updates installation

README.md

@@ -37,24 +37,41 @@ Unfortunately, a couple of executables are not available neither as a `conda` or
 
 To create a new conda environment, install third party software, install XICRA and missing dependencies, do as follows:
 
+
+```sh
+1) Get requirements file from XICRA git repo
+
 ```sh
-## clone repo
-git clone https://github.com/HCGB-IGTP/XICRA.git
+wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/devel/conda/environment.yml
+```
 
-## move to folder
-cd XICRA
+2) Create environment and install required packages using conda: 
 
-## create conda environemt
-conda env create -n XICRA -f XICRA_pip/devel/conda/requirements.txt
+```sh
+conda env create -n XICRA -f environment.yml
+```
 
+3) Activate environment and install XICRA
+```sh
 ## activate
 conda activate XICRA
 
 ## install latest python code
 pip install XICRA
+```
 
+4) Install missing software:  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`.
+
+```sh
 ## install missing software
-sh XICRA_pip/XICRA/config/software/installer.sh
+wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/XICRA/config/software/installer.sh
+sh installer.sh
+```
+
+To check everything is fine, try executing the `config` module:
+
+```sh
+XICRA config
 ```
 
 To check everything is fine, try executing the `config` module:
@@ -94,7 +111,7 @@ See a brief example on how to install and run XICRA [here](https://github.com/HC
 
 MIT License
 
-Copyright (c) 2020 HCGB-IGTP
+Copyright (c) 2020-2022 HCGB-IGTP
 
 See additional details [here](XICRA_pip/LICENSE)
 

XICRA_pip/README.md

@@ -59,32 +59,15 @@ pip install XICRA
 
 ```sh
 ## install missing software
-sh XICRA_pip/XICRA/config/software/installer.sh
+wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/XICRA/config/software/installer.sh
+sh 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:
-
-```sh
-## create enviroment
-python3 -m venv XICRA_env
-
-## activate it
-source XICRA_env/bin/activate
-
-## install XICRA and dependencies
-pip install XICRA
-
-## execute XICRA
-XICRA -h
-```
-
 ## Documentation
 
 See a full documentation, user guide and manual in [here](https://readthedocs.org/)
@@ -121,7 +104,7 @@ See a brief example on how to install and run XICRA [here](https://github.com/HC
 
 MIT License
 
-Copyright (c) 2020 HCGB-IGTP
+Copyright (c) 2020-2022 HCGB-IGTP
 
 See additional details [here](XICRA_pip/LICENSE)
 

XICRA_pip/VERSION

@@ -1 +1 @@
-1.4.1
+1.4.2

XICRA_pip/XICRA/config/software/dependencies.csv

@@ -15,6 +15,6 @@ optimir,,,na,optimir
 miraligner,,,na,miraligner.jar
 STAR,--version,([0-9\.]+).*,2.6.1,STAR
 featureCounts,-v,v([0-9\.]+).*,1.5.1,featureCounts
-MINTmap,,,na,MINTmap.pl
+MINTmap,,,na,MINTmap
 bedtools,-h,v([0-9\.]+).*,2.29.2,bedtools
 samtools,--version,samtools ([0-9\.]+).*,1.12,samtools

XICRA_pip/XICRA/config/software/installer.sh

@@ -37,6 +37,14 @@ echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++ "
 wget https://github.com/lpantano/seqbuster/raw/miraligner/modules/miraligner/miraligner.jar
 echo ""
 
+echo ""
+echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++ "
+echo "## Downloading MINTmap"
+echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++ "
+wget -O MINTmap-v2.0-alpha.zip "https://cm.jefferson.edu/?smd_process_download=1&download_id=8044"
+unzip MINTmap-v2.0-alpha.zip
+pip install markupsafe==2.0.1
+pip install MINTmap-v2.0-alpha/dist/MINTmap-2.0a0-py3-none-any.whl
 
 echo ""
 ## mv files to conda enviornment folder