Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Genomestudion in Linux Mindbomb Bioinformatics 1 04-22-2013 08:04 AM
GALAXY on Bio-Linux zgtmann Bioinformatics 3 03-22-2013 02:56 AM
BLASTP on linux syintel87 Bioinformatics 5 02-28-2013 08:29 AM
How to install Dotter in Linux shuang Bioinformatics 3 10-16-2012 12:27 AM
New to Linux and Bioinformatics johnadam33 Bioinformatics 12 09-08-2011 12:40 PM

Thread Tools
Old 08-12-2013, 12:46 PM   #1
Location: USA

Join Date: Sep 2012
Posts: 41
Question Galaxy in Linux

Hello Everyone,

Quick question. I have used galaxy before to run blastn and blastx (the gui web version). I know want to try using Galaxy installed in linux (the command mode version).
Does anyone know where to find a tutorial on this (I need things like what commands to use to make the blast run). The cluster I am using has galaxy version 1 and 2 installed and I have no idea how to start running it. Any help will be helpful and very much appreciated

Thank you in advance!
NGS_New_User is offline   Reply With Quote
Old 08-12-2013, 01:48 PM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,077

The command line manual for BLAST+ is here:

Blast family of programs must be installed on your cluster (or you could easily request your cluster administrators to install it by using the code source found at a link in the blast manual linked above). If you are new to command line the easiest thing to do would be to ask the admins for the location of the executables.

You will need to download a copy of the blast index files (at lease ones that you need). It is easiest to download the pre-built versions from this link: There is also a nice script available that the cluster admins can use to keep the indexes automatically synced with NBCI at a set interval (daily, weekly etc).

You will want to understand the syntax for the job scheduler for your cluster to submit the jobs.
GenoMax is offline   Reply With Quote
Old 08-13-2013, 02:38 AM   #3
Senior Member
Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 381

you start galaxy by navigating to the galaxy directory and use

JackieBadger is offline   Reply With Quote

blast, de novo assembly, galaxy

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:24 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO