Re: [galaxy-user] database on the cloud

[Blake L. Dixon]

Take me off this list, please.

- Original Message - 
From: Enis Afgan  
Date: Monday, April 18, 2011 1:41 pm 
Subject: Re: [galaxy-user] database on the cloud 
To: "Randall, Thomas (NIH/NIEHS) [C]"  
Cc: "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  ubuntu@ 
> # 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 
> > 
> > 
> > 
> > ___ 
> > 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: 
> > 
> >  http://lists.bx.psu.edu/ 
> > 
>
___
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Re: [galaxy-user] database on the cloud

[Enis Afgan]

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  ubuntu@
# 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
>
>
>
> ___
> 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:
>
>  http://lists.bx.psu.edu/
>
___
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:

  http://lists.bx.psu.edu/

[galaxy-user] database on the cloud

[Randall, Thomas (NIH/NIEHS) [C]]

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

___
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:

  http://lists.bx.psu.edu/