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pysqlite problem at installation
by Ross Lazarus 16 Nov '06

16 Nov '06

Apologies if I missed this (I searched the trac...) Centos 4.3, AMD 64 bit sun x4200 hardware. Python 2.4.3 sqlite-3.3.8 (latest available) pysqlite 2.3.2 (latest available at http://initd.org/pub/software/pysqlite/releases/) Short story - I get the following error when trying to build galaxy on the above system: from pysqlite2._sqlite import * ImportError: /usr/local/lib/python2.4/site-packages/pysqlite2/_sqlite.so: undefined symbol: sqlite3_enable_shared_cache Longer story: that symbol appears to be in that _sqlite.so according to grep: [root@godzilla pysqlite-2.3.2]# grep _enable_shared_cache /usr/local/lib/python2.4/site-packages/pysqlite2/_sqlite.so Binary file /usr/local/lib/python2.4/site-packages/pysqlite2/_sqlite.so matches BUT, I get the same error if I use the python2.4 shell to try the same from..import. Any suggestions welcomed... Full install log in case it helps follows below [root@godzilla galaxy_dist]# sh run.sh Architecture appears to be linux-x86_64 python path: /home/rerla/src/galaxy_dist/modules:/home/rerla/src/galaxy_dist/eggs:/home/rerla/src/galaxy_dist/arch/linux-x86_64/lib/python Traceback (most recent call last): File "paster.py", line 7, in ? command.run() File "/home/rerla/src/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 76, in run File "/home/rerla/src/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 115, in invoke File "/home/rerla/src/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 210, in run File "/home/rerla/src/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 184, in command File "/home/rerla/src/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 204, in loadapp File "/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 193, in loadapp File "/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 214, in loadobj File "/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 596, in create File "/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 96, in invoke File "/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call File "/home/rerla/src/galaxy_dist/eggs/Paste-1.0-py2.4.egg/paste/urlmap.py", line 24, in urlmap_factory File "/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 281, in get_app File "/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 596, in create File "/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 99, in invoke File "/home/rerla/src/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call File "/home/rerla/src/galaxy_dist/universe_wsgi.py", line 17, in app_factory app = UniverseApplication( **kwargs ) File "/home/rerla/src/galaxy_dist/galaxy/app.py", line 19, in __init__ create_tables = True ) File "/home/rerla/src/galaxy_dist/galaxy/model/mapping.py", line 81, in init from pysqlite2 import dbapi2 as sqlite File "/usr/local/lib/python2.4/site-packages/pysqlite2/dbapi2.py", line 27, in ? from pysqlite2._sqlite import * ImportError: /usr/local/lib/python2.4/site-packages/pysqlite2/_sqlite.so: undefined symbol: sqlite3_enable_shared_cache -- Ross Lazarus MBBS MPH, Director of Bioinformatics Channing Laboratory, 181 Longwood Ave., Boston MA 02115, USA. Voice: +617 525 2730 Fax: +617 525 0958

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Table Browser Difficulties
by Anton Nekrutenko 01 Nov '06

01 Nov '06

Galaxy users: It appears that UCSC is having temporary difficulties. If you are trying to upload data from UCSC Table Browser through Galaxy interface it may not respond. anton

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Galaxy 2.2 is down
by Ross Hardison 17 Oct '06

17 Oct '06

None of the Galaxy servers except Galaxy1 and Galaxy cluster are responding. - 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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Proxy Error Message
by Stephanie Justice 15 Oct '06

15 Oct '06

When I tried to use Galaxy 2.2 I received the following message around 2 pm on October 15, 2006: Proxy Error The proxy server received an invaild response from an upstream server. The proxy server could not handle the request *GET/.* ** Reason: Error reading from remote server. I am using Verizon DSL to access via Microsoft Explorer. I have tried to access Galaxy since 10 pm last night without success or this error message until now. The page would just refresh and say done at the bottom. Hope this helps. Stephanie Justice-Bitner Penn State Hershey Grad Student

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Tools: Operate on Genomic Intervals: Merge
by Erika 11 Oct '06

11 Oct '06

Dear Galaxy Help, I was wondering if it would be possible to get the coordinates that caused the merge as the output from "Tools: Operate on Genomic Intervals: Merge the overlapping intervals of a query", rather than the entire merged interval as the output. Kind of like the output from "Intersect: Overlapping Pieces of intervals" option, which returns the exact base pair overlap between two queries. It might be helpful in some cases to see only the coordinates that caused the merge. From my limited Galaxy knowledge, by using the "Intersect" option and comparing a file to itself, the output would also include those complete overlaps of interval_1 in file1 to it's copy interval_1 in file2. If there is already a way to get just the coordinates that caused the merge, I would be interested to learn more. Thanks again for your help! - Erika ********************************************************** E.M. Kvikstad Academic Computing Fellow IGDP Genetics Center for Comparative Genomics and Bioinformatics The Pennsylvania State University 208 Mueller Lab University Park, PA 16802 (814) 863-2185 kvik(a)bx.psu.edu

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error message when importing GC content
by Ross Hardison 11 Oct '06

11 Oct '06

When I use the Table Browser proxy in Galaxy to import data on "GC content in 5bp intervals", I get the data I want (in wiggle format). However, the information associated with the query in Galaxy says: 3: UCSC: gc5Base (chr16:1-500000) error, format: wig, database: hg17 Info: Errors: (line 100010)----------------------------------------------------------------- ---------- (line 100013)----------------------------------------------------------------- ---------- <br>UCSC: gc5Base (chr16:1-500000) As far as I can tell, the data are there and are OK (it converts from wiggle to BED OK, and the expected 100,000 lines are present). It is disconcerting to users to get the error message. 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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Galaxy screencasts
by Cathy Riemer 10 Oct '06

10 Oct '06

Hi Nate, I'm having trouble viewing the Galaxy screencasts with my Ubuntu workstation and Firefox. The default app for playing .mov files is "Movie Player" which turns out to be Totem, but I get the following error message: Totem could not play 'file:///tmp/InterFace.mov'. You do not have a decoder installed to handle this file. You might need to install the necessary plugins. It is not entirely clear which of the gstreamer plugins packages is needed for this content. Too bad Apple doesn't have a Quicktime version for Linux. :-( -Cathy

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share items between histories
by Julien Lagarde 03 Oct '06

03 Oct '06

Hi Anton or whoever else in the Galaxy, is it possible to share (or directly copy) items between different histories in galaxy? if not this would be very helpful i think. cheers j -- ----------------------------------------------------- Julien Lagarde Genome Bioinformatics Research Group Centre de Regulacio Genomica Grup de Recerca en Informatica Biomedica (IMIM) Dr. Aiguader, 88 (+34) 93 3160170 ph E-08003 Barcelona (+34) 93 3160099 fax http://genome.imim.es/~jlagarde/ --------------------------------

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history has 100 jobs i did not process/do not recognize
by Erika 02 Oct '06

02 Oct '06

hi, i was using galaxy earlier today. i came back from maybe 2hrs break and now my history has about 100 jobs i do not recognize. and i do not see my jobs in this list. unfortunately, i was not logged on as a user. this is the link i get if i click on "history options: share current history". is this someone else's history? can mine be retrieved by any chance? thanks, erika http://main.g2.bx.psu.edu/history_import?id=263 ********************************************************** E.M. Kvikstad Academic Computing Fellow IGDP Genetics Center for Comparative Genomics and Bioinformatics The Pennsylvania State University 208 Mueller Lab University Park, PA 16802 (814) 863-2185 kvik(a)bx.psu.edu

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tools: merge regions of a single query
by Erika 28 Sep '06

28 Sep '06

Hi, I've tried using the "Operate on Genomic Intervals" tool called "Merge regions of a single query" with some puzzling results. So from the example provided with the tool it seems that if regions fail to merge (i.e. they are unique) then they should be returned in the output along with the merged results, correct? I have used 3 different data files, for human hg18, chimp panTro2, and macaque rheMac2, and each of these files has returned an empty output result. However, they have successfully completed the operation (no error messages were returned). Does this indicate that all regions are unique? Does this indicate a problem with the input file? Does this indicate a problem with the tool? I have attached an example file. Thank you for your help, Erika ********************************************************** E.M. Kvikstad Academic Computing Fellow IGDP Genetics Center for Comparative Genomics and Bioinformatics The Pennsylvania State University 208 Mueller Lab University Park, PA 16802 (814) 863-2185 kvik(a)bx.psu.edu

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