preparation.rst

Preparation

Install Docker

You will need admininstration privileges to do this (or have a sys admin do it). On Debian/Ubuntu flavour machines, install the package docker.io:

sudo apt-get install docker.io

Ensure user is a member of the docker group:

groups

and add docker if that does not appear in the output above.

sudo adduser USERNAME docker

Download docker image

Download the latest version of the Pfam curation tools container from Dockerhub:

docker pull |docker-image-url|

Set up computer

Choose a directory on your machine where you will run the container; this can be anywhere you have write access but it's important that you always use this location.

mkdir pfam_curation
cd pfam_curation

Within that directory create two additional directories: one will contain the sequence files required by the pfam tools and the other will be a working directory:

mkdir seqlib
mkdir pfam_data

Also, create a pfam.conf file in the pfam_curation directory. You can use the template.

Obtain the pfamseq (and, optionally) the uniprot fasta file. Either download the pfamseq.gz (and uniprot.gz) files from Pfam ftp or run the download_pfamseq.sh script.

bash download_pfamseq.sh

If downloading manually you will need to move the files to the seqlib directory and uncompress.

In the directory above pfam_curation directory, get a checkout of the Pfam dictionary:

svn co https://xfamsvn.ebi.ac.uk/svn/pfam/trunk/Data/Dictionary/