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Old 08-12-2013, 12:46 PM   #1
NGS_New_User
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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!
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Old 08-12-2013, 01:48 PM   #2
GenoMax
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The command line manual for BLAST+ is here: http://www.ncbi.nlm.nih.gov/books/NBK1763/

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: ftp://ftp.ncbi.nih.gov/blast/db/ 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.
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Old 08-13-2013, 02:38 AM   #3
JackieBadger
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you start galaxy by navigating to the galaxy directory and use

sh run.sh
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