retropath2_wrapper.xml |
| diffstat | 3 files changed, 2 insertions(+), 36 deletions(-) [+] |
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--- a/README.md Thu Apr 20 12:30:18 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -# RetroPath2-wrapper -- Build a reaction network from a set of source compounds to a set of sink compounds. - -The open-source software package RetroPath2-wrapper is available here : https://github.com/brsynth/RetroPath2-wrapper - -## How to run RetroPath2 wrapper tests - -In order to execute tests on RetroPath2 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/RetroPath2-wrapper/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/config/job_conf.xml Thu Apr 20 12:30:18 2023 +0000 +++ b/config/job_conf.xml Thu Apr 20 12:38:17 2023 +0000 @@ -1,1 +1,1 @@ - <tool id="retropath2_wrapper" destination="local" /> + <tool id="retropath2" destination="local" />
--- a/retropath2_wrapper.xml Thu Apr 20 12:30:18 2023 +0000 +++ b/retropath2_wrapper.xml Thu Apr 20 12:38:17 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="retropath2_wrapper" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT"> +<tool id="retropath2" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT"> <description>Build a reaction network from a set of source compounds to a set of sink compounds</description> <macros> <token name="@VERSION_SUFFIX@">0</token>