25 de septiembre de 2018

SequenceServer: nice local blast

today I wanted to let you know about a tool that we discovered recently that has been very useful for us. Its name is SequenceServer (http://www.sequenceserver.com). It is simply a wrapper to let your collaborators run NCBI BLAST searches on your local sequence databases.
All you need is a copy of the NCBI folder with some BLAST+ release and a Linux distribution. Here we had ncbi-blast-2.7.1+ already in place but had to install the application, which is a ruby application, as recommended by the authors:

$ sudo gem install sequenceserver

Due to dependencies during installation I could not manage to install it in Centos5, but instead it was easy in CentOS release 7.5 (sudo yum install ruby-devel). Once this is done, and the appropriate port is open in the host, all that remains is to let the application know where the sequence databases are. You can do that with these commands:

$ sequenceserver -d /path/to/dbs  # add new databases
$ sequenceserver -l               # list installed dbs
$ sequenceserver &                # launch web application 

Now you are ready to go. Your users need to type the URL:port of your host in their browser and they can now run their searches. This is the way it looks in our server:

Cheers, Bruno

PS I will be moving to the EMBL-EBI so there might be a break in this blog, but please keep in touch

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