[galaxy-user] Seqpos output not visible in Safari/Firefox/Chrome
Hello, I am using the Cistrome/Galaxy for the ChIP-seq analysis. Recently i am encountering two problems, first is with the Genomic interval operation where i am not able to intersect or subtract the bed files. Second is with the Seqpos motif tool. The Seqpos analysis runs fine, however when i try to visualize the Cistrome motifs it gives me a blank page with the following message: Please use a frames compatible browser when viewing this output. I guess all the new browsers are frame compatible and in recent past i was able to visualize all the motifs and Seqpos output. The same is also happening with a colleague's computer. Looking forward to your response on this and any possible solution to overcome. Br, Sahu. Biswajyoti Sahu, Ph.D. Institute of Biomedicine, Physiology POB-63, Haartmaninkatu-8 FI-00014, University of Helsinki Helsinki, Finland Phone: +358 9 191 25297 Fax: +358 9 191 25302 biswajyoti.s...@helsinki.fi ___ 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] January 2013 Galaxy Update
Hello all, The January 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_01. *Highlights:* - New papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_01#New_Papers - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_01#Who.27s_Hiringat seven different institutions - GCC2013 http://wiki.galaxyproject.org/GalaxyUpdates/2013_01#GCC2013Training Day Topic Nominations and Sponsorships - January GalaxyAdmins Web Meetuphttp://wiki.galaxyproject.org/GalaxyUpdates/2013_01#January_GalaxyAdmins_Web_Meetup - Other Upcoming Events and Deadlineshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_01#Other_Upcoming_Events_and_Deadlines - New Galaxy Distributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_01#New_Galaxy_Distributions - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_01#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_01#Other_News If you have anything you would like to see in the Febrarury *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Wishing you the best possible new year, Dave Clements and the Galaxy Team -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.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] galaxy cloudman login
To be clear, your admin user still works on this instance but another one does not? If this is the case, can you log in as the admin user (and, if not, simply register a new user and make it an admin) and take a look at the user list in the admin panel? To get to the user list when in Galaxy, just click Admin at the top and then Manage Users. Are there users listed? If your user is listed but you're unable to log in, you can reset your password here. -Dannon On Dec 31, 2012, at 10:41 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Hello, I have galaxy cloudman running and had tried one time success to log in to retain the previous data and history after re-launching followed by 1sttime restart. Today I am re-launching again along with the correct size of ebs volumes that I adjusted earlier. However, my login is not recognized at all (“error:no such user….”). I tried several time of terminating and restarting and it is still the same. My admin which is same as the login was able to retained every time. What’s the issue with the log in?? It is taking time to repeat previous data/history. I need your help to retrieve my login. Thank you in advance, Kathryn ___ 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] [External] Re: galaxy cloudman login
Thank you for the reply. When I check admin from cloudman interface, I still see myself as admin user. However, when I went to galaxy web to continue my work, I couldn't login( as error message below). I can re-register with the same user name/email, however, my history is empty. I already had much work processed previously. 1. how to retain my previous work? 2. I could not find Mange User under admin, either from cloudman and galaxy web. Where is it? Thanks, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Wednesday, January 02, 2013 4:50 PM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: [External] Re: [galaxy-user] galaxy cloudman login To be clear, your admin user still works on this instance but another one does not? If this is the case, can you log in as the admin user (and, if not, simply register a new user and make it an admin) and take a look at the user list in the admin panel? To get to the user list when in Galaxy, just click Admin at the top and then Manage Users. Are there users listed? If your user is listed but you're unable to log in, you can reset your password here. -Dannon On Dec 31, 2012, at 10:41 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Hello, I have galaxy cloudman running and had tried one time success to log in to retain the previous data and history after re-launching followed by 1sttime restart. Today I am re-launching again along with the correct size of ebs volumes that I adjusted earlier. However, my login is not recognized at all (error:no such user). I tried several time of terminating and restarting and it is still the same. My admin which is same as the login was able to retained every time. What's the issue with the log in?? It is taking time to repeat previous data/history. I need your help to retrieve my login. Thank you in advance, Kathryn ___ 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] [External] Re: galaxy cloudman login
On Jan 2, 2013, at 5:17 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: 1. how to retain my previous work? If you were logged in when you were working previously, we just have to figure out who you were logged in as, and log back in. You may also want to check Saved Histories to make sure you aren't unintentionally in a fresh history instead of the one you want. 2. I could not find Mange User under admin, either from cloudman and galaxy web. Where is it? This is from within the Galaxy interface, not cloudman. Click Admin in the top masthead, and then on the left side you should see a bunch of options. The first of these should be Manage 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/
Re: [galaxy-user] Upload files from filesystem paths
Hi Ross, I think I need to clarify. I have a file in /home/galaxy/data-test/dir1/dir2/somefile.txt Under the Upload files from filesystem paths, In the path to upload window I paste /home/galaxy/data-test. This then puts the somefile.txt in the /home/galaxy/galaxy-dist/database/files/000 directory. However, I elected to keep the directory structure. I can see this if I navigate through the shared data tab but where is this information stored under the galaxt-dist structure. As my application needs to have the directory structure kept, so need to access it from the xml/command line I thought it might have been something like: /home/galaxy/galaxy-dist/database/files/000/data-test/dir1/dir2/dataset_id.dat. But this is not the case rather /home/galaxy/galaxy-dist/database/files/000/dataset_id.dat. i.e. no directory structure. So how can I access this information from the xml files in the tools directory? Thanks Neil From: Ross [ross.laza...@gmail.com] Sent: Wednesday, January 02, 2013 4:43 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user Subject: Re: [galaxy-user] Upload files from filesystem paths Try importing those library files to the history where you want them - browse the Galaxy 'shared data' tab to where you uploaded them. On Wed, Jan 2, 2013 at 11:39 AM, neil.burd...@csiro.aumailto:neil.burd...@csiro.au wrote: Hi, I have a local galaxy installation. I've created a data library, selected Upload files from filesystem paths, pasted a path in the path to upload window, and I've selected to preserve the directory structure. And the files get imported. How do I now access these files from my application? I don't want to import them into the history as then they lose the directory structure. I can't see where they are physically under the galaxy-dist structure Thanks for any help Neil ___ 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] Upload files from filesystem paths
Neil, It would help if you could point to an existing tool that works the way you want. I don't know of any that deal with arbitrary nested directories containing arbitrary files. A new composite datatype could impose a structure that a tool could be written to deal with (eg the pbed datatype used in some rgenetics tools) but arbitrary data structures are not going to be possible AFAIK. You're unlikely to get useful help without a much more complete and clear explanation of the problem. On Thu, Jan 3, 2013 at 1:50 PM, neil.burd...@csiro.au wrote: Hi Ross, I think I need to clarify. I have a file in /home/galaxy/data-test/dir1/dir2/somefile.txt Under the Upload files from filesystem paths, In the path to upload window I paste /home/galaxy/data-test. This then puts the somefile.txt in the /home/galaxy/galaxy-dist/database/files/000 directory. However, I elected to keep the directory structure. I can see this if I navigate through the shared data tab but where is this information stored under the galaxt-dist structure. As my application needs to have the directory structure kept, so need to access it from the xml/command line I thought it might have been something like: /home/galaxy/galaxy-dist/database/files/000/data-test/dir1/dir2/dataset_id.dat. But this is not the case rather /home/galaxy/galaxy-dist/database/files/000/dataset_id.dat. i.e. no directory structure. So how can I access this information from the xml files in the tools directory? Thanks Neil From: Ross [ross.laza...@gmail.com] Sent: Wednesday, January 02, 2013 4:43 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user Subject: Re: [galaxy-user] Upload files from filesystem paths Try importing those library files to the history where you want them - browse the Galaxy 'shared data' tab to where you uploaded them. On Wed, Jan 2, 2013 at 11:39 AM, neil.burd...@csiro.aumailto: neil.burd...@csiro.au wrote: Hi, I have a local galaxy installation. I've created a data library, selected Upload files from filesystem paths, pasted a path in the path to upload window, and I've selected to preserve the directory structure. And the files get imported. How do I now access these files from my application? I don't want to import them into the history as then they lose the directory structure. I can't see where they are physically under the galaxy-dist structure Thanks for any help Neil ___ 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/
