V 2.0.0

Changes to be committed:
	modified:   Dockerfile
	modified:   README.md
	modified:   docker-compose.yml
	new file:   docs/deployment/dockerDeployment.md
	new file:   docs/deployment/localDeployment.md

Dockerfile

@@ -25,6 +25,7 @@ RUN wget https://github.com/lh3/seqtk/archive/refs/tags/v1.3.tar.gz && \
 
 WORKDIR /app
 
-COPY . .
+COPY lib/censuscope.py ./lib/censuscope.py
+COPY test_data ./test_data
 
-CMD ["python", "lib/censuscope.py"]
+CMD ["python", "lib/censuscope.py"]

README.md

@@ -1,98 +1,17 @@
 # CensuScope
-We have chosen to apply the Creative Commons Attribution 3.0 Unsupported License to this version of the software.
-
-Mazumder Lab.
 
 What is CensuScope?
 ------------------------
-* CensuScope is designed and optimized for the quick detection of the components in a given NGS metagenomic dataset and provides users
-  with a standard format report of components into species or higher taxonomic node resolution.
-
-  The core of CensuScope consists of census-based reads file generation and Blast/bowtie based short-reads alignment. 
-  CensuScope is capable of sample contamination evaluation, microbiome components detection and other meta-omic related data analysis.
-
-Installation instructions: 
------------------------------------------------------------------------
-CensuScope  link: https://hive.biochemistry.gwu.edu/dna.cgi?cmd=censuscope
-
-Users must download the CensuScope package before running.
-
-
-* You need concatenated BLAST-NT database (or the MetaPhlAn Markers database) as a reference, we have already prepared 
-   this database. When the download has finished (it is a zip folder with 11.0 GB size containing all required files)
-   extract the compressed Package (censuscope.zip) into your system.(for ex. directory is c:\)
-   The compressed folder includes BLAST-NT database (17GB) and Blastn software and a bacterial
-   read datasets from prokaryotes (bacteria.fastq) for testing.
-
-CensuScope v1.2 (Windows version) README
-====================================
-
-How to use CensuScope?
----------------------------
-<<It is recommended that you use a computer with RAM capacity more than 1GB>>
-<<This version is optimized for lower than 10 Cores CPU>>
-
-  1. go to CensuScope-win directory and Run censuscope.exe
-
-  2. Set the path of your source file(for example c:\censuscope\source\bacteria.fastq)
-
-  3. Set the path of CensuScope Package where you extracted it,please do not include CensuScope main folder into path  (for example c:\ or d:\desktop\)
-
-  4.choose your desired database , you can select the Blast-NT or MetaPhlAn database 
-
-  5. Set the number of iterations and set the size of samples 
-
-  6. Press submit and wait (please do not minimize the application)
-
-  7. The output will be downloadable as a Zip file and you can check the generated output at this direction \CensuScope\sample\
+CensuScope is designed for the quick detection of the components in a given NGS metagenomic dataset. It can provide users with a standard format report of components into species or higher taxonomic node resolution.
 
-THE OUTPUT
------------------------------
-
-* Final results are in 4 different files (3 csv and 1 txt)
-
-  1. log.txt --  this text file provides all parameters which have been used to run and generate the result
-
-  2. gi_centric_table.csv -- GI_numbers sorted result
-
-  3. tax_centric_table.csv  -- TAX_ID Sorted result
-
-  4. taxslim_centric_table.csv  --  Kingdom-depth taxonomy sorted result
-
-CensuScope v1.2 (UNIX version) README
-=====================================
-
-How to use CensuScope:
----------------------------
-* Users need a PHP or ZEND server on their system for running this version.   
-<< It is recommended that you use a computer with RAM capacity more than 1GB>>
-<<this version is optimized for lower than 10 Cores CPU>>
-
-  PARAMETERS :
-  -i : set the number of iterations
-
-  -s : set the size of samples (per READ) 
+The core of CensuScope consists of census-based reads file generation and Blast/bowtie based short-reads alignment. 
+CensuScope is capable of sample contamination evaluation, microbiome components detection and other meta-omic related data analysis.
 
-  -t : set the depth of tax_slim (it is set to 3=kingdom)
-
-  -d : path to the source 
-
-  -p : path of censuscope Package
-
-
-  FOR EXAMPLE :
-  $ php censuscope.php -i 10 -s 1000 -t 3 -d '/user/desktop/fungi.fastq' -p '/user/'
-
-THE OUTPUT
------------------------------
+Deployment instructions: 
+- [Local deployment](docs/deployment/localDeployment.md) 
+- [Docker deployment](docs/deployment/dockerDeployment.md)
 
-* Final result are in 4 different files (3 csv and 1 txt)
-
-  1. log.txt --  this text file provide all parameters which have been used to run and generate the result
-
-  2. gi_centric_table.csv -- GI_numbers sorted result
-
-  3. tax_centric_table.csv  -- TAX_ID Sorted result
-
-  4. taxslim_centric_table.csv  --  Kingdom-depth taxonomy (or whatever taxonomic depth is chosen by user) sorted result
-
+## CensuScope Development and troubleshooting
+- [FAQ and trouble shooting](docs/faq.md)
+- [`.secretes` configuration](docs/config.md)
+- [Testing](docs/testing.md)

docker-compose.yml

@@ -10,11 +10,10 @@ services:
       -i 10 
       -s 5 
       -t 5 
-      -q /app/input_files/GW-04_S4_L001_R1_001.fastq
-      -d /app/input_files/blast_db/gfkb/HumanGutDB-v2.6.fasta 
+      -q /app/test_data/GW-04_S4_L001_R1_001.fastq
+      -d /app/test_data/blast_db/gfkb/HumanGutDB-v2.6.fasta 
       
     volumes:
-      - /tmp/test:/app/input_files
       - /tmp/test/outputs:/app/temp_dirs
     stdin_open: true
     tty: true

docs/deployment/dockerDeployment.md

@@ -0,0 +1,58 @@
+# CensuScope Docker Deployment
+
+
+### Requirements
+- Python 3: [3.10.6 reccomended](https://www.python.org/downloads/release/python-3106/)
+- Docker:
+    - [Docker Desktop for Linux](https://docs.docker.com/desktop/install/linux-install/)
+    - [Docker Desktop for Mac (macOS)](https://docs.docker.com/desktop/install/mac-install/)
+    - [Docker Desktop for Windows](https://docs.docker.com/desktop/install/windows-install/)
+
+## Clone the repository
+```
+git clone https://github.com/GW-HIVE/CensuScope/
+```
+
+## Enter the repository
+```
+cd CensuScope
+```
+
+**Make sure you are on the desired branch (Check for latest branch):**
+
+```
+git switch [DESIRED BRANCH TAG]
+```
+
+### Building CensuScope via Docker
+
+A docker file is provided to allow easy building of the BCO API.  This can be done from the root directory (the directory with Dockerfile in it) by running:
+
+`docker build -t  censuscope .`
+
+This will build a container named `censuscope`.
+
+The build process (via the `entrypoint.sh` script) will check for an existing database in the repository and run migrations. If no database is present one will be created and the test data will be loaded (taken from `config/fixtures/local_data.json`).
+
+### Running the container via Docker
+
+The BCO Api container can be run via docker on the command line in Linux/Windows by running:
+
+`docker run --rm --network host -it bco_api:latest`
+
+The BCO Api container can be run via docker on the command line in MacOS by running:
+
+`docker run --rm -p 8000:8000 -it bco_api:latest`
+
+This will expose the server at `http://127.0.0.1:8000`, whitch is where all of the default settings will expect to find the BCODB. 
+
+#### Overriding the port
+
+It is possible to override the port 8000 to whatever port is desired.  This is done by running the container with 8080 representing the desired port.
+
+`docker run --rm --network host -it bco_api:latest 0.0.0.0:8080`
+
+
+NOTE: The ip address of 0.0.0.0 is to allow the web serer to properly associate with 127.0.0.1 - if given 127.0.0.1 it will not allow communications outside of the container!
+
+You can also give it a specific network created with `docker network create` if you wanted to give assigned IP addresses.