October 2010 - galaxy-dev - lists.galaxyproject.org

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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API?
by Davide Cittaro 06 Oct '10

06 Oct '10

Hi there, I've been reading the last devnewsbrief... I've probably missed something, but I see that API should be available... where can I find docs about? thanks 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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October 5, 2010 Galaxy Development News Brief
by Jennifer Jackson 05 Oct '10

05 Oct '10

----- October 5, 2010 Galaxy Development News Brief ----- http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… Here are the highlights of what you will get if you perform the following upgrade: hg pull -u -r d681ef7538ed ----- What's New ----- - Enhanced Data Library Features 1. Add the ability to make any library item public (and it's contents, if any) * There are now options on library item pop-up menus to make a library dataset public, make all contents of a folder public, or make an entire data library public. These new menu items are displayed only if the current item (dataset) is not public or if the current item (data library, folder) contains items that are not public. * The following image shows a data library that contains a restricted dataset and a folder that contains a restricted dataset. Since the data library contains items that are not public (restricted), it's Library Actions menu includes a "Make public" option. Selecting this option will make all of the contents of the entire data library public. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… * Similarly, the folder popup menu includes a "Make public" option since it contains a restricted dataset. Selecting this option at the folder level will only make the contents of the particular folder public. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… * The popup menu associated with any restricted library dataset will also include a "Make public" option. Selecting this option will make only that particular dataset public. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… 2. Upload Option changes * Move the upload options (ie., file, directory, filesystem paths, import from history), which used to be in the data library upload form's title bar popup menu, into a select list on the upload form. * Selecting a different upload option now performs a refresh on the upload form so that any form contents entered before selecting the option are now retained. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… - Extended Workflow and related History/Dataset Features 1. You can now flag a workflow step as an output within the editor. * To do this, hover over any output, click the asterisk to flag/unflag an output. If a workflow has outputs flagged, only those particular results will show in the history and all other outputs will be hidden. If no outputs are flagged, everything is shown (same as previous behavior). Note that workflow output flagging overrides HideDatasetActions; if a HideDatasetAction exists on a dataset flagged as a workflow output, it is removed. * This feature makes it much easier to take an existing workflow, and hide all of the outputs except for a small number of desired results. * It is worth noting that non-output results are only hidden, not deleted, and that they can be viewed in the history at any time by going to "View Hidden Datasets" in the history panel. 2. More options for Exporting, Searching, and Annotating * Both workflows and histories can now be exported to files. Importing workflows and histories is coming soon. * Annotations preserved when importing histories and workflows. * Tool search is now available in workflow editor so that you can search for tools when creating workflows. * Improvements for annotating histories and workflows to make it easier to add annotations. 3. Workflow Tool Form changes * Output extensions are now properly separated by ', ' (including space) instead of just slammed together. * Width is calculated better, taking into account the length of input and output rows, with an upper bound of 250px, and lower bound of 150px. 4. Post Job Actions * Separated into immediate and delayed actions. Immediate actions run when the job is created, as opposed to when it is finished. * Set Datatype is now an immediate action. This has no impact on the execution of the job, but it allows following jobs to queue with the correct subsequent datatypes. * RenameDatasetAction also happens immediately, rather than waiting for a job to complete. This makes the history less confusing to watch, as things don't randomly change names. 5. Updated UI - screenshots * Hovering for the tooltip on the asterisk. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… * A larger segment of a workflow, showing two Group steps flagged as outputs, one intermediary join not flagged as an output, and then a final cut that is flagged. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… * And, for larger workflows, note that the overview in the editor panel colors outputs, so you can find them at a glance. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… ----- Updated & Improved ----- - Application Programming Interface (API) * API now returns data template information associated with a library dataset. * Added library dataset file_path to API captured information. - Data Upload * Allow for bz2 compressed uploads. Datasets can now be gzipped, bzipped, or zipped (only one file per zip, however). - Data Libraries * Clicking on a folder name now expands the folder instead of displaying information/description. * Moved folder icon to be next to the folder name and text (removing extra whitespace). * Rephrase naming for available compression schemes. * When viewing library dataset information under the Admin interface, a field is now present that displays the real path to the file on disk. - Mutation Visualization Tool * Requirement to enter the default columns indicating reference base, position, and start of sample. * New interactive zoom option: image can be zoomed in or out using the mouse wheel. - Trackster Visualization Tool * Better drawing of features at the bottom of viewing window. * Added track name dropdown for setting overview preferences. * Improved packing when zoomed (done on a w_scale basis instead of rounding to levels). - Documentation & Screencasts * Added more screencasts and topics in sample tracking documentation http://main.g2.bx.psu.edu/u/rkchak/p/sts - Community * Community ratings for all published items plus ratings are visible in published items lists. - Reproducibility * Tool parameters captured fresh when rerunning a process within an imported or copied history. - Functional Test Framework * Significant improvements to the functional test framework, especially those tests related to Galaxy forms and data libraries. * Allow the defining of a cluster job runner when running functional tests. - General * Changes to grids to make sorting order clear and reduce clutter from tags and annotations. * Adjusted BWA, Bowtie, and PerM wrappers so they now use verified use-case parameters. * Modified the 'file_path' field type in 'sample_dataset' table to 'TEXT' to support large file paths exceeding 255 characters. * Make the grouping, join, sort, and and any tool which uses r_wrapper.sh compatible with non-bash shells like bourne and dash (the default under modern Debian systems). - Bug Fixes! * Corrected bug that was causing Page item selection grids to be initialized twice and hence causing grid paging to fail. * Corrected bug in full parameter setting specification for Lastz. * Corrected typos in Tool Executed template and in Compute Motifs Frequency tool information. * Corrected import errors that would cause indel_analysis to fail under Python 2.6. ---- Galaxy Project Team http://usegalaxy.org http://bitbucket.org/galaxy/galaxy-central This project is supported in part by NSF, NHGRI, and the Huck Institutes of the Life Sciences, and The Institute for CyberScience at Penn State.

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