readme.md

How to use

1. Clone this repository
2. Build the image with docker build -t image_name .
3. Run the container with docker run image_name ncbiblast_lwp.pl --email docker@ebi.ac.uk --stype protein --database uniprotkb_swissprot --program blastp sp:wap_rat
4. Alternatively, to save results it can be run as docker run --rm -w /results -v /path/local/destination:/results image_name ncbiblast_lwp.pl --email docker@ebi.ac.uk --stype protein --database uniprotkb_swissprot --program blastp sp:wap_rat

How to update clients

1. Add the jdispatcher clients' repo as a remote: git remote add -f -t master --no-tags clients git@github.com:ebi-wp/webservice-clients.git
2. Load the remote repo's master branch: git checkout clients/master
3. Remove everything from the branch except the folder with perl clients: git subtree split -P perl/lwp -b perl_clients
4. Go back to master branch: git checkout master
5. Insert the modified branch into master: git subtree add --squash -P clients perl_clients
6. Clean up the branch: git branch -D perl_clients

Quick guide for the new tools, Hmmer3 phmmer & hmmscan

How to use the clients

How to use hmmer3 hmmscan :

To use the client directly (without Docker) :

./clients/hmmer3_hmmscan_lwp.pl --email yours@email.ac.uk --hmmDatabase Pfam ./sequence/single.seq

With Docker :

docker run image_name hmmer3_hmmscan_lwp.pl --email yours@email.ac.uk --hmmDatabase Pfam ./sequence/single.seq

How to use hmmer3 phmmer :

To use the client directly (without Docker) :

./clients/hmmer3_phmmer_lwp.pl --email yours@email.ac.uk --seqdb uniprotkb ./sequence/single.seq

With Docker :

docker run image_name ./clients/hmmer3_phmmer_lwp.pl --email yours@email.ac.uk --seqdb uniprotkb ./sequence/single.seq

The recent retired tool :

hmmer_hmmscan