- galaxy-user - lists.galaxyproject.org

PS on problem with intersection (bx)
by Ross Hardison 13 Jul '06

13 Jul '06

I forgot to tell you that I'm using the test version of Galaxy (http://test.g2.bx.psu.edu/) - Ross Ross Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology The Pennsylvania State University 304 Wartik Laboratory University Park, PA 16802 e-mail: rch8(a)psu.edu phone: 814-863-0113 FAX: 814-863-7024

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Problem with intersect (bx)
by Ross Hardison 13 Jul '06

13 Jul '06

The intersection tool under "Operate on Genomic Intervals (bx)" is not working for returning either overlapping regions or overlapping pieces. The intersection and overlaps in the non-bx operations section are working. I was running intersection (bx) on a set of Mathieu Blanchette's PReMods (118,402 regions) with our RP>0.05 intervals (314,040 regions), in hg17, requiring at least 10bp overlap. Here are the error messages. For returning overlapping pieces: An error occurred running this job: Traceback (most recent call last): File "./tools/new_operations/gops_intersect.py", line 63, in ? main() File "./tools/new_operations/gops_intersect.py", line 56, in main for line in intersect([g1,g2], pieces=pieces, mincols=mincols): File " For returning overlapping regions: An error occurred running this job: Traceback (most recent call last): File "./tools/new_operations/gops_intersect.py", line 63, in ? main() File "./tools/new_operations/gops_intersect.py", line 56, in main for line in intersect([g1,g2], pieces=pieces, mincols=mincols): File " I'll leave the files and results in my history for a while in case that is helpful. Thanks, Ross Ross Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology The Pennsylvania State University 304 Wartik Laboratory University Park, PA 16802 e-mail: rch8(a)psu.edu phone: 814-863-0113 FAX: 814-863-7024

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ENCODE data partioning
by Angelika Merkel 09 Jul '06

09 Jul '06

Hi, I am new Galaxy user and trying to figure out how the ENCODE partitioning works. It says on the webpage that this is based on GENECODE experimentally verified coding sets - is this species specific or a universal prediction? Thanks a lot Angie -- Angelika Merkel Molecular Ecology Lab School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch, New Zealand Ph: ++64 3 364 2987 ext. 7048; 4878

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inconsistent sequences
by Melissa Wilson 06 Jul '06

06 Jul '06

Can anyone help figure out the following problem? I am interested in the exon positions and sequences of EIF1AX. I used Galaxy to find the coding exon positions through UCSC (RefSeq gene NM_001412) using the hg18 (and subsequently hg17 and hg16) sequences. Then I used Fetch Sequences and Alignments to Extract genomic DNA corresponding to query coordinates. The functions work well on the surface, and while there are 435nt extracted for the EIF1AX cds the composition of those 435nt is not the same as the 435nt I get from NCBI NM_001412 CDS nor when I go through UCSC directly to extract the CDS for EIF1AX. This is the same for hg17 and then almost the same for hg16 except for a few additional exons (not clear about those). Perhaps I'm running my search incorrectly, but would someone please check this out. I think a fresh view might clarify things. Best, Melissa

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a suggestion - compressing download files
by Yogeshwar Kelkar 06 Jul '06

06 Jul '06

Hi it takes long time for downloading some huge files from galaxy. how about asking the user whether he/she wants to zip the file before saving / downloading it on local computer? cheers yogeshwar __________________ Yogeshwar Kelkar Makova Lab (517 Mueller University Park, PA 16802)

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Latest genome builds?
by Mike Schaffer 06 Jul '06

06 Jul '06

Hi, It doesn't appear your database has the latest genome builds for human (hg18) and mouse (mm8). Will these be supported soon? Additionally, I was interested in acquiring human/mouse alignments for syntenic introns. When I tried to acquire this from your site for hg17/mm6, it returned a list of alignments, but many of the intron sequences are fragmented across many multiple alignment entries. Is it possible to acquire full "global-like" human/mouse BLASTZ alignments for intron regions from Galaxy, including gapped regions where the sequences aren't alignable? Thanks for any help you can provide. Best regards, Mike Schaffer Ph.D. Candidate Bioinformatics Program Boston University Boston, MA

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Re: [Galaxy-user] Thanks for the answer
by Prachi Shah 28 Jun '06

28 Jun '06

Hi Anton and the galaxy group, Tests of the ENCODEdb connection on the galaxy test site as Anton suggested generates this new set of errors: -------- URL: http://test.g2.bx.psu.edu:9001/async/encode_db1 Module paste.exceptions.errormiddleware:138 in __call__ Module paste.lint:65 in lint_app Module flup.middleware.session:743 in __call__ Module paste.recursive:54 in __call__ Module paste.httpexceptions:619 in __call__ Module paste.wsgilib:112 in catch_errors_app Module galaxy.web.framework:104 in __call__ << kwargs = trans.request.params.copy() kwargs.update( map ) body = method( trans, **kwargs ) # Now figure out what we got back and try to get it to the browser in # a smart way >> body = method( trans, **kwargs ) Module galaxy.interfaces.async:85 in index << GALAXY_BUILD = params.GALAXY_BUILD or params.galaxyFreeze or 'hg17' data = datatypes.factory(ext=GALAXY_TYPE)() data.ext = GALAXY_TYPE data.name = GALAXY_NAME>> data = datatypes.factory(ext=GALAXY_TYPE)() exceptions.AttributeError: 'module' object has no attribute 'factory' -------- Thanks Prachi > -----Original Message----- > From: Elnitski, Laura (NIH/NHGRI) [E] [mailto:elnitski@mail.nih.gov] > Sent: Wednesday, June 28, 2006 3:16 PM > To: prachi(a)stanford.edu; Umayam, Lowell (NIH/NHGRI) [C] > Cc: Wolfsberg, Tyra (NIH/NHGRI) [E]; Baxevanis, Andy (NIH/NHGRI) [E] > Subject: Thanks for the answer > > > FYI- here's the response from Anton > > -----Original Message----- > From: Anton Nekrutenko [mailto:anton@bx.psu.edu] > Sent: Wed 6/28/2006 5:38 PM > To: Elnitski, Laura (NIH/NHGRI) [E] > Cc: galaxy-user(a)bx.psu.edu > Subject: Re: [Galaxy-user] FW: Fwd: Fw: FW: Is Galaxy down? > > The Encode db datasource was not loaded into running galaxy. It is > corrected now and running at http://test.g2.bx.psu.edu > > Use this URL for testing and let us know. > > anton > > > Anton Nekrutenko > Assistant Professor > Department of Biochemistry and Molecular Biology > Center for Comparative Genomics and Bioinformatics > 505 Wartik Building > PennState University > University Park, PA 16802 > 814 865-4752 > 814 863-6699 FAX > anton(a)bx.psu.edu > http://www.bx.psu.edu/~anton > http://g2.bx.psu.edu > > > On Jun 28, 2006, at 5:07 PM, Elnitski, Laura ((NIH/NHGRI)) [E] wrote: > > > > > Hi- > > > > thanks for your help. the message below shows another error we're > > getting. Normally, we'd take more time to investigate the problem > > before asking you, but our manuscript is out for review right now > > and we need resolution of this ASAP. If you think it can only be > > handled on our end, let me know, but if you have suggestions for > > the fix- we would greatly appreciate hearing them. > > > > Thanks again, > > Laura > > > > -----Original Message----- > > From: Umayam, Lowell (NIH/NHGRI) [C] > > Sent: Wed 6/28/2006 5:02 PM > > To: Elnitski, Laura (NIH/NHGRI) [E]; prachi(a)stanford.edu > > Cc: Wolfsberg, Tyra (NIH/NHGRI) [E]; Baxevanis, Andy (NIH/NHGRI) [E] > > Subject: Re: Fwd: Fw: [Galaxy-user] FW: Is Galaxy down? > > > > Hi Laura, > > Switched the URL so it's pointing to the correct public port. So now > > it's getting access to the galaxy server but now another error has > > developed. It looks like they must have changed the script on their > > end > > and that it's now taking different arguments. This error is out of my > > scope since I really don't have any expertise with the scripts on > > Galaxy. I think Prachi should look into this. > > > > -Lowell > > > > > > Server Error > > > > URL: http://g2.bx.psu.edu:8085/async/encode_db1 > > Module paste.exceptions.errormiddleware:*138* in |__call__| > > Module paste.lint:*65* in |lint_app| > > Module flup.middleware.session:*743* in |__call__| > > Module paste.recursive:*54* in |__call__| > > Module paste.httpexceptions:*619* in |__call__| > > Module paste.wsgilib:*112* in |catch_errors_app| > > Module galaxy.web.framework:*104* in |__call__| > > |<< <http://g2.bx.psu.edu:8085/async/encode_db1#> kwargs *=* > > trans*.*request*.*params*.*copy*(**)* > > kwargs*.*update*(* map *)* > > body *=* method*(* trans*,* ****kwargs *)* > > # Now figure out what we got back and try to get it to the browser in > > # a smart way > > ||>> <http://g2.bx.psu.edu:8085/async/encode_db1#>body *=* method*(* > > trans*,* ****kwargs *)*| > > *exceptions.TypeError: default() takes at least 3 non-keyword > > arguments > > (2 given) > > > > * > > > > Tyra Wolfsberg wrote: > > > >> > >> > >> > >>> Subject: Fw: [Galaxy-user] FW: Is Galaxy down? > >>> Date: Wed, 28 Jun 2006 16:04:56 -0400 > >>> Thread-Topic: [Galaxy-user] FW: Is Galaxy down? > >>> Thread-Index: Acaau6b4nybF168GSgeMfrMVI4hHmAAMnsjC > >>> From: "Elnitski, Laura \(NIH/NHGRI\) [E]" <elnitski(a)mail.nih.gov> > >>> To: "Wolfsberg, Tyra \(NIH/NHGRI\) [E]" <tyra(a)nhgri.nih.gov> > >>> > >>> Hi can you forward this to Lowell? I'm in italy :-) > >>> Laura > >>> -------------------------- > >>> Sent from my BlackBerry Wireless Device > >>> > >>> > >>> ----- Original Message ----- > >>> From: Nate Coraor <nate(a)bx.psu.edu> > >>> To: Elnitski, Laura (NIH/NHGRI) [E] > >>> Cc: galaxy-user(a)bx.psu.edu <galaxy-user(a)bx.psu.edu> > >>> Sent: Wed Jun 28 10:04:35 2006 > >>> Subject: Re: [Galaxy-user] FW: Is Galaxy down? > >>> > >>> On Jun 28, 2006, at 7:49 AM, Elnitski, Laura ((NIH/NHGRI)) [E] > >>> wrote: > >>> > >>>> Can you give us any guidance on our ENCODEdb connection problem? > >>> > >>> > >>> Laura, > >>> > >>> It's on port 8885, although the "public" interface is now just: > >>> > >>> <http://main.g2.bx.psu.edu/>http://main.g2.bx.psu.edu/ > >>> > >>> --nate > >> > >> > > > > > > _______________________________________________ > > Galaxy-user mailing list > > Galaxy-user(a)bx.psu.edu > > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user > > > >

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FW: Fwd: Fw: FW: Is Galaxy down?
by Elnitski, Laura (NIH/NHGRI) [E] 28 Jun '06

28 Jun '06

Hi- thanks for your help. the message below shows another error we're getting. Normally, we'd take more time to investigate the problem before asking you, but our manuscript is out for review right now and we need resolution of this ASAP. If you think it can only be handled on our end, let me know, but if you have suggestions for the fix- we would greatly appreciate hearing them. Thanks again, Laura -----Original Message----- From: Umayam, Lowell (NIH/NHGRI) [C] Sent: Wed 6/28/2006 5:02 PM To: Elnitski, Laura (NIH/NHGRI) [E]; prachi(a)stanford.edu Cc: Wolfsberg, Tyra (NIH/NHGRI) [E]; Baxevanis, Andy (NIH/NHGRI) [E] Subject: Re: Fwd: Fw: [Galaxy-user] FW: Is Galaxy down? Hi Laura, Switched the URL so it's pointing to the correct public port. So now it's getting access to the galaxy server but now another error has developed. It looks like they must have changed the script on their end and that it's now taking different arguments. This error is out of my scope since I really don't have any expertise with the scripts on Galaxy. I think Prachi should look into this. -Lowell Server Error URL: http://g2.bx.psu.edu:8085/async/encode_db1 Module paste.exceptions.errormiddleware:*138* in |__call__| Module paste.lint:*65* in |lint_app| Module flup.middleware.session:*743* in |__call__| Module paste.recursive:*54* in |__call__| Module paste.httpexceptions:*619* in |__call__| Module paste.wsgilib:*112* in |catch_errors_app| Module galaxy.web.framework:*104* in |__call__| |<< <http://g2.bx.psu.edu:8085/async/encode_db1#> kwargs *=* trans*.*request*.*params*.*copy*(**)* kwargs*.*update*(* map *)* body *=* method*(* trans*,* ****kwargs *)* # Now figure out what we got back and try to get it to the browser in # a smart way ||>> <http://g2.bx.psu.edu:8085/async/encode_db1#>body *=* method*(* trans*,* ****kwargs *)*| *exceptions.TypeError: default() takes at least 3 non-keyword arguments (2 given) * Tyra Wolfsberg wrote: > > > >> Subject: Fw: [Galaxy-user] FW: Is Galaxy down? >> Date: Wed, 28 Jun 2006 16:04:56 -0400 >> Thread-Topic: [Galaxy-user] FW: Is Galaxy down? >> Thread-Index: Acaau6b4nybF168GSgeMfrMVI4hHmAAMnsjC >> From: "Elnitski, Laura \(NIH/NHGRI\) [E]" <elnitski(a)mail.nih.gov> >> To: "Wolfsberg, Tyra \(NIH/NHGRI\) [E]" <tyra(a)nhgri.nih.gov> >> >> Hi can you forward this to Lowell? I'm in italy :-) >> Laura >> -------------------------- >> Sent from my BlackBerry Wireless Device >> >> >> ----- Original Message ----- >> From: Nate Coraor <nate(a)bx.psu.edu> >> To: Elnitski, Laura (NIH/NHGRI) [E] >> Cc: galaxy-user(a)bx.psu.edu <galaxy-user(a)bx.psu.edu> >> Sent: Wed Jun 28 10:04:35 2006 >> Subject: Re: [Galaxy-user] FW: Is Galaxy down? >> >> On Jun 28, 2006, at 7:49 AM, Elnitski, Laura ((NIH/NHGRI)) [E] wrote: >> >>> Can you give us any guidance on our ENCODEdb connection problem? >> >> >> Laura, >> >> It's on port 8885, although the "public" interface is now just: >> >> <http://main.g2.bx.psu.edu/>http://main.g2.bx.psu.edu/ >> >> --nate > >

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galaxy-Encodedb connection issues
by Prachi Shah 28 Jun '06

28 Jun '06

Hi Istvan, It seems the connection between galaxy and encodedb is broken again. Nothing has changed at the ENCODEdb end that may have caused this problem. Here is the traceback error we receive: -------- URL: http://main.g2.bx.psu.edu:8085/async/encode_db1 File 'build/bdist.darwin-8.5.1-i386/egg/paste/exceptions/errormiddleware.py', line 138 in __call__ File 'build/bdist.darwin-8.5.1-i386/egg/paste/lint.py', line 65 in lint_app File '/var/opt/universe/wsgi-postgres-main/eggs/flup-0.5-py2.4.egg/flup/middlewar e/session.py', line 743 in __call__ File 'build/bdist.darwin-8.5.1-i386/egg/paste/recursive.py', line 54 in __call__ File 'build/bdist.darwin-8.5.1-i386/egg/paste/httpexceptions.py', line 619 in __call__ File 'build/bdist.darwin-8.5.1-i386/egg/paste/wsgilib.py', line 112 in catch_errors_app File '/var/opt/universe/wsgi-postgres-main/galaxy/web/framework.py', line 104 in __call__ body = method( trans, **kwargs ) exceptions.TypeError: default() takes at least 3 non-keyword arguments (2 given) -------- As a way for galaxy to identify where the data request is coming from, you had set up a dedicated link to send params to (.../async/encode_db1). Is that still valid? Thanks Prachi

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FW: Is Galaxy down?
by Elnitski, Laura (NIH/NHGRI) [E] 28 Jun '06

28 Jun '06

hi- Can you give us any guidance on our ENCODEdb connection problem? Thanks! Laura -----Original Message----- From: Umayam, Lowell (NIH/NHGRI) [C] Sent: Tue 6/27/2006 3:33 PM To: Prachi; Elnitski, Laura (NIH/NHGRI) [E] Cc: Wolfsberg, Tyra (NIH/NHGRI) [E]; Baxevanis, Andy (NIH/NHGRI) [E] Subject: Is Galaxy down? Hi Laura and Prachi, I'm working on migrating the ENCODE scripts to the new webserver we plan to switch over to at the end of the year and I notice that the Consortium script recieved and error when trying to query Galaxy. I then checked to see if I could contact the Galaxy server using the production script on research and I got the same error "The connection was refused when attempting to contact g2.bx.psu.edu:9000." So did they close this port on the galaxy server? I don't know who to contact over there to figure out why it isn't working at the moment

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