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Installation Instructions
Jaci Saunders edited this page Oct 1, 2020
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These instructions assume that you are running within a Unix operating system.
- Git:
git clone https://github.com/saitomics/metatryp.git
OR - download https://github.com/WHOIGit/metatryp-2.0/archive/master.zip
- Unzip the repository:
gzip master.zip
- Unzip the repository:
- Create a virtual environment with conda
conda create -f environment.yml
- Activate the environment:
conda activate metatryp2_env
- Activate the environment:
- PostgreSQL must already be installed on your machine. It comes pre-installed on many Linux operating systems, such as Ubuntu.
- If you do not have postgreSQL installed already, see: Installation guide for postgreSQL
- Create a new postgreSQL user for METATRYP. User here is called
metatryp2_user
. We set the password topeptides
.
$ createuser --interactive metatryp2_user -P
Enter password for new role:
Enter it again:
Shall the new role be a superuser? (y/n) y
- Check that the user was created successfully:
- Start the postgreSQL prompt by running under the admin user
postgres
(need sudo priveleges).$ sudo -u postgres psql
- Once in the postgreSQL prompt, lookup all users with
\du
command - Output should resemble the following:
$ sudo -u postgres psql [sudo] password for userX: psql (10.12 (Ubuntu 10.12-0ubuntu0.18.04.1)) Type "help" for help. postgres=# \du List of roles Role name | Attributes | Member of ----------------+------------------------------------------------------------+----------- metatryp2_user | Superuser, Create role, Create DB | {} postgres | Superuser, Create role, Create DB, Replication, Bypass RLS | {}
- Start the postgreSQL prompt by running under the admin user
- Create an empty postgreSQL database :
- While still in the postgreSQL prompt:
postgres=# CREATE DATABASE metatryp2_proteins;
- Check that the database was created successfully:
postgres=# \l
- Should produce similar output to the following:
postgres=# \l List of databases Name | Owner | Encoding | Collate | Ctype | Access privileges ---------------------+----------+----------+-------------+-------------+--------------------------- metatryp2_proteins | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 | postgres | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 |
- Assign the user you created priveleges to use this new database:
postgres=# GRANT ALL PRIVILEGES ON DATABASE metatryp2_proteins TO metatryp2_user;
- Check that the database was created successfully:
postgres=# \l
- Should resemble the following:
postgres=# GRANT ALL PRIVILEGES ON DATABASE metatryp2_proteins TO metatryp2_user; GRANT postgres=# \l List of databases Name | Owner | Encoding | Collate | Ctype | Access privileges --------------------+----------+----------+-------------+-------------+----------------------------- metatryp2_proteins | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =Tc/postgres + | | | | | postgres=CTc/postgres + | | | | | metatryp2_user=CTc/postgres postgres | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 |
- Quit the postgreSQL prompt and return to working directory:
postgres=# \q
- While still in the postgreSQL prompt:
- Open the file
/conf/db_config.py
and add in the necessary connection configurations for postgreSQL. If following this tutorial explicitly, it would be the following:#Connection Settings for the metatryp database, need to be set for program to run DB_NAME="metatryp2_proteins" DB_CONN_PREFIX="postgresql" DB_HOST="localhost" DB_PORT="5432" DB_PASS="peptides" DB_USER="metatryp2_user"
- If building a database from the pre-built database with 136 pre-loaded marine microbial genomes, follow instructions at: Tutorial.
-
OR, If building a database from scratch use the following:
$ pg_restore --dbname=metatryp2_proteins --no-owner db_schema/metatryp_base_schema.backup
- Check that the database successfully imported the schema:
$ sudo -u postgres psql postgres=# \connect metatryp2_proteins metatryp2_proteins=# \dt
- Output should resemble the following:
$ sudo -u postgres psql [sudo] password for userX: psql (10.12 (Ubuntu 10.12-0ubuntu0.18.04.1)) Type "help" for help. postgres=# \connect metatryp2_proteins You are now connected to database "metatryp2_proteins" as user "postgres". metatryp2_proteins=# \dt List of relations Schema | Name | Type | Owner --------+-------------------------------------+-------+--------- public | digest | table | protein public | metagenome | table | protein public | metagenome_annotations | table | protein public | metagenome_sequence | table | protein public | metagenome_sequence_digest_peptide | table | protein public | metagenome_taxon | table | protein public | ncbi_taxonomy | table | protein public | peptide | table | protein public | protease | table | protein public | protein | table | protein public | protein_digest | table | protein public | protein_digest_peptide | table | protein public | specialized_assembly | table | protein public | specialized_assembly_digest_peptide | table | protein public | specialized_assembly_sequence | table | protein public | taxon | table | protein public | taxon_digest | table | protein public | taxon_digest_peptide | table | protein public | taxon_protein | table | protein (19 rows) metatryp2_proteins=# \q