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

Re: [galaxy-user] ABySS
by Shaun Jackman 08 Oct '10

08 Oct '10

Hi Jennifer, I'm happy to help if I can be of any assistance in bringing ABySS to Galaxy. Cheers, Shaun ABySS team Jennifer Jackson wrote... > > Hello Jesse, > > > > We are currently working on this. There isn't an estimate for > > completion yet, but it should be soon if nothing unexpected comes > > up. > > > > Thanks, > > > > Jen > > Galaxy team > > > > On 9/28/10 1:51 PM, Jesse Erdmann wrote: > > > I've done a little searching but haven't found anyone that has > > > wrapped > > > ABySS for Galaxy. Does anyone know of an existing wrapper or is > > > anyone willing to share one? If nothing else it would be nice if > > > we > > > could find a starting spot. Thanks!

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ABySS
by Jesse Erdmann 08 Oct '10

08 Oct '10

I've done a little searching but haven't found anyone that has wrapped ABySS for Galaxy. Does anyone know of an existing wrapper or is anyone willing to share one? If nothing else it would be nice if we could find a starting spot. Thanks! -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann(a)umn.edu 612-626-3123 jesse(a)jesseerdmann.com Twitter: http://twitter.com/jesseerdmann

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searching for data
by Yury Bukhman 08 Oct '10

08 Oct '10

Hi, I would like to annotate my data sets and enable users to search on these annotations. For example, suppose I have datasets from different microbial species and strains, grown on different media under different conditions. I can attach templates to all of my data that would have fields for species, strain, growth medium and treatment. Suppose now I want to look at all of the data from S.cerevisae, strain ABC, grown on a medium XYZ, under heat stress. How do I do that? I have looked around my Galaxy instance and on the Wiki, but I could not figure out how to search on template fields. Thanks. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman(a)glbrc.wisc.edu

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conditional cluster/merge
by Agnes Williams 08 Oct '10

08 Oct '10

Hi, I have a dataset of some 1000 individuals and I'd like to merge consecutive intervals within 50kb that are within an individual. I know how to do it per person (first filter an individual into one file, and use the "cluster" function at the "operate on genomic intervals". But to do this in 1000 times is obviously not ideal, unless it can be automated. Either that, or perform cluster/merge with an additional condition (only merge for intervals from the same individual). I'm an experimentalist without programming background, so I rely on using galaxy to perform my analyses. I'm wondering if you have any suggestion for this? many thanks in advance! AW

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Input contain special characters
by Zhe Chen 07 Oct '10

07 Oct '10

Hi, I was implementing a galaxy tool. A problem occurs when my input contains ">", linebreak, galaxy seems traslate them to __gt__, __cr____cn__. Is there a way to stop this translation? Or suggestion to fix this problem? Thanks

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Expression data
by Hsu, Amy (NIH/NIAID) [E] 06 Oct '10

06 Oct '10

I have a set of genomic regions, about 8000 intervals, and I'd like to sort them by expression in certain tissues - does anyone know if that is possible? I am not having much luck in UCSC determining which track of data corresponds to a certain tissue. For example - I would like to filter on only those expressed in lymphoctyes (which may mean combining on several fields - whole blood, T cells, B cells, monocytes). Any insight or suggestions would be appreciated. Thanks - Amy

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Re: [galaxy-user] galaxy-user Digest, Vol 52, Issue 4
by Inma Barrasa 06 Oct '10

06 Oct '10

UNSUBSCRIBE ----- Original Message ----- From: galaxy-user-request(a)lists.bx.psu.edu To: galaxy-user(a)lists.bx.psu.edu Sent: Wednesday, October 6, 2010 11:05:29 AM Subject: galaxy-user Digest, Vol 52, Issue 4 Send galaxy-user mailing list submissions to galaxy-user(a)lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-user or, via email, send a message with subject or body 'help' to galaxy-user-request(a)lists.bx.psu.edu You can reach the person managing the list at galaxy-user-owner(a)lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-user digest..." Today's Topics: 1. October 5, 2010 Galaxy Development News Brief (Jennifer Jackson) 2. Reannotate microarray data (NONELL MAZELON, LARA) 3. Re: how to cancel a upload to data library? (Jennifer Jackson) 4. Re: Reannotate microarray data (Jennifer Jackson) ---------------------------------------------------------------------- Message: 1 Date: Tue, 05 Oct 2010 20:52:21 -0700 From: Jennifer Jackson <jen(a)bx.psu.edu> To: "galaxy-user(a)bx.psu.edu" <galaxy-user(a)bx.psu.edu>, "galaxy-dev(a)bx.psu.edu" <galaxy-dev(a)bx.psu.edu> Subject: [galaxy-user] October 5, 2010 Galaxy Development News Brief Message-ID: <4CABF275.8040801(a)bx.psu.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed ----- 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. ------------------------------ Message: 2 Date: Wed, 6 Oct 2010 09:13:09 +0200 From: "NONELL MAZELON, LARA" <lnonell(a)imim.es> To: "galaxy-user(a)bx.psu.edu" <galaxy-user(a)bx.psu.edu> Subject: [galaxy-user] Reannotate microarray data Message-ID: <BB3B87345736EE45843CC0ADF9EEEB0D2AE8CD85CE(a)hermes2.imim.es> Content-Type: text/plain; charset="us-ascii" Dear Galaxy team, I just discovered your tool and is fantastic!. I want to reannotate the porcine affymetrix microarray. So I wanted to perform the following steps: 1. Run blat/blast to the porcine genome SGSC sscrofa9.2/susScr2 with the sequences of all probes on the array (which i have in a csv file) 2. Get genes 3. Do the same with human genome I can load my file and the entire pig genome but i do not know how to perform the "alignment" Is it possible to perform blat/blast (or any other alignment tool similar) through Galaxy? Thanks very much in advance, <mailto:lnonell@imim.es>Lara Nonell Microarray Analysis Service Scientific and Technical Services IMIM-Hospital del Mar Barcelona Biomedical Research Park (office 166) Doctor Aiguader, 88 | 08003 Barcelona Tel.+34 933 160 577 | Fax +34 933 160 410 lnonell(a)imim.es<mailto:lnonell@imim.es> www.imim.es<http://www.imim.es/>

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Reannotate microarray data
by NONELL MAZELON, LARA 06 Oct '10

06 Oct '10

Dear Galaxy team, I just discovered your tool and is fantastic!. I want to reannotate the porcine affymetrix microarray. So I wanted to perform the following steps: 1. Run blat/blast to the porcine genome SGSC sscrofa9.2/susScr2 with the sequences of all probes on the array (which i have in a csv file) 2. Get genes 3. Do the same with human genome I can load my file and the entire pig genome but i do not know how to perform the "alignment" Is it possible to perform blat/blast (or any other alignment tool similar) through Galaxy? Thanks very much in advance, <mailto:lnonell@imim.es>Lara Nonell Microarray Analysis Service Scientific and Technical Services IMIM-Hospital del Mar Barcelona Biomedical Research Park (office 166) Doctor Aiguader, 88 | 08003 Barcelona Tel.+34 933 160 577 | Fax +34 933 160 410 lnonell(a)imim.es<mailto:lnonell@imim.es> www.imim.es<http://www.imim.es/>

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October 5, 2010 Galaxy Development News Brief
by Jennifer Jackson 06 Oct '10

06 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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Re: [galaxy-user] Tophat
by Jeremy Goecks 05 Oct '10

05 Oct '10

[cc'ing galaxy-user] Test and Main do not share databases, so you'll need to create an account on Test and (re)upload your data to Test as well. However, here's a trick for moving datasets between Galaxy servers: use the 'save' link next to a dataset (the link for the 'disk' icon) as the URL for a dataset that you want to 'upload.' This will enable you to quickly move datasets between Galaxy servers without having to upload again from your computer. Also, we're working on functionality that will make it easier to move Galaxy histories between servers, but it's not quite ready yet. Best, J. On Oct 5, 2010, at 10:18 AM, giovanni stefani wrote: > Thank you very much, Jeremy; > sorry to be such a nag, but I can't log in the test site with my e-mail address and password. I entered my e-mail, username and password in the test site as a new user but I can't see the data I uploaded in the main site from the test site. Can you please advise on how to analyze data from my main account in the test site? > Thank you very much, > > Giovanni > >> Hi Giovanni, >> >> Tophat is available on our test server ( http://test.g2.bx.psu.edu/ ), and it will be available on our main server soon. FYI, our test server can be somewhat unreliable, but you're welcome to try your Tophat analyses there. >> >> Thanks, >> J. >> >> On Oct 5, 2010, at 1:10 AM, giovanni stefani wrote: >> >>> Hello, >>> >>> I am a new galaxy user, still trying to find my way around. Is there a way to run Tophat on Galaxy? >>> Thanks >>> >>> Giovanni >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-user >> >> >> >> > J.

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