Update README.md

HCGB-IGTP · Mar 24, 2021 · ecf1e39 · ecf1e39
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Showing 1 changed file with 16 additions and 2 deletions.
diff --git 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: