Take me off this list, please.

----- Original Message ----- 
From: Enis Afgan <afg...@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.rand...@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.rand...@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 
> > 
> > randall...@niehs.nih.gov 
> > 
> > 919-541-2271 
> > 
> > 
> > 
> > ___________________________________________________________ 
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> > 
>
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