Outdated install instructions

[Danoontjes]

Hi,

The install instructions in INSTALL.md are outdated. More specifically, any modern Linux distribution has python >= 3.9

It might be possible to create a conda environment with python 3.6.7 as is required now. Personally, I could not get it to work.

Regards

[Danoontjes]

Nevermind, I just saw this: Python Notes Mian must be run with Python < 3.7 due to limitations in how the function timeout works. The multiprocessing library in these newer versions appears to trigger infinite reloading of the main file.

[Danoontjes]

Here are my results of installing mian in a 'modern' environment.

Install on modern OS with python > 3.6.x

Method 1: Docker

• You can use the procedure and Dockerfile below to create a docker image that runs mian.

  mkdir main_docker
  cd mian_docker
  git clone https://github.com/tbj128/mian.git

• Create a file called requirements.txt filled with:

  biom-format
  flask==1.1.1
  flask-login==0.4.0
  Flask-Mail==0.9.1
  h5py
  rpy2==3.1.0
  scikit-learn
  scipy
  werkzeug==1.0.1
  scikit-bio
  pandas==1.0.3
  Keras==2.3.1
  Boruta
  tensorflow==2.5.0
  traitlets==4.3.3
  numpy
  cython

• Dockerfile

  
  FROM python:3.6.7

set working directory in container

WORKDIR /usr/src/app

Copy and install packages

COPY requirements.txt / RUN pip install --upgrade pip RUN pip install -r /requirements.txt

Install needed system tools

RUN apt-get update \ && apt-get install -y --no-install-recommends \ software-properties-common apt-transport-https gfortran libblas-dev liblapack-dev \ && rm -rf /var/lib/apt/lists/*

Install R

RUN gpg --batch --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E19F5F87128899B192B1A2C2AD5F960A256A04AF && gpg -a --export E19F5F87128899B192B1A2C2AD5F960A256A04AF | apt-key add - RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/debian stretch-cran35/' RUN apt-get update \ && apt-get install -y --no-install-recommends --allow-unauthenticated \ r-base \ && rm -rf /var/lib/apt/lists/*

Install R packages

RUN R -e "install.packages(c('vegan', 'RColorBrewer', 'ranger', 'Boruta', 'BiocManager', 'remotes'), repos='https://cloud.r-project.org/')" RUN R -e "library('remotes'); install_version('locfit', '1.5.9.4'); install_version('Hmisc', '4.4')" RUN R -e "BiocManager::install('DESeq2')"

Copy app folder to app folder in container

COPY /mian /usr/src/app/

Run app

CMD python run.py

- Build the image and run. The first step will take a while.

docker build -t mian . docker run -d --name mian -p 5000:5000 mian

- This is good for testing, but there is no persistence. You will have to make sure the database and data dirs (/usr/src/app/mian/mian.db and /usr/src/app/mian/data) are not inside the container.
___  

## Method 2: Conda
Follow the procedure below to install inside a conda environment. This procedure also installs and uses apache mod_wsgi that is controlled by systemd.  
This example was developed on ALmaLinux 9.1

- Donwload conda with python==3.6.5 https://repo.anaconda.com/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh
- Install conda into **/opt/miniconda3**:

bash Miniconda3-4.5.4-Linux-x86_64.sh

- Activate conda with:

echo ". /opt/miniconda3/etc/profile.d/conda.sh" >> ~/.bashrc . /opt/miniconda3/etc/profile.d/conda.sh conda create -n mian gxx_linux-64 conda activate mian

- upgrade pip:

conda install pip=9 pip install --upgrade pip

- create a requirements.txt file and paste the following:

biom-format flask==1.1.1 flask-login==0.4.0 Flask-Mail==0.9.1 flask-ldap3-login h5py rpy2==3.1.0 scikit-learn scipy werkzeug==1.0.1 scikit-bio pandas==1.0.3 Keras==2.3.1 Boruta tensorflow==2.5.0 traitlets==4.3.3 numpy cython configparser

- Install requirements:

pip install -r requirements.txt

- Optionally set compile threads to speed up R package compilation a bit.

export MAKE="make -j$(nproc)"

- Install R packages:

conda install r-base r-RColorBrewer r-ranger r-Boruta r-Hmisc r-XML r-remotes r-BiocManager r-permute R -e "library('remotes'); install_version('locfit', '1.5-9.4', repos='https://cloud.r-project.org/')" R -e "install.packages('vegan', repos='https://cloud.r-project.org/')" R -e "BiocManager::install('DESeq2')"

- Setup apache

dnf install httpd httpd-devel pip install mod_wsgi

- Clone the mian repo and set permissions  
I'm using user webdev here, but it can be any other user

cd /opt git clone https://github.com/tbj128/mian.git chown -R webdev:apache /opt/mian chown -R webdev:apache /opt/miniconda3

- Create the file **/opt/mian/mian.wsgi** for mod_wsgi:

import sys

sys.path.insert(0, '/opt/mian')

print("App Startup")

from mian.main import app as application

application.secret_key = 'Twilight Sparkle' application.config['SESSION_TYPE'] = 'filesystem'

- Create the config files for the webserver (replace variables with your actual values).

mkdir /etc/mian mod_wsgi-express setup-server /opt/mian/mian.wsgi --user webdev --group apache --https-port 443 --https-only --server-name 10.5.87.61 --ssl-certificate-key-file /etc/pki/tls/private/vlan87.key --ssl-certificate-file /etc/pki/tls/certs/vlan87.pem --server-root=/etc/mian/mod_wsgi-express-443

- Add the following two lines directly after the shebang (#!/usr/bin/bash) in **/etc/mian/mod_wsgi-express-443/apachectl**

source /opt/miniconda3/etc/profile.d/conda.sh conda activate mian

- Change the following in /etc/mian/mod_wsgi-express-443/httpd.conf  
  The first enables slightly more verbose logging, the second enables uploads of files larger than 10MB

LogLevel info LimitRequestBody 2073741824

- You can now start, stop or restart the server with:

/etc/mian/mod_wsgi-express-443/apachectl start

- If you want to use systemd so you can have it automatically start at system startup, create a systemd file. Create **/etc/systemd/system/mian.service** that contains the following.

[Unit] Description=The Mian app After=network.target remote-fs.target nss-lookup.target

[Service] Type=forking ExecStart=/etc/mian/mod_wsgi-express-443/apachectl -k start ExecReload=/etc/mian/mod_wsgi-express-443/apachectl -k graceful ExecStop=/etc/mian/mod_wsgi-express-443/apachectl -k graceful-stop PrivateTmp=true

[Install] WantedBy=multi-user.target

- First reload systemd, then you can start and stop the app with:

systemctl daemon-reload systemctl start mian.service

- To make the app start at boot:

systemctl enable mian.service

[tbj128]

Hey this is amazing - thank you for doing this! Did you want to make a pull request into the README?

[tbj128]

Sorry, I noticed you actually submitted a PR - thank you! Small comment left on https://github.com/tbj128/mian/pull/10 otherwise happy to merge in.