Update README.md with Docker/Singularity/Conda/Mamba/Manual installat…

…ion steps

README.md

@@ -13,52 +13,124 @@ Our approach is amenable to include sequences generated by *de novo* Illumina as
 
 Extended documentation is hosted on ReadTheDocs: http://mikado.readthedocs.org/
 
+## Contents
+- [Installation](#installation)
+  - [Docker Installation](#docker-installation)
+  - [Singularity Installation](#singularity-installation)
+  - [Conda Installation](#condamambamanual-installation)
+
 ## Installation
 
-Using mamba
+### Docker Installation
+Mikado can be installed with docker. If you don't have docker, please install [docker](https://docs.docker.com/get-docker/) first. Then you can pull the docker image with mikado installed
+```console
+VERSION=2.3.5rc2
+docker run gemygk/mikado:v${VERSION} mikado -h
+```
+
+### Singularity Installation
+Mikado can be installed with singularity. If you don't have singularity, please install [singularity](https://docs.sylabs.io/guides/3.9/user-guide/quick_start.html#quick-installation-steps) first. Then you can pull the singularity image with mikado installed.
+```console
+VERSION=2.3.5rc2
+singularity exec docker://gemygk/mikado:v${VERSION} mikado -h
+```
+
+### Conda/Mamba/Manual Installation
+Mikado can be installed with conda. If you don't have conda, please install [mamba](https://github.com/conda-forge/miniforge?tab=readme-ov-file#miniforge-pypy3) first. Then you can create a new environment with mikado installed.
+
+Install mamba with PyPy 3.9 in the base environment (https://github.com/conda-forge/miniforge?tab=readme-ov-file#miniforge-pypy3)
 
-download mamba using pip
+Replace `/path/to` with your installation directory when following the steps below:
 
-```bash
-pip install mamba=0.27.0
+```console
+/path/to/src
+[src]$ wget -c https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge-pypy3-Linux-x86_64.sh
+[src]$ bash Miniforge-pypy3-Linux-x86_64.sh
 ```
 
-Create a mamba environment using the environment.yml file
+I have installed the base to `/path/to/x86_64/` location
 
-```bash
-mamba env create -f environment.yml
-conda activate mikado2
+If you have chosen to not have conda modify your shell scripts at all, to activate conda's base environment in your current shell session, please do:
+
+```console
+/path/to/src
+[src]$ eval "$(/path/to/x86_64/bin/conda shell.bash hook)"
 ```
 
-Check and run mikado
+Install Git
 
-```bash
-mikado --help
+```console
+/path/to/src
+(base) [src]$ mamba install -y git
 ```
 
+Clone mikado
+```console
+/path/to/src
+(base) [src]$ git clone [email protected]:EI-CoreBioinformatics/mikado.git
+(base) [src]$ cd mikado
+```
 
+Install Mikado dependencies
+```console
+/path/to/src/mikado
+(base) [mikado]$ mamba env create -f environment.yml --prefix /path/to/x86_64/envs/mikado_env
+```
 
-Mikado can also be be installed from PyPI with pip (**deprecated**):
+Activate mikado_env
+```console
+/path/to/src/mikado
+(base) [mikado]$ conda activate mikado_env
+(mikado_env) [mikado]$
+```
 
-``pip3 install mikado``
+Do checks if all dependencies are installed. A full list of library dependencies can be found in the file ``requirements.txt``
+```console
+/path/to/src/mikado
+(mikado_env) [mikado]$ pip3 install wheel
+(mikado_env) [mikado]$ pip3 install -r requirements.txt
+(mikado_env) [mikado]$ pip3 install Cython
+```
+- For the above commands - wheel, requirements.txt, Cython should all have the status 'Requirement already satisfied'
 
-Alternatively, you can clone the repository from source and install with:
 
-    pip wheel -w dist .
-    pip install dist/*whl
+We need gcc for bdist_wheel (tested on gcc v5.2.0, v9.4.0)
+
+```console
+/path/to/src/mikado
+(mikado_env) [mikado]$ python3 setup.py bdist_wheel
+(mikado_env) [mikado]$ pip3 install dist/*.whl
+```
+Now that installation is complete, run Mikado help
+```console
+/path/to/src/mikado
+(mikado_env) [mikado]$ mikado -h
+usage: Mikado [-h] [--version] {configure,prepare,serialise,pick,compare,util} ...
+
+Mikado is a program to analyse RNA-Seq data and determine the best transcript for each locus in accordance to user-specified criteria.
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --version             Print Mikado current version and exit.
+
+Components:
+  {configure,prepare,serialise,pick,compare,util}
+                        These are the various components of Mikado:
+    configure           This utility guides the user through the process of creating a configuration file for Mikado.
+    prepare             Mikado prepare analyses an input GTF file and prepares it for the picking analysis by sorting its transcripts and performing some simple consistency checks.
+    serialise           Mikado serialise creates the database used by the pick program. It handles Junction and ORF BED12 files as well as BLAST XML results.
+    pick                Mikado pick analyses a sorted GTF/GFF files in order to identify its loci and choose the best transcripts according to user-specified criteria. It is dependent on files produced by the "prepare" and "serialise"
+                        components.
+    compare             Mikado compare produces a detailed comparison of reference and prediction files. It has been directly inspired by Cufflinks's cuffcompare and ParsEval.
+    util                Miscellaneous utilities
+```
 
-You can verify the correctness of the installation with the unit tests (*outside of the source folder*, as otherwise Python will get confused and try to use the `Mikado` source folder instead of the system installation):
 
-    python -c "import Mikado; Mikado.test(); Mikado.test(label='slow')"
 
-An alternative way of installing using `setuptools`:
+You can verify the correctness of the installation with the unit tests (*outside of the source folder*, as otherwise Python will get confused and try to use the `Mikado` source folder instead of the system installation):
 
-    pip install -r requirements.txt
-    pip install Cython
-    python setup.py bdist_wheel
-    pip install dist/*whl
+    python -c "import Mikado; Mikado.test(); Mikado.test(label='slow')"
 
-The steps above will ensure that any additional python dependencies will be installed correctly. A full list of library dependencies can be found in the file ``requirements.txt``
 
 ### Additional dependencies