Merge pull request #149 from bioinfo-chru-strasbourg/options_and_docs

Fix requirements, fix parse_args, add docs #4

README.md

@@ -37,15 +37,25 @@ HOWARD is multithreaded through the number of variants and by database (data-sca
 
 ## Python
 
-Install using Python Pip tool:
-
+Install HOWARD using Python Pip tool, and run HOWARD for help options:
 ```
 python -m pip install -e .
+howard --help
+```
+
+Install HOWARD Graphical User Interface using Python Pip tool with supplementary packages, and run as a tool:
 ```
+python -m pip install -r requirements-gui.txt
+howard gui
+```
+
+![HOWARD Graphical User Interface](images/howard-gui.png "HOWARD Graphical User Interface")
+
+
 
 ## Docker
 
-In order to build, setup and create a persitent CLI (running container), docker-compose command build images and launch services as containers.
+In order to build, setup and create a persitent CLI (running container with all useful external tools such as [BCFTools](https://samtools.github.io/bcftools/), [snpEff](https://pcingola.github.io/SnpEff/), [Annovar](https://annovar.openbioinformatics.org/), [Exomiser](https://www.sanger.ac.uk/tool/exomiser/)), docker-compose command build images and launch services as containers.
 
 ```
 docker-compose up -d
@@ -57,7 +67,13 @@ A setup container (HOWARD-setup) will download useful databases (take a while).
 docker-compose up -d HOWARD-CLI
 ```
 
-A Command Line Interface container (HOWARD-CLI) is started with host data and databases folders mounted (by default in ${HOME}/HOWARD folder)
+A Command Line Interface container (HOWARD-CLI) is started with host data and databases folders mounted (by default in ${HOME}/HOWARD folder). Let's play within Docker HOWARD-CLI service!
+
+```
+docker exec -ti HOWARD-CLI bash
+howard --help
+```
+
 
 ## Databases
 

docs/user_guide.md

@@ -38,11 +38,33 @@ HOWARD is multithreaded through the number of variants and by database (data-sca
 
 ## Python
 
-Install using Python Pip tool:
+### Quick install
+
+Install HOWARD using Python Pip tool:
 ```
 python -m pip install -e .
 ```
 
+Run HOWARD for help options:
+```
+howard --help
+```
+
+### GUI install
+
+Install HOWARD Graphical User Interface using Python Pip tool with supplementary packages:
+```
+python -m pip install -r requirements-gui.txt
+```
+
+Run HOWARD Graphical User Interface as a tool:
+```
+howard gui
+```
+
+![HOWARD Graphical User Interface](../images/howard-gui.png "HOWARD Graphical User Interface")
+
+
 ## Docker
 
 ### Quick Start
@@ -53,6 +75,17 @@ In order to build images, launch default setup and create a persitent CLI (Comma
 docker-compose up -d
 ```
 
+The persitent CLI contains external tools, such as:
+| External tool | Description |
+| -- | -- |
+| [BCFTools](https://samtools.github.io/bcftools/) | Utilities for variant calling and manipulating VCFs and BCFs |
+| [snpEff](https://pcingola.github.io/SnpEff/) | Genomic variant annotations, and functional effect prediction toolbox |
+| [Annovar](https://annovar.openbioinformatics.org/) | Efficient software tool to utilize update-to-date information to functionally annotate genetic variants |
+| [Exomiser](https://www.sanger.ac.uk/tool/exomiser/) | Program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data |
+
+
+
+
 ### Setup container
 
 Docker service HOWARD-setup creates HOWARD image and download useful databases to start with HOWARD tools. 
@@ -105,6 +138,17 @@ See [HOWARD Help](docs/help.md) for more options.
 
 Let's play within Docker HOWARD-CLI service!
 
+### Tests
+
+In order to test HOWARD within Docker, use this command:
+```
+docker exec -ti HOWARD-CLI bash
+cd /tool
+# Basic test
+coverage run -m pytest .
+# Debug test
+coverage run -m pytest . -x -v --log-cli-level=DEBUG --capture=tee-sys
+```
 
 # Databases
 

howard/main.py

@@ -56,7 +56,7 @@ def main() -> None:
     parser = help_generation(arguments_dict=arguments_dict, parser=parser, setup=setup_cfg, output_type="parser")
 
     # Parse args
-    args, remaining = parser.parse_known_args()
+    args = parser.parse_args()
 
     # Quiet
     if "quiet" in args and args.quiet:

requirements-gui.txt

@@ -22,10 +22,11 @@ jproperties==2.1.1
 psutil==5.9.6
 markdown==3.5.2
 tabulate==0.9.0
-Pillow>=4.3.0
-colored>=1.3.93
-pygtrie>=2.3.3
-re-wx>=0.0.2
+Pillow==10.2.0
+colored==2.2.4
+pygtrie==2.5.0
+re-wx==0.1.0
 typing-extensions==3.10.0.2
 mypy-extensions==0.4.3
-wxpython>=4.1.0
+wxpython==4.2.1
+gooey==1.0.8.1