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
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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
-
Blake L. Dixon -
Enis Afgan -
Randall, Thomas (NIH/NIEHS) [C]