/bionella

Legionella genome annotation

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bionella

Legionella genome annotation

Prerequesites

$ conda install pandas

To start the Jupyter Notebook:

$ make start-nb

To generate the site:

$ make site

To run each of the steps first, second and third:

$ make first
$ make second
$ make third

Build docker image

$ cd Dockerfiles/
$ docker build -t vitorenesduarte/swissprot_blast -f swissprot_blast.

This will build a docker image with blast. This docker image only has one database called swissprot. Check here more details about UniProtKB Swiss-Prot.

Push the docker image

$ docker push vitorenesduarte/swissprot_blast

Run blast in docker

Place in a folder, for example .query_dir, a set of FASTA files and run:

$ docker run -e QUERY_DIR=.query_dir \
             -e DB=swissprot -v $PWD/.query_dir:/.query_dir \
             -ti vitorenesduarte/swissprot_blast

In the end, for each of the FASTA files, you should have a correspondent XML file.

Useful links: