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Invalid request ID
by nsfox＠uwaterloo.ca 14 Dec '10

14 Dec '10

When I try to import a sample from a csv file, it's failing and I'm getting the error message : Invalid request ID. Any suggestions as to what I might be doing wrong would be great. Thanks, Natalie

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Nested structure or sections in drop down lists (select parameters)
by Peter 14 Dec '10

14 Dec '10

Hi all, I'm about to add all our existing BLAST nucleotide databases into the blastdb.loc file, plus all our protein databases into blastdb_p.loc, for use in Galaxy. I've realised these will result in some quite long drop down lists, which will not be very user-friendly. Currently in wwwblast, we have listed our BLAST databases by organism, and inserted dummy disabled options as spacers (e.g. species names). Perhaps a similar mechanism would work in Galaxy? According to the tool configuration page on the wiki the <option> tag only has value and selected tags, it would need something like an enabled tag (default true), and a way to select this from a loc file column. Alternatively I'm wondering if a (multiple select?) drill down select would be possible, something like that used in the Multiple Alignment Viewer tool (file visualization/GMAJ.xml). Are there any other similar situations elsewhere in Galaxy, and how was it handled? Thanks, Peter

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Wiki erratum...
by Richard Bruskiewich 14 Dec '10

14 Dec '10

Galaxy Colleagues, I don't know who is maintaining the Galaxy wiki page at http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup but I noticed that the Python script under the Megablast instructions has an error: the "defline" operation after the "line.startswith" should be moved *after* the if length > 0 statement, otherwise, the defline is reset incorrectly before the previous sequence is written out. This results in a frameshift in the FASTA header line identifiers (i.e. the current sequence gets the next sequence identifier). I've commented out the erroneous defline below and added the right one: import sys length = 0 defline = '' seq = [] for line in sys.stdin : line = line.rstrip( '\r\n' ) if line.startswith( '>' ): # defline = line.split( "|" )[1] # defline should NOT be here if length > 0: print ">%s_%s" % ( defline, length ) print "\n".join( seq ) length = 0 seq = [] defline = line.split( "|" )[1] # defline should be here else: seq.append( line ) length += len( line ) print ">%s_%s" % ( defline, length ) print "\n".join( seq ) While on the topic of this page, perhaps the software versions need to be revisited. Megablast has been superseded already by Blast+. Perhaps new releases of Galaxy should update this? BTW, when is the new Galaxy release (cloud man AMI too...) coming out? I heard rumors that it was due this week. Cheers Richard Bruskiewich -- *Richard Bruskiewich, PhD* Senior Scientist, Computational and Systems Biology Applications Team for Computational Genomics T.T. Chang Genetic Resources Center International Rice Research Institute

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Column order on Tool Shed
by Peter 13 Dec '10

13 Dec '10

Hi all, In Galaxy itself, a tool ID is shown (as a link) followed immediately by its description in the left hand column. As a result many tools have their description written as an extension of the ID text. For example, "Join two Queries" as the ID and "side by side on a specified field" as the description. In these cases the description on its own is not meaningful. This is a problem on the Galaxy Tool Shed since the column order is ID, type (tool vs suite), version, description, categories, uploaded by, and rating. I'd suggest putting the description column immediately after the name. Or maybe even combining the columns, with the ID in bold or something? Alternatively, perhaps Galaxy could try and use self standing descriptions? What do you think? Regards, Peter

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Bug report for uploading tool updates to Tool Shed
by Peter 13 Dec '10

13 Dec '10

Hi all, I have an already approved tool on the Tool Shed, TMHMM and SignalP suite version 0.0.1 I uploaded a new tar ball for version 0.0.2, but did not click approve - I realised I needed to update the REAME file. So I deleted this update. [Note the UI could be clearer about what delete does, thankfully it did not delete the original approved version as well.] This aborted update now shows under "Browse your tools" with status "deleted". I now tried to upload a revised tar ball for version 0.0.2, but it complains "The new version (0.0.2) matches an old version. Check your version in the tool suite config file." The version it matches is the deleted one (my aborted 0.0.2 update). I would expect the version check to ignore deleted tools. Can this be changed? Thanks, Peter

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displaying data in Gbrowse
by Nicki Gray 13 Dec '10

13 Dec '10

Hi, I have been trying to send data to our Gbrowse2 servers from within Galaxy. I found some information from Greg Von Kuster (below) explaining how to change the configuration settings. I edited ~/universe_wsgi.ini and ~/tool-data/shared/gbrowse/ gbrowse_build_sites.txt We have python 2.6 and the file ~/lib/galaxy/datatypes/interval.py has the following in the class Gff section: self.add_display_app( 'gbrowse', 'display in Gbrowse', 'as_gbrowse_display_file', 'gbrowse_links' ) but I still only see "display at UCSC" - there is no "display at GBrowse" link Is there another file I need to edit in order to get this link to show as an option? Thanks, Nicki --------------------- Nicki Gray MRC Molecular Haematology Unit 01865 222434 >> > On Mon, Mar 15, 2010 at 10:46 AM, Jelle Scholtalbers < >> > j.scholtalbers at gmail.com> wrote: >> > >> >> Hi Greg, >> >> >> >> thank you for the explanation, could this also be included >> somewhere in >> >> the wiki? >> >> Although I do get far I don't get the tracks to display in my >> GBrowse. The >> >> link does redirect me to the appropriate gbrowse that I >> specified, the >> >> uploaded track is displayed as: >> >> "could not fetch data for >> >> http://galaxyserver/galaxy/root/display_as?id=4047&display_app=c_elegans&au… >> " >> >> with the label "galaxyserver/display_as". >> >> When I then follow that link I actually see the data as GFF, but >> it seems >> >> GBrowse can't retrieve it somehow. >> >> >> >> This was tested under: >> >> Galaxy-central - 3528:48e83411aa91 >> >> and GBrowse 1.995 >> >> >> >> Two other things: >> >> - under python 2.6 the links appear, under 2.4 they don't. >> >> - The links are displayed as "display in wormbase" and the >> >> display_app="c_elegans". This seems to be harcoded at >> >> galaxy.datatypes.interval line 572, would be nice to have that >> dynamically >> >> generated from for example the >> >> ~/tool-data/shared/gbrowse/gbrowse_build_sites.txt >> >> >> >> Cheers, >> >> Jelle >> >> >> >> >> >> On Fri, Mar 12, 2010 at 3:25 PM, Greg Von Kuster <greg at >> bx.psu.edu> wrote: >> >> >> >>> This requires only configuration settings, not an actual tool >> like >> >>> Epigraph. Displaying in GBrowse is done the same way as >> displaying in UCSC. >> >>> >> >>> In you universe_wsgi.ini file, look for hte following setting, >> and set >> >>> your GBrowse accordingly - you may only want 1 site instead of >> the 3 in the >> >>> sample. >> >>> >> >>> # Comma separated list of bx / UCSC / gbrowse / GeneTrack >> browsers to use >> >>> for viewing >> >>> bx_display_sites = main >> >>> ucsc_display_sites = main,test,archaea,ucla >> >>> gbrowse_display_sites = main,test,tair >> >>> >> >>> Next, make the setting in >> >>> ~/tool-data/shared/gbrowse/gbrowse_build_sites.txt - here are >> the sample >> >>> settings ( note that each corresponds to what you configured in >> your >> >>> universe_wsgi.ini file ). White spaces are tabs in this file, >> and the first >> >>> value in each line ( e.g., main, test ) is the link label that >> points to the >> >>> GBrowse site whose URL is in the 2nd column. The 3rd column of >> each line is >> >>> the valid builds for which the link will be displayed ( see >> below ). Note >> >>> that the sample builds are no longer valid, they should be >> value slike ce2, >> >>> ce3, etc - see ~/tool-data/shared/ucsc/builds.txt for valid >> values ). >> >>> >> >>> # wormbase sites / supported genomes >> >>> main http://www.wormbase.org/db/seq/gbgff/c_elegans/ >> >>> >> c_elegans >> ,c_briggsae,c_remanei,c_brenneri,c_japonica,p_pristionchus,b_malayi >> >>> test http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ >> >>> >> c_elegans >> ,c_briggsae,c_remanei,c_brenneri,c_japonica,p_pristionchus,b_malayi >> >>> tair http://arabidopsis.org/cgi-bin/gbrowse/ >> >>> arabidopsis_tair8,arabidopsis >> >>> >> >>> When you have the correct configuration settings, you'll see a >> link in >> >>> history items ( here is an example - display in Wormbase main ) >> whose genome >> >>> build matches one of the configured builds.

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Warning message display on the main galaxy website
by Assaf Gordon 13 Dec '10

13 Dec '10

Hi, On the main website there's a yellow warning message about the cooling hardware failure - it's very nice (not the failure, the message display). Is there a standard way to add those on a local instance (through the "admin" pages, perhaps) ? or did you just temporarily changed "base_panels.mako" ? Thanks, -gordon

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galaxy lims issues
by nsfox＠uwaterloo.ca 10 Dec '10

10 Dec '10

Hi, I'm having a few issues with the galaxy lims system. First, when I try to upload a dataset with the Upload files from filesystem paths option, I'm getting the following error: Traceback (most recent call last): File "/share/galaxy/tools/data_source/upload.py", line 414, in ? __main__() File "/share/galaxy/tools/data_source/upload.py", line 389, in __main__ output_paths = parse_outputs( sys.argv[4:] ) File "/share/ error Any ideas as to what might be wrong would be great! Also, I think the following might be bugs. 1. I can log out twice and then I have to log in twice. When I log out, galaxy goes to the analyze data tab rather than the login page but it does say that I am logged out. The user tab however says that I am logged in and gives me the option to log out again. If I refresh the page it acts like I'm logged out and redirects to the login page. 2. In the lims system, the order of the fields in the grid level for when entering the information about a sample changes from the order in the sample sequencing form. Lastly I was wondering if it was changed on purpose so that a non-admin user can change the information about a sample once the sequencing request is submitted. It used to be that a regular user could not edit data after they had submitted the sequencing request. Thanks so much, Natalie

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[patch] remote user custom genomes
by Ry4an Brase 10 Dec '10

10 Dec '10

We use external authentication for our Galaxy setup and custom reference genomes weren't working until JJ made this small patch: https://bitbucket.org/Ry4an/galaxy-umn-msi-changes/src/1d3e4c47468e/remote-… Please consider it for addition to galaxy-central. Thanks, -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institute http://www.msi.umn.edu

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Re: [galaxy-dev] invoking galaxy standalone
by Kelly Vincent 10 Dec '10

10 Dec '10

Hi Sean, It's pretty standard that if you close a terminal window with a process running in it, that process doesn't necessarily shut down properly, though after a while it will clean itself up. Shutting the browser or not will have absolutely no impact. So you can either leave open the terminal window with Galaxy running, or stop the server before exiting the terminal window. Alternatively, you can also run Galaxy as a background process if you don't want to bother with leaving the terminal window open ("sh run.sh --daemon" to start it and "sh run.sh --stop-daemon" to stop it). Just bear in mind that if you run it as a background process, you won't see any error messages unless you inspect the paster log. As far as which port number to use, 8080 is a very common default, but anything higher than that is a good bet. It's usually good to just choose an arbitrary "odd" number (8976 rather than 9000, for instance). There's always a small chance you'll run into a conflict with another program, so if you ever see an error referencing a port number, just try changing Galaxy's. For moving it to another directory, I think that should be okay. You may need to rerun setup.sh. Regards, Kelly On Dec 10, 2010, at 9:50 AM, Sean Rogers wrote: > I shut quit the terminal and safari which were both running from > yesterday. Galaxy opened through the new terminal command using the > default port. This is semi-inconvenient. Any suggestions as to which > port number to change to? Do I pull a number from a hat or are there > only certain numbered ports available? > > I installed galaxy in my home directory. Can I move it to /usr/ > local/ with the mv command and still have everything work? > > Thanks again,Sean > > > > > Quoting Kelly Vincent <kpvincent(a)bx.psu.edu>: > > > Sean, > > > > This message means that the port specified in universe_wsgi.ini is > > being used by something else (or possibly Galaxy if you never > stopped > > the server you started yesterday). You should probably change port > > from the default 8080 if you haven't already. Let us know if you > have > > any further questions. > > > > Regards, > > Kelly > > > > > > > > On Dec 10, 2010, at 9:01 AM, Sean Rogers wrote: > > > >> Hello, > >> > >> I downloaded and set up galaxy yesterday. It opened up the local > >> host fine at that time. I went to reopen galaxy today by using > >> run.sh from the command line. Galaxy did not open and I got the > >> message: > >> > >> File > >> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/ > SocketServer.py", line 413, in > >> server_bind > >> > >> self.socket.bind(self.server_address) > >> > >> File "<string>", line 1, in bind > >> > >> socket.error: [Errno 48] Address already in use > >> > >> > >> > >> > >> > >> Sean A. Rogers > >> > >> ************************************** > >> Visiting Research Associate > >> Department of Horticulture > >> A314 - Plant & Soil Sciences Building > >> Michigan State University > >> East Lansing, MI 48824-1325 > >> > >> Phone: (517) 355-5191 x1373 > >> > **************************************_______________________________________________ > >> galaxy-dev mailing list > >> galaxy-dev(a)lists.bx.psu.edu > >> http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > > > Sean A. Rogers > > ************************************** > Visiting Research Associate > Department of Horticulture > A314 - Plant & Soil Sciences Building > Michigan State University > East Lansing, MI 48824-1325 > > Phone: (517) 355-5191 x1373 > **************************************

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