Database On The Cloud

Question: Database On The Cloud

7.6 years ago by

Randall, Thomas (NIH/NIEHS) [C] • 30 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<mailto:randallta2@niehs.nih.gov> 919-541-2271

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modified 7.6 years ago by Enis Afgan • 690 • written 7.6 years ago by Randall, Thomas (NIH/NIEHS) [C] • 30

7.6 years ago by

Enis Afgan • 690

United States

Enis Afgan • 690 wrote:

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] <

ADD COMMENT • link written 7.6 years ago by Enis Afgan • 690

Take me off this list, please. 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>

ADD REPLY • link written 7.6 years ago by Blake L. Dixon • 20

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