From ecf1e390c6d2e361a06c573fbf238a55d71acd65 Mon Sep 17 00:00:00 2001 From: Jose Francisco Sanchez-Herrero Date: Wed, 24 Mar 2021 14:41:19 +0100 Subject: [PATCH] Update README.md --- XICRA_pip/README.md | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/XICRA_pip/README.md b/XICRA_pip/README.md index a4fe96f..e334283 100644 --- a/XICRA_pip/README.md +++ b/XICRA_pip/README.md @@ -28,9 +28,13 @@ Python XICRA module will install itself along some python modules dependencies ( But additionally, XICRA depends on third party software that we listed in the following [table](https://github.com/HCGB-IGTP/XICRA/blob/master/XICRA_pip/XICRA/config/software/soft_dependencies.csv). -### Conda installation +### Conda environment -We encourage you to install XICRA and all dependencies using the `conda` environment we created. To do so: +We encourage you to install XICRA and all dependencies using the `conda` environment we created and following these instructions. + +Unfortunately, a couple of executables are not available neither as a `conda` or `pip` packages. These packages are `miraligner` and `sRNAbench`. We have generated a `shell` script to retrieve and include within your `conda environment`. + +To create a new conda environment, install third party software, install XICRA and missing dependencies, do as follows: ```sh ## clone repo @@ -44,7 +48,17 @@ conda activate XICRA ## install latest python code pip install XICRA + +## install missing software +sh XICRA_pip/XICRA/config/software/installer.sh +``` + +To check everything is fine, try executing the `config` module: +```sh +XICRA config ``` + + ### Python environment If you are not using a `conda` environment as you might have previously installed all dependencies, we encourage you to create a python environment containing all python modules required for XICRA. See as an example this code: