Easy download/setup of Bacterial Genbank and multiple alignment files from UCSC?
Happy new year to you! First of all, well done on a fabulous system. It really is going to make my life as a bioinformatician a lot easier and hopefully empower my wet-lab biologists. I'm trying to setup the 'Get microbial data' tool. Is there an easy way to get hold of these datasets easily with the location files and tool configuration files preset. I wouldn't like to have to try to setup thousands of genomes manually. Better still, can I set up my galaxy instance to send the request to your server directly? Thanks! Konrad. Dr Konrad Paszkiewicz Exeter Sequencing Service, Biosciences, Stocker Road, University of Exeter, Exeter EX4 4QD, UK. http://biosciences.exeter.ac.uk/facilities/sequencing/
On Thu, Jan 6, 2011 at 3:24 PM, Paszkiewicz, Konrad <K.H.Paszkiewicz@exeter.ac.uk> wrote:
Happy new year to you!
First of all, well done on a fabulous system. It really is going to make my life as a bioinformatician a lot easier and hopefully empower my wet-lab biologists.
I’m trying to setup the ‘Get microbial data’ tool. Is there an easy way to get hold of these datasets easily with the location files and tool configuration files preset. I wouldn’t like to have to try to setup thousands of genomes manually. Better still, can I set up my galaxy instance to send the request to your server directly?
Thanks!
Konrad.
See this thread: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004074.html The summary is that the current code needs some updating to work with the current NCBI FTP site (see my branch for some fixes), and Dan will hopefully be looking at updating things - possibly to take advantage of the Galaxy Library functionality (so that using the data doesn't needless make a copy of it). Peter
Hi all, Many thanks for that Peter. It worked a charm. There does seem to be a bug in there somewhere. If more than one item is selected for retrieval at a time, only a single item is returned. The other items all return a 'This file cannot be found' error. Finally as an aside, could this system be adapted to retrieve the PTT files from Genbank? All the very best, Konrad. -----Original Message----- From: p.j.a.cock@googlemail.com [mailto:p.j.a.cock@googlemail.com] On Behalf Of Peter Sent: 06 January 2011 15:55 To: Paszkiewicz, Konrad Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Easy download/setup of Bacterial Genbank and multiple alignment files from UCSC? On Thu, Jan 6, 2011 at 3:24 PM, Paszkiewicz, Konrad <K.H.Paszkiewicz@exeter.ac.uk> wrote:
Happy new year to you!
First of all, well done on a fabulous system. It really is going to make my life as a bioinformatician a lot easier and hopefully empower my wet-lab biologists.
I'm trying to setup the 'Get microbial data' tool. Is there an easy way to get hold of these datasets easily with the location files and tool configuration files preset. I wouldn't like to have to try to setup thousands of genomes manually. Better still, can I set up my galaxy instance to send the request to your server directly?
Thanks!
Konrad.
See this thread: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004074.html The summary is that the current code needs some updating to work with the current NCBI FTP site (see my branch for some fixes), and Dan will hopefully be looking at updating things - possibly to take advantage of the Galaxy Library functionality (so that using the data doesn't needless make a copy of it). Peter
On Wed, Jan 12, 2011 at 1:15 AM, Paszkiewicz, Konrad <K.H.Paszkiewicz@exeter.ac.uk> wrote:
Hi all,
Many thanks for that Peter. It worked a charm.
There does seem to be a bug in there somewhere. If more than one item is selected for retrieval at a time, only a single item is returned. The other items all return a 'This file cannot be found' error.
Given Dan's comments earlier, that doesn't surprise me. Is this on your local Galaxy (I didn't get as far that before Christmas), or on the main Penn State instance?
Finally as an aside, could this system be adapted to retrieve the PTT files from Genbank?
You certainly could use the PTT files to get the gene CDS co-ordinates, but as I recall the scripts just extract this information from the GenBank files (*.gbk) instead.
All the very best,
Konrad.
Peter
Hi Peter, Thanks for getting back to me. I've tested this on both my own Galaxy install and on the galaxy test server - both give the same error. I'm not sure what's causing it. All the very best! Konrad. -----Original Message----- From: p.j.a.cock@googlemail.com [mailto:p.j.a.cock@googlemail.com] On Behalf Of Peter Sent: 12 January 2011 17:54 To: Paszkiewicz, Konrad Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Easy download/setup of Bacterial Genbank and multiple alignment files from UCSC? On Wed, Jan 12, 2011 at 1:15 AM, Paszkiewicz, Konrad <K.H.Paszkiewicz@exeter.ac.uk> wrote:
Hi all,
Many thanks for that Peter. It worked a charm.
There does seem to be a bug in there somewhere. If more than one item is selected for retrieval at a time, only a single item is returned. The other items all return a 'This file cannot be found' error.
Given Dan's comments earlier, that doesn't surprise me. Is this on your local Galaxy (I didn't get as far that before Christmas), or on the main Penn State instance?
Finally as an aside, could this system be adapted to retrieve the PTT files from Genbank?
You certainly could use the PTT files to get the gene CDS co-ordinates, but as I recall the scripts just extract this information from the GenBank files (*.gbk) instead.
All the very best,
Konrad.
Peter
participants (2)
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Paszkiewicz, Konrad -
Peter