[galaxy-user] comparing data sets with different coordinates
Hello, May I use galaxy to do correlation analyses with two continuous quantitative data sets containing different coordinates (two different microarray designs)? How can I create sliding windowed averages for these data sets to accomplish this? How can I perform a correlation analysis with a wiggle and a bed (e.g., microarray data VS gene density). Would I need to do a grouping of my microarray data with another spreadsheet defining the window coordinates? Thanks, Dan ___ 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] Finding Galaxy version
On Dec 13, 2011, at 5:33 AM, Paul-Michael Agapow wrote: A perhaps obvious question: how do I work out what version of Galaxy an instance is? This has come up a few times because of apparent bugs and different behaviour across various development and production instances. Now if you’re installed straight from the repo, you can use “hg log” for the repo number. But that doesn’t work if it’s been installed in another way, say from a tarball or via another versioning system (we use git to synchronize tool development to a production server). Simple solution? Hi Paul, Since the hg changeset id is the Galaxy version, there's not a great way to determine the version without hg. I'd suggest making a note of the id when you fetch the tarball. --nate Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Health Protection Agency ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk** ___ 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/
Re: [galaxy-user] Tophat jobs not starting
On Dec 14, 2011, at 11:19 AM, Magdalena Strzelecka wrote: Hi, I have submitted some jobs to Tophat, but they have not started since yesterday (Dec 13th); i.e they were in a queue for 12 hrs. I have re-submitted everything again (2 jobs), but the same situation is happening. Is there some issue with Tophat at the moment? Hi Magdalena, This was due to a problem with the cluster Galaxy uses to run certain jobs. This was resolved early last week, although there may have been a few intermittent problems after that time. If tophat still has not run successfully, please let us know. Our sincere apologies for the inconvenience, Best, --nate Thanks. M. -- Magdalena Strzelecka, PhD Heald Lab University of California, Berkeley Department of Molecular Cell Biology 315 Life Sciences Addition # 3200 Berkeley, CA 94720-3200 phone: (510) 643-5002 fax: (510) 643-6791 e-mail: strzele...@berkeley.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/ ___ 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] Workflows Multiple datasets
Hi, I was searching for how to run a workflow for multiple input files and I was very happy to find it's already implemented as mentioned here: http://wiki.g2.bx.psu.edu/News%20Briefs/2011_05_20 The problem is that it's not working for me. When I select two files, for example, it runs the workflow only in the first file. Even if I check 'Send results to a new history', it only creates a new history called 'test 1' and not the others. Is my instance somehow misconfigured or it's happening to others as well? I'm also looking for a way to add datasets to a library from different histories. Do I really need to open each history one by one and use 'Import datasets from your current library'? Thank you, Adhemar ___ 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] Workflows Multiple datasets
Dannon, Thanks for the immediate reply. I just retrieved the latest code from the repository and it's not working $ hg summary parent: 6298:b258de1e6cea tip I also tried 'hg pull -u -r 6368:de03f821784b' but it says: pulling from https://bitbucket.org/galaxy/galaxy-dist abort: unknown revision '6368:de03f821784b'! How or when can I update to the release you mentioned? Thanks, -Adhemar 2011/12/19 Dannon Baker dannonba...@me.com Adhemar, This was a bug that has been fixed as of changeset 6368:de03f821784b, which should be available on main.g2.bx.psu.edu in the near future. If you're running a local instance, you'll find this resolved as soon as you update to that changeset or higher. Unfortunately, there isn't a fast way to copy datasets into a data library from multiple histories at once. I think you might find it faster to use the standard Copy Datasets functionality in the history Options menu to move everything you'd like into a single new history, and from there move it into a library. This Copy Datasets action allows you to select an individual history to copy from, instead of manually changing to the history first, so it should save you some time to do it that way. -Dannon On Dec 19, 2011, at 12:12 PM, Adhemar wrote: Hi, I was searching for how to run a workflow for multiple input files and I was very happy to find it's already implemented as mentioned here: http://wiki.g2.bx.psu.edu/News%20Briefs/2011_05_20 The problem is that it's not working for me. When I select two files, for example, it runs the workflow only in the first file. Even if I check 'Send results to a new history', it only creates a new history called 'test 1' and not the others. Is my instance somehow misconfigured or it's happening to others as well? I'm also looking for a way to add datasets to a library from different histories. Do I really need to open each history one by one and use 'Import datasets from your current library'? Thank you, Adhemar ___ 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/
Re: [galaxy-user] Workflows Multiple datasets
I already tested and it's working like a charm. Thank you very much Dannon. -Adhemar 2011/12/19 Dannon Baker dannonba...@me.com Ahh, I should have specified, that changeset is in the galaxy-central repository and has not been moved to galaxy-dist yet. I think we're testing a few more things, but this should happen in the near future, at which point you could simply update from galaxy-dist as usual, or you could pull directly from galaxy-central right now if you'd like. -Dannon On Dec 19, 2011, at 12:50 PM, Adhemar wrote: Dannon, Thanks for the immediate reply. I just retrieved the latest code from the repository and it's not working $ hg summary parent: 6298:b258de1e6cea tip I also tried 'hg pull -u -r 6368:de03f821784b' but it says: pulling from https://bitbucket.org/galaxy/galaxy-dist abort: unknown revision '6368:de03f821784b'! How or when can I update to the release you mentioned? Thanks, -Adhemar 2011/12/19 Dannon Baker dannonba...@me.com Adhemar, This was a bug that has been fixed as of changeset 6368:de03f821784b, which should be available on main.g2.bx.psu.edu in the near future. If you're running a local instance, you'll find this resolved as soon as you update to that changeset or higher. Unfortunately, there isn't a fast way to copy datasets into a data library from multiple histories at once. I think you might find it faster to use the standard Copy Datasets functionality in the history Options menu to move everything you'd like into a single new history, and from there move it into a library. This Copy Datasets action allows you to select an individual history to copy from, instead of manually changing to the history first, so it should save you some time to do it that way. -Dannon On Dec 19, 2011, at 12:12 PM, Adhemar wrote: Hi, I was searching for how to run a workflow for multiple input files and I was very happy to find it's already implemented as mentioned here: http://wiki.g2.bx.psu.edu/News%20Briefs/2011_05_20 The problem is that it's not working for me. When I select two files, for example, it runs the workflow only in the first file. Even if I check 'Send results to a new history', it only creates a new history called 'test 1' and not the others. Is my instance somehow misconfigured or it's happening to others as well? I'm also looking for a way to add datasets to a library from different histories. Do I really need to open each history one by one and use 'Import datasets from your current library'? Thank you, Adhemar ___ 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/
Re: [galaxy-user] CloudMan - The connection has timed out
Hi guys, It looks like my security group rules didn't get saved. I'm going to try again and report back. I actually asked this question on Biostar too. I thought my email didn't make it to the user group. It probably makes sense to consolidate in one place so I'm continuing the updates over there: http://biostar.stackexchange.com/questions/15554/galaxy-cloudman-cant-get-an-instance-started-the-connection-has-timed-out -Greg On Sat, Dec 17, 2011 at 3:36 AM, Enis Afgan eaf...@emory.edu wrote: Hi Greg, Sorry to hear you're having trouble. Can you please confirm that you followed the step for creating a security group on the wiki and opened all the specified ports? Enis On Fri, Dec 16, 2011 at 7:58 PM, mailing list margeem...@gmail.com wrote: Hi Everyone, I'm trying to set up Cloud man. I believe I followed the instructions listed here to a T: http://wiki.g2.bx.psu.edu/Admin/Cloud After launching the instance I even waited 20 minutes before trying to access the public DNS ec2-xxx-xx-xx-xx.compute-1.amazonaws.com/cloud, but my browser just says: The connection has timed out The server at ec2-xxx-xx-xx-xx.compute-1.amazonaws.com is taking too long to respond. Any ideas what I should check? I'm stuck. What information would be useful? Info: Zone is us-east-1a Type is m1.large root devide is ebs AMI Name: galaxy-cloudman-2011-03-22 Region is US East (Virginia) I used this format for user data: cluster_name: DESIRED CLUSTER NAME password: DESIRED Galaxy CloudMan WEB UI PASSWORD access_key: YOUR AWS ACCESS KEY secret_key: YOUR AWS SECRET KEY However this screenshot shows a pipe delimited deal? Maybe I should try that? http://userwww.service.emory.edu/~eafgan/content/galaxy_cloud/AWSconsole-4.jpg Thanks, Greg ___ 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/
