galaxy-user November 2006

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Downtime
by Anton Nekrutenko 27 Nov '06

27 Nov '06

Galaxy and all other Penn State bx services will be down November 28 between 5:00am and 7:00am EST. Galaxy team

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modified "merge" tool
by Iris Vargas Jentzsch 19 Nov '06

19 Nov '06

Dear Galaxy team, I just realized that the "merge" tool in the 'Operate on Genomic intervals" section has been modified (for both the test and the main sites). When I used it before, it gave me only three columns as output (start, end and chromosome) regardless of the number of columns present in the original file. That was actually very handy for me, because it meant that after merging output files from different programs individually, I could join those into one without problem because the columns ended up being the same in all files. Now the tool conserves the column number by adding dot columns to reproduce the original number of columns. I wonder if there is the possibility to leave this as an option, so that the user can choose among conserving number of columns or getting a simplified version with only three output columns like before. I know I can simply cut the columns I want out to another file, but it is an additional step, and when processing a lot of files, if the connection is slow or the server is busy it takes ages :( Otherwise I would be very happy if someone can tell me how to use galaxy directly from the command line. That would make my life so much easier :) Thank you, Iris ====================================== Iris M. Vargas Jentzsch School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch - New Zealand phone: +64 (0) 3 364 2987 ext 7048

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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-user November 2006