April 2006 - galaxy-user - lists.galaxyproject.org

Could you check this for me?
by Ying Zhang 27 Apr '06

27 Apr '06

Hi, the day before yesterday, Anton sent out an email to announce the publicity of g2.bx.psu.edu:8887, so I tried it yesterday. I submit two operations, and they are still pending. By the way, I think the explanation of Coverage ( one tool for operating genomic regions ) is a little confusing. Which is the query 1, the within part or the other? best, Ying

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Galaxy Ka/Ks?
by Ryan Morin 26 Apr '06

26 Apr '06

Hello. I remember reading that Galaxy can perform Ka/Ks calculations on aligned sequences. I can't seem to find this function in the current version at http://g2.bx.psu.edu:8889/. Am I missing it or has this functionality been removed? Thanks. Ryan

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New instance of test server. http://g2.bx.psu.edu:8887/
by Dan Blankenberg 25 Apr '06

25 Apr '06

The newest version of galaxy2.2 test is running at http://g2.bx.psu.edu:8887/. This version utilizes a different database, and will (hopefully) not suffer the downfalls of sqllite. Dan

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lost history panel
by Ross Hardison 23 Apr '06

23 Apr '06

This again is with Galaxy2.2test My history panel was replaced by a large Server Error message, and I cannot see any way to get back to a history: Server Error URL: http://g2.bx.psu.edu:8889/history 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__ >> body = method( trans, **kwargs ) Module galaxy.interfaces.root:67 in history >> return trans.fill_template(template, history=history, mode=mode ) Module galaxy.web:153 in fill_template >> return str(template) Module Cheetah.Template:175 in respond Module galaxy.model:166 in display_info >> return self.datatype.display_info( self ) Module galaxy.datatypes.data:27 in display_info >> return escape(dataset.info) Module cgi:1039 in escape >> s = s.replace("&", "&") # Must be done first! exceptions.AttributeError: 'NoneType' object has no attribute 'replace' extra data CGI Variables HTTP_ACCEPT '*/*' HTTP_ACCEPT_ENCODING 'gzip, deflate' HTTP_ACCEPT_LANGUAGE 'en' HTTP_CONNECTION 'keep-alive' HTTP_COOKIE 'universe=125; universe_user=12; universe_ui=info704' HTTP_HOST 'g2.bx.psu.edu:8889' HTTP_IF_MODIFIED_SINCE 'Sat, 22 Apr 2006 11:52:13 GMT' HTTP_REFERER 'http://g2.bx.psu.edu:8889/history' HTTP_USER_AGENT 'Mozilla/5.0 (Macintosh; U; PPC Mac OS X; en) AppleWebKit/418 (KHTML, like Gecko) Safari/417.9.2' PATH_INFO '/history' REMOTE_ADDR '69.162.62.23' REMOTE_HOST '69-162-62-23.stcgpa.adelphia.net' REQUEST_METHOD 'GET' SERVER_NAME '128.118.201.89' SERVER_PORT '8889' SERVER_PROTOCOL 'HTTP/1.1' Configuration __file__ '/var/opt/universe/james-wsgi/universe_wsgi.ini' database_file 'database/universe.sqlite' debug 'true' file_path 'database/files' here '/var/opt/universe/james-wsgi' job_queue_workers '5' template_path 'templates' test_conf 'test.conf' tool_config_file 'tool_conf.xml' tool_path 'tools' use_interactive 'False' WSGI Variables application <function lint_app at 0xb6d85a3c> com.saddi.service.session <flup.middleware.session.SessionService object at 0xadc3a22c> paste.cookies (<SimpleCookie: universe='125' universe_ui='info704' universe_user='12'>, 'universe=125; universe_user=12; universe_ui=info704') paste.expected_exceptions [<class paste.httpexceptions.HTTPException at 0xb7b746ec>] paste.httpexceptions <paste.httpexceptions.HTTPExceptionHandler instance at 0xb6d8650c> paste.parsed_formvars ({}, ('', <paste.lint.InputWrapper instance at 0xadc3a5ac>, 'GET', False, True)) paste.printdebug_listeners [<cStringIO.StringO object at 0xadc3a020>, <paste.script.serve.LazyWriter object at 0xb7c7378c>] paste.recursive.forward <paste.recursive.Forwarder from /> paste.recursive.include <paste.recursive.Includer from /> paste.recursive.script_name '' paste.remove_printdebug <function remove_printdebug at 0xae2ed87c> paste.throw_errors True wsgi process 'Multithread CGI (?)' full traceback URL: http://g2.bx.psu.edu:8889/history 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__ >> body = method( trans, **kwargs ) Module galaxy.interfaces.root:67 in history >> return trans.fill_template(template, history=history, mode=mode ) Module galaxy.web:153 in fill_template >> return str(template) Module Cheetah.Template:175 in respond Module galaxy.model:166 in display_info >> return self.datatype.display_info( self ) Module galaxy.datatypes.data:27 in display_info >> return escape(dataset.info) Module cgi:1039 in escape >> s = s.replace("&", "&") # Must be done first! exceptions.AttributeError: 'NoneType' object has no attribute 'replace' text version URL: http://g2.bx.psu.edu:8889/history 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/james-wsgi/eggs/flup-0.5-py2.4.egg/ flup/middleware/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/ james-wsgi/galaxy/web/framework.py', line 104 in __call__ body = method( trans, **kwargs ) File '/var/opt/universe/james-wsgi/galaxy/ interfaces/root.py', line 67 in history return trans.fill_template (template, history=history, mode=mode ) File '/var/opt/universe/james- wsgi/galaxy/web/__init__.py', line 153 in fill_template return str (template) File '<string>', line 175 in respond File '/var/opt/ universe/james-wsgi/galaxy/model/__init__.py', line 166 in display_info return self.datatype.display_info( self ) File '/var/opt/ universe/james-wsgi/galaxy/datatypes/data.py', line 27 in display_info return escape(dataset.info) File '/usr/lib/python2.4/ cgi.py', line 1039 in escape s = s.replace("&", "&") # Must be done first! exceptions.AttributeError: 'NoneType' object has no attribute 'replace' 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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error in "filter"
by Ross Hardison 22 Apr '06

22 Apr '06

This is with Galaxy2.2-test (http://g2.bx.psu.edu:8889/) For a file with this format: chr7 115444940 115447120 input_line_1 400 + intronic_proximal 1.0000 0.153597 0.000300 0.944100 330.387200 2151 chr7 115447433 115448233 input_line_2 400 + intronic_proximal 1.0000 0.378290 0.000800 0.994800 302.632000 800 chr7 115448438 115449021 input_line_3 400 + intronic_proximal 1.0000 0.117626 0.001000 0.572000 67.046900 570 chr7 115451858 115452630 input_line_4 500 + intronic_distal 1.0000 0.245333 0.000300 0.954500 189.397301 772 chr7 115453188 115453306 input_line_5 500 + intronic_distal 1.0000 0.161356 0.000400 0.609000 19.040000 118 chr7 115453387 115454302 input_line_6 500 + intronic_distal 1.0000 0.100500 0.000300 0.723800 91.957300 915 I tried to "filter" on column 7, selecting 'intronic_proximal' The error says: 36: Filter on data 34 An error occurred running this job: Cannot recognize the word <b>intronic</b> in condition <b>c7 == 'intronic_proximal'</b> delete 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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server error
by Ross Hardison 21 Apr '06

21 Apr '06

This error came up while trying to sort on column 5 of a file, the first several lines are: chr7 115444940 115447120 3.222082 2180.0 chr7 115447433 115448233 2.294320 800.0 chr7 115448438 115449021 1.155959 583.0 chr7 115449882 115450724 1.604342 842.0 chr7 115451288 115452630 2.87653 1342.0 chr7 115453112 115454302 2.138354 1190.0 chr7 115457980 115458979 1.16 999.0 chr7 115463940 115465249 3.093321 1309.0 chr7 115473798 115474797 2 999.0 chr7 115505514 115506426 1.529573 912.0 chr7 115550504 115551734 5.27437 1230.0 chr7 115587898 115587933 1.25 35.0 chr7 115588088 115590342 3.762417 2254.0 chr7 115590672 115590934 1.5 262.0 chr7 115591492 115592337 1.16 845.0 chr7 115637298 115638032 1.5 734.0 chr7 115733400 115735454 5.649392 2054.0 chr7 115745332 115747197 4.390654 1865.0 chr7 115758594 115761798 4.289223 3204.0 chr7 115761893 115762754 1.919954 861.0 chr7 115810867 115811730 1.33 863.0 chr7 115816924 115817256 1.33 332.0 chr7 115822010 115823009 1.16 999.0 chr7 115826503 115827652 3.731661 1149.0 chr7 115848264 115848894 1.5 630.0 chr7 115861341 115861943 2.98 602.0 chr7 115864830 115866222 2.767889 1392.0 chr7 115866396 115866788 1.670789 392.0 chr7 115905030 115908212 4.927685 3182.0 chr7 115908466 115909276 2.786252 810.0 chr7 115920701 115921284 1.33 583.0 chr7 115921462 115921700 2 238.0 chr7 115932824 115933280 1.268972 456.0 chr7 115938942 115939561 1.33 619.0 chr7 115940006 115942238 2.228168 2232.0 chr7 115950570 115951532 2.781931 962.0 chr7 116006585 116007584 1.26151 999.0 chr7 116012092 116012712 1.724638 620.0 chr7 116031529 116032528 1.1695 999.0 Server Error URL: http://g2.bx.psu.edu:8889/display?id=609 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__ >> body = method( trans, **kwargs ) Module galaxy.interfaces.root:90 in display >> return open( data.file_name ) exceptions.IOError: [Errno 2] No such file or directory: './database/ files/dataset_609.dat' 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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Fwd: Problem in set-up of "coverage" operation
by Ross Hardison 20 Apr '06

20 Apr '06

I just noticed that this is fixed on Galaxy2.2-test, but it is not fixed on Galaxy2.1ENCODE. My understanding is that we are directing people to use Galaxy2.1ENCODE, so it is imperative that it be fixed on the recommended version. Of course, it seems like it should be fixed on all versions that have this tool. - Ross Begin forwarded message: > From: yizhang(a)bx.psu.edu (Yi Zhang) > Date: April 17, 2006 10:34:22 AM EDT > To: Ross Hardison <rch8(a)psu.edu> > Subject: Re: [Galaxy-user] Problem in set-up of "coverage" operation > > Fixed. Thanks for letting us know the problem. > > Yi > > On Sat, Apr 15, 2006 at 10:45:11AM -0400, Ross Hardison wrote: >> The "coverage" tool is a great addition to the set, but I think the >> description is backwards from the execution. >> >> The user selects: >> The density of elements of Query: (call it query 1) >> within Query: (call it query 2) >> >> The explanation says: >> "Return entire regions from query 1 that overlap query2, and append >> two more fields at the end of the returned region: (1) the number of >> nucleotides for each returned region from query 1 that overlap a >> region from query 2 and (2) the percentage of the overlap for each >> region of query1: ..." >> >> >> What you get is actually the opposite of the explanation. You get >> the regions from the 2nd query that contain regions from query 1, >> etc. The selection tools have query 2 as the target for finding >> elements from query 1, but the explanation treats query 1 as the >> target. >> >> I think the first choice should be query 1 and the second choice be >> query 2. You could change the explanation, but I think it would be >> better to change the selection display. In that case, you would have >> something like: >> >> Within Query: (pull down menu of choices for the target) >> Find the density of elements of Query: (pull down menu of choices for >> elements to find in the target). >> >> Then the explanation will fit. >> >> >> >> >> >> >> 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 >> >> >> >> >> > >> _______________________________________________ >> Galaxy-user mailing list >> Galaxy-user(a)bx.psu.edu >> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user > > 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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redundant datasets
by Ross Hardison 19 Apr '06

19 Apr '06

I wanted to repeat a request that when datasets of the same name are deposited on different dates, that only the more recent one be shown on the Galaxy menu. For instance, under ENCODE/Transcriptional Regulation, users can get either TR (20060204) or TR (20060206) The latter is the one they should use. 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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slow loading home page
by Ross Hardison 19 Apr '06

19 Apr '06

Do you have any idea why it takes so long to load the homepage http://www.bx.psu.edu/cgi-bin/trac.cgi when you come from the Center home www.bx.psu.edu ? It used to be instant, but now it takes several seconds. Yesterday, I just stopped showing Galaxy to a visitor because the page did not load after what seemed like a long time (maybe 10-15 sec). - 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 in set-up of "coverage" operation
by Ross Hardison 16 Apr '06

16 Apr '06

The "coverage" tool is a great addition to the set, but I think the description is backwards from the execution. The user selects: The density of elements of Query: (call it query 1) within Query: (call it query 2) The explanation says: "Return entire regions from query 1 that overlap query2, and append two more fields at the end of the returned region: (1) the number of nucleotides for each returned region from query 1 that overlap a region from query 2 and (2) the percentage of the overlap for each region of query1: ..." What you get is actually the opposite of the explanation. You get the regions from the 2nd query that contain regions from query 1, etc. The selection tools have query 2 as the target for finding elements from query 1, but the explanation treats query 1 as the target. I think the first choice should be query 1 and the second choice be query 2. You could change the explanation, but I think it would be better to change the selection display. In that case, you would have something like: Within Query: (pull down menu of choices for the target) Find the density of elements of Query: (pull down menu of choices for elements to find in the target). Then the explanation will fit. 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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