Re: [galaxy-user] generic filenames with Export to File

2011-11-14 Thread Jeremy Goecks
There is currently no way to do this but it would definitely be a useful option to have. I've opened a ticket that you can follow and/or comment on if you're interested: https://bitbucket.org/galaxy/galaxy-central/issue/680/preserve-dataset-names-when-exporting I forgot to mention that

Re: [galaxy-user] Lastz

2011-11-14 Thread Nate Coraor
On Nov 12, 2011, at 6:30 AM, Andrew South wrote: Dear Nate - It seems I may have upset the cluster again: I have 3 Lastz jobs running and cannot upload any more data. I had been uploading fine; started 3 lastz mapping jobs (Fasta (1 sequence) vs Fasta (~3000 sequences) output as SNP,

[galaxy-user] trimming

2011-11-14 Thread dtrejo
Does anyone know if it is possible to trim sequencing adaptor sequences away in Galaxy? and what is the necessary format for trimming sequences? because in Clip adapter sequences I can not to see my files. thaks Diana Trejo, PhD -- This message has been scanned for viruses and dangerous

Re: [galaxy-user] Trouble in extracting species on maf imported from UCSC

2011-11-14 Thread Jennifer Jackson
Hi Aurelie, The dataset from the UCSC Table browser did not transfer completely, which lead to the other errors. There is a limit to the number of rows of data that can be extracted, to Galaxy or any other type of download. It is around ~100k, but it depends on the data type. The UCSC group

Re: [galaxy-user] https://galaxy.jgi-psf.org/

2011-11-14 Thread Peter Cock
On Mon, Nov 14, 2011 at 10:08 PM, Chauhan, Archana achau...@utk.edu wrote: Dear Sir/Madam,     I am registered with galaxy http://main.g2.bx.psu.edu/. But I recently came across another link as  https://galaxy.jgi-psf.org/ . This has some very good applications especially

[galaxy-user] enabling regular users to upload large data volumes to a local Galaxy server

2011-11-14 Thread Yury V Bukhman
Hi, we are running a local Galaxy server, administered by a bioinformatics core group. Our end users increasingly come to us with sets of large NGS files that they can't upload to Galaxy on their own through a web browser. We copy their data to a Galaxy filesystem and upload into data

Re: [galaxy-user] enabling regular users to upload large data volumes to a local Galaxy server

2011-11-14 Thread Chorny, Ilya
FTP server. Ilya -Original Message- From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Yury V Bukhman Sent: Monday, November 14, 2011 3:01 PM To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] enabling regular users to upload large