- galaxy-dev - lists.galaxyproject.org

Embed Galaxy into my own website
by Zhe Chen 11 Oct '10

11 Oct '10

Hi, Is it possible to embed Galaxy in my own website instead of embed my website into Galaxy framework? Or can I change the look and feel of Galaxy framework, such as header, footer? Thanks

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Nuitka
by Davide Cittaro 11 Oct '10

11 Oct '10

Hi all, did somebody tried this? http://kayhayen24x7.homelinux.org/blog/ d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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Nucleotide vs Protein FASTA files
by Peter 11 Oct '10

11 Oct '10

Hi all, For several tools it is useful to restrict input to just protein FASTA files, or just nucleotide FASTA files (or even just DNA or just RNA). Galaxy has the concept of file types, e.g. "tabular" or "fasta". Is there any way to add additional meta-data on top of this, or file sub-types? I remember asking James Taylor about this particular example (types of FASTA file) at a conference a few years ago (probably BOSC/ISMB), and I recall at the time he said there were no plans in this direction... is that still true? Thanks, Peter

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Re: [galaxy-dev] [galaxy-bugs] Sequence Read Archive (SRA)
by James Taylor 08 Oct '10

08 Oct '10

On Fri, Oct 08, 2010 at 01:40:01PM -0700, Shaun Jackman wrote: > Could the Sequence Read Archive (SRA) be added to the list of data > sources? To do this we need some way to communicate with the datasource, either some Galaxy awareness in the web site, or a reasonable API we can query data with, preferably both. Does anybody know what sort of API is avaialble for SRA?

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lib/galaxy/tools/parameters/basic.py
by Peter 08 Oct '10

08 Oct '10

Hi all, I've got a couple of minor fixes I'd like to propose for inclusion in galaxy-central: http://bitbucket.org/peterjc/galaxy-central/changeset/7ffc52983c92 http://bitbucket.org/peterjc/galaxy-central/changeset/8e8f1c8d8273 Is there an estabilish mechanism for this kind of request? Thanks, Peter

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Redirect from page "/tool_runner"
by Zhe Chen 08 Oct '10

08 Oct '10

Hi, On the site: http://genome.ucsc.edu/cgi-bin/hgTables, when I click "Send to Galaxy" button. It will redirect to Galaxy main page after running the tool. How is it implemented? It is related to the tool (Get Data)->(UCSC main). Thanks

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Admin Feature suggestion
by SHAUN WEBB 08 Oct '10

08 Oct '10

Would it be possible to create an admin function to send an email to all registered users? Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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publicity for core labs?
by Ross 08 Oct '10

08 Oct '10

Sigh. FTP is state of the art? At least we got a plug. Some more wouldn't do any harm... 2010/10/7 Michael Cho <mikecho95(a)gmail.com> > Thought you would find this conversation amusing. > > > ---------- Forwarded message ---------- > From: solexa+noreply <solexa+noreply(a)googlegroups.com<solexa%2Bnoreply(a)googlegroups.com> > > > Date: Thu, Oct 7, 2010 at 4:52 PM > Subject: Digest for solexa(a)googlegroups.com - 9 Messages in 1 Topic > To: Digest Recipients <solexa+digest(a)googlegroups.com<solexa%2Bdigest(a)googlegroups.com> > > > > > Today's Topic Summary > > Group: http://groups.google.com/group/solexa/topics > > Data delivery for HiSeq [9 Updates] > > Topic: Data delivery for HiSeq > > Sivakumar Gowrisankar <siva80(a)gmail.com> Oct 07 10:04AM -0400 ^ > > Hi, > > For those of you who are in a core lab, would you please share how you > deliver data to your customers? I am especially interested in the HiSeq > data. > > Thank you > Siva > > > > Davide Cittaro <daweonline(a)gmail.com> Oct 07 04:06PM +0200 ^ > > On Oct 7, 2010, at 4:04 PM, Sivakumar Gowrisankar wrote: > > > Hi, > > > For those of you who are in a core lab, would you please share how you > deliver data to your customers? I am especially interested in the HiSeq > data. > > We are testing galaxy (http://usegalaxy.org) for that. > > d > > > -- > Davide Cittaro > daweonline(a)gmail.com > http://daweonline.googlepages.com/ > > > > "Kittler, Ellen Ph. D." <Ellen.Kittler(a)umassmed.edu> Oct 07 10:26AM -0400 > ^ > > I'm ordering a blue ray disk burner for off campus users ! On-campus > users have a pick up area at nearline storage on the high performance > cluster. > > Ellie > > -----Original Message----- > From: solexa(a)googlegroups.com [mailto:solexa@googlegroups.com] On > Behalf Of Davide Cittaro > Sent: Thursday, October 07, 2010 10:07 AM > To: solexa(a)googlegroups.com > Subject: Re: Data delivery for HiSeq > > > On Oct 7, 2010, at 4:04 PM, Sivakumar Gowrisankar wrote: > > > Hi, > > > For those of you who are in a core lab, would you please share how you > deliver data to your customers? I am especially interested in the HiSeq > data. > > We are testing galaxy (http://usegalaxy.org) for that. > > d > > > -- > Davide Cittaro > daweonline(a)gmail.com > http://daweonline.googlepages.com/ > > -- > You received this message because you are subscribed to the Google > Groups "solexa" group. > To post to this group, send email to solexa(a)googlegroups.com. > To unsubscribe from this group, send email to > solexa+unsubscribe(a)googlegroups.com<solexa%2Bunsubscribe(a)googlegroups.com> > . > For more options, visit this group at > http://groups.google.com/group/solexa?hl=en. > > > > Terry Camerlengo <terry.camerlengo(a)gmail.com> Oct 07 10:32AM -0400 ^ > > Depending on specifics....website and/or FTP server. > > > > > Chulhong Kim <cybog337(a)gmail.com> Oct 07 11:11PM +0900 ^ > > Dear Siva > In our case we deliver the seq data to customer using Hdd. If you use the > FTP then it spend too much time. > Brst regards. > Chul Kim > > 2010. 10. 7. 오후 11:04에 "Sivakumar Gowrisankar" <siva80(a)gmail.com>님이 작성: > > Hi, > > For those of you who are in a core lab, would you please share how you > deliver data to your customers? I am especially interested in the HiSeq > data. > > Thank you > Siva > > -- > You received this message because you are subscribed to the Google Groups > "solexa" group. > To post to this group, send email to solexa(a)googlegroups.com. > To unsubscribe from this group, send email to > solexa+unsubscribe(a)googlegroups.com<solexa%2Bunsubscribe(a)googlegroups.com> > <solexa%2Bunsubscribe(a)googlegroups.com<solexa%252Bunsubscribe(a)googlegroups.com> > >. > For more options, visit this group at > http://groups.google.com/group/solexa?hl=en. > > > > aubin thomas <aubinthomas(a)gmail.com> Oct 07 04:37PM +0200 ^ > > Hi, > > it depends on the type of the files that you want to share. A FTP with > secure connection is suitable if you share only the reads that pass the > filter > > On Thu, Oct 7, 2010 at 16:32, Terry Camerlengo > > > > Ammar Husami <ammar.husami(a)gmail.com> Oct 07 03:16PM -0400 ^ > > We use a secure file sharing tool that is only available to cchmc faculty > and staff, and we purchased 20GB of space for $50/year. http://bmixythos > .cchmc.org > but we can use it to send data inside and outside the organization. > > Ammar Husami > Applications Specialist > Molecular Diagnostics Laboratory > Department of Human Genetics > Cincinnati Children's Hospital Medical Center > > > On Thu, Oct 7, 2010 at 10:32 AM, Terry Camerlengo < > > > > Terry Camerlengo <terry.camerlengo(a)gmail.com> Oct 07 03:50PM -0400 ^ > > Why would you say FTP takes too much time? A typical export file compressed > is around 7-8 GB per lane. On a network connection around 15 Mbs (the > average rates at our institution) you are looking at a download time of > 7-10 > minutes per lane. > > Not fast by any means, but considering the size of the files, it certainly > beats burning things to DVDs and mailing it. > > 2010/10/7 Chulhong Kim <cybog337(a)gmail.com> > > > > > Andrew Gagne <agagne(a)gmail.com> Oct 07 04:08PM -0400 ^ > > We generally distribute data via ftp, although some of our users request > their entire run folder and we transfer that on our internal shared storage > system. > > andrew > > 2010/10/7 Terry Camerlengo <terry.camerlengo(a)gmail.com> > > > > > -- > You received this message because you are subscribed to the Google > Groups "solexa" group. > To post to this group, send email to solexa(a)googlegroups.com. > To unsubscribe from this group, send email to > solexa+unsubscribe(a)googlegroups.com<solexa%2Bunsubscribe(a)googlegroups.com> > . > For more options, visit this group at > http://groups.google.com/group/solexa?hl=en. >

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Optional integer or float parameters
by Peter 07 Oct '10

07 Oct '10

Hello all, I'm trying to define an optional integer and float parameter, for example I'd like to do this: <param name="max_hits" type="integer" value="" optional="true" label="Maximum hits to show" help="Use blank (or zero) for default limits"> <validator type="in_range" min="0" /> </param> However, that insists on having an integer (on pressing execute, this parameter goes red and says "An integer is required"), overriding the optional setting. The problem isn't coming from the validator, consider this example: <param name="max_hits" type="integer" value="" optional="true" label="Maximum hits to show" help="Use blank (or zero or negative) for default limits" /> That allows negative values to be entered, but also still insists on a value. Looking at the code, in lib/galaxy/tools/parameters/basic.py only DataToolParameter currently seems to look at the optional element from the XML. The following patch makes it explicit that 'optional' is not currently supported on integer and float parameters (I intend to try and fix that next). http://bitbucket.org/peterjc/galaxy-central/changeset/f6a6c998a015 Peter

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Question w.r.t. local data on local galaxy
by Stein Aerts 06 Oct '10

06 Oct '10

Dear galaxy-dev, Thank you for the wonderful software. I have installed Galaxy locally on a server that is connected directly to a big storage (DAS). On this DAS we are storing our NGS and other data sets. Would it be possible to configure Galaxy in such a way that we can use Get Data to point directly to local data sets on the server? It would be useless to copy the data to my client, and then upload again. Thank you in advance for any suggestion, Stein Aerts Stein Aerts, PhD Assistant Professor Laboratory of Computational Biology Center for Human Genetics University of Leuven Herestraat 49, P.O. Box 602 3000 Leuven, Belgium Office +32 16 330710 Lab + 32 16 330142 Mobile +32 486 659003 http://med.kuleuven.be/lcb/

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