Installation Instructions

These instructions assume that you are running within a Unix operating system.

1. Download this Repository (follow A OR B)

• A: Git: git clone https://github.com/saitomics/metatryp.git
• B: download https://github.com/saitomics/metatryp/archive/master.zip
  • Unzip the repository: gzip master.zip

2. Create a virtual environment (follow A OR B)

• A: Create a virtual environment with conda conda create -f environment.yml
  • Activate the environment: conda activate metatryp1
• B: Create an environment with virtualenv
  • Will need python 2.7 and pip
  • Install virtualenv: https://virtualenv.pypa.io/en/latest/installation.html
  • Create a virtualenv: Navigate into the unzipped directory you created above metatryp-master (. It should contain this README.md file. Then run this command: virtualenv py2.7. This will create a new python virtual environment directory named 'py2.7'.
  • Install dependencies via pip: Still in the same directory, run this command: bin/install_requirements.sh. This will install other python libraries that are necessary for these tools to work. (currently, just the SqlAlchemy library).
  • (optional). Install the sqlite3 command-line client: If you wish run your own SQL queries on the protein db, it is recommended that you install the sqlite3 client. This should be possible through your system's package manager. E.g. on Ubuntu, the command to do this would look like sudo apt-get install sqlite3.

3. Run tests

• Make sure everything is installed correctly. Run the command ./bin/run_tests.sh. You should see a bunch of output, with the last line reading 'OK'.

4. Initialize the sqlite database (follow A OR B)

• A: Create an empty database names 'proteomics.db.sqlite': ./bin/initialize_db.sh
• B: Build the pre-constructed marine microbial tutorial database: zcat ./tutorial/proteomics.dump.gz | sqlite3 proteomics.db.sqlite. For more on information on what is in the marine microbial database: Tutorial.