# genenetwork3 [](https://penguin2.genenetwork.org/jobs/genenetwork3) [](https://penguin2.genenetwork.org/jobs/genenetwork3-pylint) [](https://penguin2.genenetwork.org/jobs/genenetwork3-mypy) GeneNetwork3 REST API for data science and machine learning ## Installation #### GNU Guix packages Install GNU Guix - this can be done on every running Linux system. There are at least three ways to start GeneNetwork3 with GNU Guix: 1. Create an environment with `guix shell` 2. Create a container with `guix shell -C` 3. Use a profile and shell settings with `source ~/opt/genenetwork3/etc/profile` #### Create an environment: Simply load up the environment (for development purposes): ```bash guix shell -Df guix.scm ``` Also, make sure you have the [guix-bioinformatics](https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics) channel set up. ```bash guix shell --expose=$HOME/genotype_files/ -Df guix.scm python3 import redis ``` #### Run a Guix container ``` guix shell -C --network --expose=$HOME/genotype_files/ -Df guix.scm ``` #### Using a Guix profile (or rolling back) Create a new profile with ``` guix package -i genenetwork3 -p ~/opt/genenetwork3 ``` and load the profile settings with ``` source ~/opt/genenetwork3/etc/profile start server... ``` Note that GN2 profiles include the GN3 profile (!). To roll genenetwork3 back you can use either in the same fashion (probably best to start a new shell first) ``` bash source ~/opt/genenetwork2-older-version/etc/profile set|grep store run tests, server etc... ``` #### Troubleshooting Guix packages If you get a Guix error, such as `ice-9/boot-9.scm:1669:16: In procedure raise-exception: error: python-sqlalchemy-stubs: unbound variable` it typically means an update to guix latest is required (i.e., guix pull): ``` guix pull source ~/.config/guix/current/etc/profile ``` and try again. Also make sure your ~/guix-bioinformatics is up to date. See also instructions in [.guix.scm](.guix.scm). ## Running Tests (assuming you are in a guix container; otherwise use venv!) To run tests: ```bash python -m unittest discover -v ``` Running pylint: ```bash pylint *py tests gn3 ``` Running mypy(type-checker): ```bash mypy . ``` ## Running the GN3 web service To spin up the server on its own (for development): ```bash env FLASK_DEBUG=1 FLASK_APP="main.py" flask run --port=8080 ``` And test with ``` curl localhost:8080/api/version "1.0" ``` To run with gunicorn ``` gunicorn --bind 0.0.0.0:8080 wsgi:app ``` consider the following options for development `--bind 0.0.0.0:$SERVER_PORT --workers=1 --timeout 180 --reload wsgi`. And for the scalable production version run ``` gunicorn --bind 0.0.0.0:8080 --workers 8 --keep-alive 6000 --max-requests 10 --max-requests-jitter 5 --timeout 1200 wsgi:app ``` (see also the [.guix_deploy](./.guix_deploy) script) ## Using python-pip IMPORTANT NOTE: we do not recommend using pip tools, use Guix instead 1. Prepare your system. You need to make you have python > 3.8, and the ability to install modules. 2. Create and enter your virtualenv: ```bash virtualenv --python python3 venv . venv/bin/activate ``` 3. Install the required packages ```bash # The --ignore-installed flag forces packages to # get installed in the venv even if they existed # in the global env pip install -r requirements.txt --ignore-installed ``` #### A note on dependencies Make sure that the dependencies in the `requirements.txt` file match those in guix. To freeze dependencies: ```bash # Consistent way to ensure you don't capture globally # installed packages pip freeze --path venv/lib/python3.8/site-packages > requirements.txt ``` ## Genotype Files You can get the genotype files from http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL and save them on your host machine at, say `$HOME/genotype_files` with something like: ```bash $ mkdir -p $HOME/genotype_files $ cd $HOME/genotype_files $ yes | 7z x genotype_files.tar.7z $ tar xf genotype_files.tar ``` The `genotype_files.tar.7z` file seems to only contain the **BXD.geno** genotype file. ## QTLReaper (rust-qtlreaper) and Trait Files To run QTL computations, this system makes use of the [rust-qtlreaper](https://github.com/chfi/rust-qtlreaper.git) utility. To do this, the system needs to export the trait data into a tab-separated file, that can then be passed to the utility using the `--traits` option. For more information about the available options, please [see the rust-qtlreaper](https://github.com/chfi/rust-qtlreaper.git) repository. ### Traits File Format The traits file begins with a header row/line with the column headers. The first column in the file has the header **"Trait"**. Every other column has a header for one of the strains in consideration. Under the **"Trait"** column, the traits are numbered from **T1** to **T<n>** where **<n>** is the count of the total number of traits in consideration. As an example, you could end up with a trait file like the following: ```txt Trait BXD27 BXD32 DBA/2J BXD21 ... T1 10.5735 9.27408 9.48255 9.18253 ... T2 6.4471 6.7191 5.98015 6.68051 ... ... ``` It is very important that the column header names for the strains correspond to the genotype file used. ## Partial Correlations The partial correlations feature depends on the following external systems to run correctly: - Redis: Acts as a communications broker between the webserver and external processes - `sheepdog/worker.py`: Actually runs the external processes that do the computations These two systems should be running in the background for the partial correlations feature to work correctly.