Take me off this list, please.

----- Original Message -----
From: Enis Afgan <afgane@gmail.com>
Date: Monday, April 18, 2011 1:41 pm
Subject: Re: [galaxy-user] database on the cloud
To: "Randall, Thomas (NIH/NIEHS) [C]" <thomas.randall@nih.gov>
Cc: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>

> Hi Thomas,
> It turns out you discovered a bug in the cloud setup. We're
> missing a 2bit
> file and a respective reference to the file for the extract
> genomic DNA
> tool. We'll update the deployment but in the mean time you can
> configure the
> instance yourself with just a few commands:
> # connect to the instance
> [local] $ ssh -i <AWS private key file> ubuntu@<instance public IP>
> # Become galaxy user
> [ec2] $ sudo su galaxy
> # Change to the data dir and create 2bit file
> [ec2] $ cd /mnt/galaxyIndices/genomes/Hsapiens/hg18/seq;
> faToTwoBit hg18.fa
> hg18.2bit
> # Update respective .loc file:
> [ec2]: vi /mnt/galaxyTools/galaxy-central/tool-data/alignseq.loc
> # add this line at the bottom (use TAB to separate the 3 columns)
> seq     hg18    /mnt/galaxyIndices/genomes/Hsapiens/hg18/seq/hg18.2bit
>
> That should do it.
> Let us know if you have any more trouble and we'll fix this issue
> when we
> release a new version of the deployment.
>
> Enis
>
>
> On Fri, Apr 15, 2011 at 11:55 AM, Randall, Thomas (NIH/NIEHS) [C] <
> thomas.randall@nih.gov> wrote:
>
> > I set up a galaxy instance on the cloud, but got the following
> error when
> > trying to convert a bed file of hg18 coordinates to fasta
> sequence with the
> > “Extract Genomic DNA” tool as a test of the functionality of
> this instance:
> >
> > *No sequences are available for 'hg18', request them by
> reporting this
> > error.*
> >
> > * *
> >
> > Where did I go wrong? Likely I would get a similar error for other
> > databases and indexes I might need and the instructions on the
> bitbucket> site does not cover this (
> > https://bitbucket.org/galaxy/galaxy-central/wiki/cloud).
> >
> > Otherwise this is a very nice setup.
> >
> >
> >
> > Thomas Randall, PhD
> >
> > Bioinformatics Scientist, Contractor
> >
> > National Institute of Environmental Health Sciences
> >
> > P.O. Box 12233, Research Triangle Park, NC 27709
> >
> > randallta2@niehs.nih.gov
> >
> > 919-541-2271
> >
> >
> >
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