Re: [galaxy-user] Datasets Disappear following import of additional datasets
Hello Josh, Would you please generate a shared history link and send that back to me? If you could note the dataset # of the one that is missing, that would be helpful. Use "Options (gear icon) -> Share or Publish", click on the first button to create link, copy and past into a reply to this email, send directly to me (off-list) to keep your data private. Thanks for reporting the issue. I will watch for your reply, Jen Galaxy team On 10/4/12 6:28 AM, Josh Romney wrote: Galaxy, I am able to upload fastqsanger files via FTP and import them to my various histories without a problem. When I import additional files from the Shared Data library CloudMap into my various histories, my fastqsanger files disappear 'they are no longer visible in the history panel'. The amount of disk usage suggests that my files are still there and the saved histories page shows that there are six datasets even though only five are visible. Any help would be appreciated. Josh ___ 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/
[galaxy-user] Datasets Disappear following import of additional datasets
Galaxy, I am able to upload fastqsanger files via FTP and import them to my various histories without a problem. When I import additional files from the Shared Data library CloudMap into my various histories, my fastqsanger files disappear 'they are no longer visible in the history panel'. The amount of disk usage suggests that my files are still there and the saved histories page shows that there are six datasets even though only five are visible. Any help would be appreciated. Josh ___ 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] Fastq-groomer help
On Oct 3, 2012, at 2:02 PM, Kshama Aswath wrote: > Hello: > I have this 20GB data that I have uploaded onto my history and trying to get > it run thr groomer. Just the first data set was uploaded yesterday and ran > groomer on it and it was not done this morning. The message indicated taht it > is still waiting to be run !!! I have 57 data sets to run and would > appreciate if you could inform me about how long it may take to even get > started or any other suggestion to get my job done will help. > Thanks so much, user name :genenart > Kshama. Hi Kshama, There were some problems dispatching jobs that have been resolved. Sorry for the inconvenience, and thanks for using Galaxy. --nate > > -- > Kshama Aswath > Graduate Student-(PhD) > Bioinformatics and computational Biology > Prince Williams Campus > George Mason University > Manasses,VA-20110 > > ___ > 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] Trim Galore Galaxy Integration
Hello. I would like to integrate this great tool "Trim Galore" in the local Galaxy. How can I do that? Thanks in advance. ___ 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] Trim Galore Galaxy Integration
Hi Sachit! > Hello. I would like to integrate this great tool "Trim Galore" in the > local Galaxy. Has anyone did this before? If so, please provide me > with the wrapper and .xml file? How can I integrate it? I have a beta version of it, also a working Bismark (from the same group) wrapper. I will finish it and get back to you. Thanks, Bjoern > Best wishes, > Sachit > ___ > 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/ -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.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/
[galaxy-user] Trim Galore Galaxy Integration
Hello. I would like to integrate this great tool "Trim Galore" in the local Galaxy. Has anyone did this before? If so, please provide me with the wrapper and .xml file? How can I integrate it? Best wishes, Sachit ___ 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] Galaxy in cloud (not Amazon)
Hi Anatoliy, If you're going to keep that cluster alive continuously, just set it up as per the page whose link you provided and you should be ok. If you plan on having multiple users have their own cloud clusters with Galaxy, you'll probably want to do what I suggested in my previous email. Good luck, Enis On Thu, Oct 4, 2012 at 6:10 PM, Anatoliy Pandorin wrote: > Hi. > Thanks for your help! > > At the moment, we have organized a system like this: > In the cloud OpenStack running several virtual machines (on them built > virtual cluster torqui (with scheduler maui)) and the Galaxy set for > cluster(http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster). > > We need Galaxy for large biological data quickly (faster than a stand > alone machine). > > Maybe we do not understand something? > > Best regards, > Anatoly > > 2012/10/3 Enis Afgan > >> Yes there is, the setup is just not documented very well at this point... >> >> Also, are you familiar with the cloud concepts or just looking to use >> Galaxy? >> >> The basic approach is to setup a CloudMan (usecloudman.org) machine >> image on the local cloud (using the image building process from >> https://github.com/chapmanb/cloudbiolinux is the recommended method). >> Install Galaxy as well as all of its tools, dependencies, and reference >> data on the appropriate block storage volumes and turn those into snapshots >> (see this paper for the architecture overview >> http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full and then >> Galaxy's wiki (http://wiki.g2.bx.psu.edu/Admin) for the details on how >> to set everything up). Beyond that, it's a matter of making sure it all >> works as desired on your setup. You'll probably also want to use a version >> of the code similar to https://github.com/chapmanb/biocloudcentral to >> launch instances because for the non-amazon case, the user data ( >> http://wiki.g2.bx.psu.edu/CloudMan/UserData) required by an instance is >> a bit tedious to compose by hand (the user data link just explains what the >> user data is but the full set of user data fields required for non-amazon >> clouds is not yet documented - I'll do that soon). >> >> Hope this helps. I'm also CCing the galaxy-dev mailing list because >> others may be interested in this topic as well. >> Enis >> >> On Tue, Oct 2, 2012 at 9:37 PM, wrote: >> >>> Hi Enis! >>> In our institute we process biological data. And we have cloud, based on >>> OpenStack. >>> We want to use the Galaxy in the cloud (OpenStack). Are there any >>> solutions for this? (or just Amazon) >>> >>> Thank you so much for the Galaxy! :) And sorry for my English. >>> >> >> > ___ 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/
