[galaxy-user] sharing and publishing workflows using myExperiment
We are pleased to announce a new facility in Galaxy for sharing and publishing Galaxy workflows via the myExperiment social website, which is the leading social website for scientific workflow sharing. myExperiment can now be accessed easily while you're using the Galaxy servers - you can export your workflows to myExperiment to store and share them, and import Galaxy workflows from myExperiment. This means you can: - Share Galaxy workflows in a controlled way (e.g. within a project), publish them with a stable myExperiment reference for your papers (which is linked-data compatible), and use myExperiment's discovery facilities to find more Galaxy workflows as content grows. - Use the social website features directly to document, tag and discuss workflows, add licensing, credit and attribution, and to bundle your Galaxy workflows with associated data, documents, presentations etc into myExperiment packs for ease of reuse and preservation. - Benefit from a central workflow website with a broad community, which means you can manage workflows for multiple Galaxy installations, attract visitors to your workflows and research, and network with others. Instructions are below and in more detail on http://wiki.myexperiment.org/index.php/Galaxy_Help This new facility is brought to you by a myExperiment-Galaxy collaboration and will increase in value as more Galaxy workflows are uploaded so we encourage you to do so - we hope you find it useful and we welcome feedback (contact details are on the help page). Best regards -- Dave 1. When using Galaxy you can import Galaxy workflows from myExperiment by choosing Upload or import workflow in Galaxy's workflow menu, then the new Visit myExperiment link at the bottom of the page. Within the myExperiment interface you can then view a Galaxy workflow and select Import this workflow into Galaxy. Some Galaxy tutorial workflows are currently available to help you try this out. 2. To export Galaxy workflows to myExperiment you'll first need a myExperiment username and password, then you'll be able to upload Galaxy workflows and also make them visible to others if you wish. To create a username and password go to http://www.myexperiment.org/ and register. Having a username and password enables you to benefit from all the features of the site. 3. To export a Galaxy workflow to myExperiment select Download or Export from Galaxy's workflow menu, enter your myExperiment username and password in the Export to myExperiment section and click the Export button. Exported workflows are set to be Private by default but you can make them visible publicly or to friends, groups etc by clicking on Click here to view the workflow on myExperiment and changing the Sharing settings. 4. Visit http://www.myexperiment.org/ at any time to change settings, add further description, tags, license etc, and to create packs. You can also create and administer groups, link up with friends and network with other workflow users. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] cufflinks reference annotation
HI guys, how do we know when to select a refernce annotation when running cufflinks?And if yes, which one from UCSC should we chose: refgene or knowngenes? Thanks, ib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] cufflinks reference annotation
Hello, Using a reference annotation combines what is known with what is novel in your experiment. The Common uses section of this web page explains this concept: http://cufflinks.cbcb.umd.edu/tutorial.html The UCSC Known Genes track incorporates all of RefSeq Genes with other sources, giving it an advantage. But it is also created at a particular time (updated recently, check UCSC for exact dates for any track's last update). Tracks from Genbank are updated daily, includes RefSeq Genes, giving it an different advantage as time passes. One or both tracks may or may not be available, depending on the target genome. Another choice are the iGenomes builds at the Cufflinks web site for UCSC. The iGenomes 'genes.gtf. files have specific attributes populated that activate the full functionality of Cufflinks and related tools. These are: gene_id, transcript_id, gene_name, p_id, and tss_id. For an example of how these are used, see Cuffdiff usage, as explained here http://cufflinks.cbcb.umd.edu/howitworks.html#hdif. The iGenomes data are a popular choice and were recently updated. http://cufflinks.cbcb.umd.edu/igenomes.html (scroll down) Note: mm9 'genes.gtf' is in Shared Data Libraries on Galaxy main. Others are welcome to add to the post to share other good sources for GTF datasets that include the attributes this tool package can utilize. Best, Jen Galaxy team On 7/16/12 8:33 AM, Irene Bassano wrote: HI guys, how do we know when to select a refernce annotation when running cufflinks?And if yes, which one from UCSC should we chose: refgene or knowngenes? Thanks, ib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] galaaxy history size (gb)
Hi Irene, Hi, I deleted several jobs from my history (and purged history as well), however the used space on history hasn't changed. What is the limit of Gb that can e stored?Can this be updated when files are deleted permanently Have a look @ allow_user_dataset_purge = False in universe_wsgi.ini.sample Also, please find find more information about removing datasets from galaxy under: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Purge%20Histories% 20and%20Datasets Cheers, Bjoern Thanks, ib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] cuffdiff
Hi, just few questions about cuffdiff if anyone can answer: 1.how can I load more than two sam/bam files?Galaxy gives spaceonly for two files 2.what to use as input: cufflinks, cuffcompare or cuffmerge? Thanks a lot! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] galaaxy history size (gb)
Hi Irene, If your question is about the public Main Galaxy server, then the current quota is one account per user, 250G per account. http://wiki.g2.bx.psu.edu/Main (see #2). The numbers in the UI will update in a few minutes up to a few hours, it just depends on the load. Going to User - Preferences will show your current usage vs. quota allotment. Within a history, use Options (gear icon) - Show Hidden Datasets or Show Deleted Datasets to check for those that are deleted, but not Permanently deleted (aka Purged). To view your accounts contents across all histories, showing size and status, use Options (gear icon) - Saved Histories, then Advanced Search - status: all. Permanently deleted/Purged data are what do not count in a quota. This wiki has more help/details, including a screencast that walks through how to check where data in an account may be: http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Delete_vs_Delete_Permanently If you still have questions or unaccounted for data after several hours on the public Main server, please let us know, Jen Galaxy team On 7/16/12 1:12 PM, Irene Bassano wrote: Hi, I deleted several jobs from my history (and purged history as well), however the used space on history hasn't changed. What is the limit of Gb that can e stored?Can this be updated when files are deleted permanently? Thanks, ib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
