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README.md

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Building the PostgreSQL extension

To build the extension run:

mkdir build
cd build
cmake -D PostgreSQL_TYPE_INCLUDE_DIR=<postgres include directory> ..
make
sudo make install

in the pg directory. You can also add optional variables in cmake:

  • MMSEQ_HOSTNAME - "localhost" by default
  • MMSEQ_PORT - 8080 by default
  • MMSEQ_TIMEOUT - timeout in milliseconds, 30000 by default (30 seconds)

For example:

cmake -D PostgreSQL_TYPE_INCLUDE_DIR=/usr/include/postgresql/14/server/ -D MMSEQ_TIMEOUT=60000 ..

Then run CREATE EXTENSION mmseq2; in a PostgreSQL database.

Building the MMSeqs2 computational service

To build the MMSeqs2 computational service run:

mkdir build
cd build
cmake -D PostgreSQL_TYPE_INCLUDE_DIR=<postgres include directory> ..
make

in the mmseq2 directory. You can also optionally set the following environment variables:

  • PG_HOST - "localhost" by default
  • PG_PORT - 5432 by default
  • PG_DBNAME - "bioseqdb" by default
  • PG_USER - "postgres" by default
  • PG_PASSWORD - "password" by default

to specify for MMSeqs2 from what database to fetch the data such as the target sequences and the indexes.

Then you can run MMSeqs2 by executing the command:

echo <MMSeqs2 port> | ./mmseq2

Running the project as a containerized application

Another way to build the project is to use the ops/bin/up.sh shell script which creates two docker containers - one for the PostgreSQL database and one for the MMSeqs2 computational service.