- galaxy-user - lists.galaxyproject.org

New tools available on Galaxy
by yizhang＠bx.psu.edu 19 Feb '07

19 Feb '07

New tools released to Galaxy Test at http://test.g2.bx.psu.edu. 1. Gene BED to Exon/Intron BED ("Convert Formats" tool set) - This tool is an enhancement to the old tool "Gene BED to Exon BED". It converts a UCSC gene bed format file to a list of bed format lines corresponding to requested features of each gene. The new feature is to convert gene bed lines to intron bed lines. And the interface is more user friendly. 2. yn00 ("PAML" tool set) - this tool finds the ratio of the number of non-synonymous substitutions per non-synonymous site (Ka) to the number of synonymous substitutions per synonymous site (Ks) for the alignments in the input file.

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Install problem: SQLite DBAPI not found
by Thomas Junier 16 Feb '07

16 Feb '07

Hi folks, First of all, I'm not sure if this is the right list to post to, so my apologies if it isn't. I'm trying to install Galaxy on my machine, according to the instructions at http://g2.trac.bx.psu.edu/wiki/HowToInstall. Everything works fine until I try to do: $ sh run.sh at which point I get a Python traceback in which the last call raises the following error: File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.3.3-py2.4.egg/sqlalchemy/engine/strategies.py", line 52, in create sqlalchemy.exceptions.InvalidRequestError: Cant get DBAPI module for dialect '<sqlalchemy.databases.sqlite.SQLiteDialect object at 0x2a983a6fd0>' (whole traceback at end of mail) I'm using Python version 2.4.3. on a Linux box (SuSE 9) The eggs/ directory does contain a bunch of pysqlite*.egg files, but apparently Python can't find them or else they're not the right ones, or whatnot. Is there a step I missed during install? Any other ideas? Thanks in advance. Thomas ------------ Whole traceback: $ sh run.sh Architecture appears to be linux-x86_64 python path: /home/galaxy/galaxy_dist/lib:/home/galaxy/galaxy_dist/eggs Traceback (most recent call last): File "./scripts/paster.py", line 7, in ? command.run() File "/home/galaxy/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 76, in run File "/home/galaxy/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 115, in invoke File "/home/galaxy/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 210, in run File "/home/galaxy/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 184, in command File "/home/galaxy/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 204, in loadapp File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 193, in loadapp File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 214, in loadobj File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 596, in create File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 96, in invoke File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call File "/home/galaxy/galaxy_dist/eggs/Paste-1.0-py2.4.egg/paste/urlmap.py", line 24, in urlmap_factory File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 281, in get_app File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 596, in create File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 99, in invoke File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call File "/home/galaxy/galaxy_dist/lib/galaxy/app.py", line 48, in app_factory app = UniverseApplication( **kwargs ) File "/home/galaxy/galaxy_dist/lib/galaxy/app.py", line 23, in __init__ create_tables = True ) File "/home/galaxy/galaxy_dist/lib/galaxy/model/mapping.py", line 201, in init metadata.connect( url, **kwargs ) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.3.3-py2.4.egg/sqlalchemy/schema.py", line 936, in connect File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.3.3-py2.4.egg/sqlalchemy/engine/__init__.py", line 91, in create_engine File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.3.3-py2.4.egg/sqlalchemy/engine/strategies.py", line 52, in create sqlalchemy.exceptions.InvalidRequestError: Cant get DBAPI module for dialect '<sqlalchemy.databases.sqlite.SQLiteDialect object at 0x2a983a6fd0>'

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News From the Galaxy Development Team
by yizhang＠bx.psu.edu 09 Feb '07

09 Feb '07

Hello Galaxy Users, The Galaxy development team is starting a new initiative for communicating important announcements about Galaxy to our users. We will be sending announcements like this one to the galaxy-user(a)bx.psu.edu email list, so if you are interested in receiving these announcements, please be sure to subscribe to this list. We are also in the process of adding a "News" page to our Galaxy wiki documentation, so some announcements will be available there as well. Here are the highlights of the new features that are currently available on our Galaxy test environment at http://test.g2.bx.psu.edu/. Maf Limit to Species Tool This tool offers the ability to remove any undesired species from a MAF file. Columns which contain only gaps are removed. The user can choose to keep or discard blocks which do not have all the desired species. The user can also choose to include blocks which contain only a single species. Enhanced LAJ Tool We have added a dialog box for filtering the input data. This eliminates a problem we were having with integer overflow. Enhanced Build Lists of the Upload Tool and Edit Attributes Build lists are now alphabetized (by display name) in edit attributes and the upload tool. Miscellaneous We have made several miscellaneous improvements throughout the application, including (but not limited to) better descriptions of errors encountered with invalid data source files (even more improvements coming in this area). As stated above, we'll continue to contact you with new about important Galaxy enhancements and updates. Thanks very much, The Galaxy Development Team

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Re: [galaxy-user] modified "merge" tool
by Iris Vargas Jentzsch 09 Jan '07

09 Jan '07

Hello, I had an issue with the "merge tool some time ago and I sent a message to this board on the 20th of November last year. I got a reply linking me to the explanation of the new operations, which I found awesome! Especially for the Cluster tool :) I did reply to that message, but it seems like it did not come through. In that mail I wrote the following: --- If the Merge tool should output only three columns then there might be something wrong with it because it actually replaces all the columns that are not start, end and chromosome with dots instead of eliminating them, resulting in files with different numbers of columns. On the other hand, the concatenate tool does combine datasets that have the same columns in different orders. But if there are additional columns beside of start, end and chromosome (like the dot columns in the results from the merge tool), then it gives me an error: An error occurred running this job: Traceback (most recent call last): File "./tools/new_operations/gops_concat.py", line 69, in ? main() File "./tools/new_operations/gops_concat.py", line 62, in main for line in concat([g1, g2], sameformat=sameformat): File "build/bdist.linux Here I can’t see the whole error message, so I don’t know if this is useful. --- The "merge" tool actually continues adding those funny dots for the additional columns, which I then need to eliminated to continue performing operations on the file. Therefore I would ask you please to have a look at it and maybe give the user the choice as to how many columns are needed in the output (i.e. 1-conserve number of columns or 2-reduce to three columns). Thanks again, 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 ----- Original Message ----- From: "Anton Nekrutenko" <anton(a)bx.psu.edu> To: "Iris Vargas Jentzsch" <imj15(a)student.canterbury.ac.nz> Cc: <galaxy-dev(a)bx.psu.edu> Sent: Wednesday, November 22, 2006 3:01 AM Subject: Re: [galaxy-user] modified "merge" tool Iris: The merge tool still gives you three columns as before. The concatenate tool now fills absent fields with dots. Here is a detailed description of new operations: http://www.bx.psu.edu/cgi-bin/trac.cgi/wiki/GopsDesc You can use new operation from command line. For this you will need to download Galaxy and look at how commands are formed within tool configuration files. Let us know if you need any help with that. 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 Nov 19, 2006, at 8:46 PM, Iris Vargas Jentzsch wrote: > 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 > _______________________________________________ > 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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error with EMBOSS tools
by Ross Hardison 05 Jan '07

05 Jan '07

Using Galaxy test I tried to run three different ORF-finders from EMBOSS: "getorf", "sixpack" and "transeq". All of them gave the same error: "An error occurred running this job: sixpack: error while loading shared libraries: libX11.so.6: cannot open shared object file: No such file or directory" 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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(no subject)
by E Bouhassira 05 Jan '07

05 Jan '07

I am trying to use the gencode partition software but when I tried to access the lnked with the documentation I get a login windows to login to genome.imem.es Is this software restricted to some users? How can I get access? -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/

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Fetch sequence and alignments: extract blastz alignments
by Erika 29 Dec '06

29 Dec '06

Is it possible to get hg18 alignments to panTro2 on the server? the latest are at : http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsPanTro2/ please do NOT use the ones currently in /depot/data1/cache/human/hg18/align/panTro2/axtNet/ as they were run using an incorrect substitution matrix. Thanks a lot! - 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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Re: [galaxy-user] ENCODEdb
by yizhang＠bx.psu.edu 18 Dec '06

18 Dec '06

Hi Laura, How are you doing? Thanks for letting us know the connection problem between EncodeDB and Galaxy. After some minor fix, EncodeDB should work now. Please let us know, if there are still problems. Wish you have happy Holidays, Yi

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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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