From 835d28be88298e8eb66cab0f551645388170115d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joan=20H=C3=A9risson?= Date: Mon, 3 Jan 2022 16:58:33 +0100 Subject: [PATCH] doc(README): update --- README.md | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index f52800a..a22859b 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ Implementation of the KNIME retropath2.0 workflow. Takes for input the minimal ( ## Prerequisites * Python 3 -* KNIME (code was tested on 4.3.0 version) +* KNIME (code was tested on 4.5.0 version) ## Install @@ -19,18 +19,11 @@ On Linux system, the tool tries to install the KNIME Anlytical Platform as well On MacOS, the user needs to first install by himself KNIME, and be sure that the RetroPath2.0 node dependancies are installed. To install node dependancies, we recommand to follow the RetroPath2.0 instructions from https://www.myexperiment.org/workflows/4987.html. -### conda environment - -In case a new conda environment `` need to be set up, first start with: -```shell -conda create -n my_env python=3 -``` - ### conda package Install in the `` conda environment: ```shell -conda install -c brsynth -c conda-forge -n retropath2_wrapper +conda install -c conda-forge -n retropath2_wrapper ``` ## Run @@ -113,12 +106,12 @@ Test can be run with the following commands: ### Natively ```sh -cd tests -pytest -v +conda install -c conda-forge pytest +python -m pytest tests ``` # CI/CD -For further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](ci/README.md)). +For further tests and development tools, a CI toolkit is provided in `cicd-toolkit` folder (see [cicd-toolkit/README.md](cicd-toolit/README.md)). ### How to cite RetroPath2.0?