- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] [galaxy-user] FastQ Import
by Nate Coraor 22 Nov '10

22 Nov '10

Martin Laforest wrote: > Hello, > > I'm currently trying out Galaxy and I like a lot thus far. We have our own > instance on a test server. > > I have one issue with the time it takes to import large fastq files > (s_x_sequence.txt files from the GAIIx actually). I think it may be our > set up or something. How long is it suppose to take to upload a 5 > gigabytes file? Hi Martin, I've moved this conversation over to our development list since it pertains to a local installation of Galaxy. It's difficult to say how long it should take since it's going to depend on connection speed and write performance on the server. Also, browsers may not be able to handle file uploads > 2GB. Is the dataset still in the "uploading" state, or has it changed to queued/running? Thanks, --nate > > Many thanks in advance > > > Martin > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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problems with MACS peak calling tool
by Yuelin Zhu 22 Nov '10

22 Nov '10

Hi all, We got the Galaxy installed locally in our cluster and most tools are working well. But for some reason the MACS peak calling tool is not working. Basically it runs very quickly (a few seconds) with empty bed file. When I try to download the html file (very small, just 377.0 bytes) I always get this error: "Unable to remove temporary library download archive and directory" Our Galaxy is installed on a Linux system (Linux 2.6.31.12 #16 SMP Sat Jun 19 11:23:12 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux). Our another Galaxy instance on a Mac OS does not have such any problems with the MACS. Apparently I did not install the MACS correctly. Could anyone give me any clues about this? Your help will be greatly appreciated. Jack

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Skipping BLAST+ tests
by Peter 22 Nov '10

22 Nov '10

Hi Nate, Regarding this: http://bitbucket.org/galaxy/galaxy-central/changeset/cb6787fcc256 Do you plan to install BLAST+ on the Galaxy Test machine? [I think you could even install it on the main Galaxy instance if you avoid all the large databases. The NCBI vector database is tiny and useful, also FASTA vs FASTA is handy.] Also, I made sure all the tests to date use FASTA vs FASTA so that you don't need to worry about the blastdb.loc file for the tests. However, some things like XML output are not supported like this (you have to BLAST against a DB). Regards, Peter

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Local Galaxy installation
by Singh, Indresh 22 Nov '10

22 Nov '10

Greetings, First of all you guys are doing exceptional job building and supporting Galaxy! I would like to download and install galaxy for our JCVI users and hopefully also contribute building and enhancing Galaxy. Is there any documentation which described installation and configuration, I'm mainly looking for document which will help me estimate server requirement. Regards, Indresh Singh J. Craig Venter Institute(JCVI) 9704 Medical Center Drive Rockville, MD 20850, USA Phone: (301)-795-7129 Fax: (240)-243-0600 www.jcvi.org <http://www.jcvi.org>

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Sample tracking dataset upload file browser
by Sarah Diehl 22 Nov '10

22 Nov '10

Hi, I just updated our Galaxy to the newest version in http://bitbucket.org/galaxy/galaxy-dist/. Now I am wondering why I don't have the nice dynamic file browser in the sample tracking dataset upload anymore. There is no extra window with a scroll bar and when I select a file and press "select datasets" nothing happens. I attached a screenshot so you can see what I'm talking about. Thank you very much for your help! Best regards, Sarah

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Error in requests_admin.py
by Sarah Diehl 22 Nov '10

22 Nov '10

Hi again, I think I found another error. After I solved the last issue, I got an error in line 568 of GALAXY_ROOT/lib/galaxy/web/controllers/requests_admin.py. I think the line should be if option == options.EXPERIMENT_NAME: Can somebody confirm this? Best regards, Sarah

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Display of tabular data in Galaxy
by Peter 22 Nov '10

22 Nov '10

Hi all, I've noticed in the right hand column for tabular data Galaxy shows the first few lines with a nice column based layout. Looking at the source, you actually define an HTML table for this. However, on the main central column, when viewing a tabular dataset (by clicking on the eye icon from an entry in the right hand column), the data is shown as raw text. As long as the data in each column is about the same length, this works OK. However, if you have variable length fields then the columns do not line up. It would be nice if the main display showed the data respecting the columns. Has this been considered? My guess is that doing this was rejected due to the computational load to reformat it, and the network load to send the marked up data. (I did try and search the mailing list archives but didn't find any discussion of this) Regards, Peter

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Safe to have Apache serve datasets?
by Branden Timm 19 Nov '10

19 Nov '10

Hi, The notes for deploying Galaxy in production using Apache with mod_proxy advise serving static content from Apache. Is there a good reason not to do the same for <galaxy_home>/database/files? -- Branden Timm System Administrator Great Lakes Bioenergy Research Center btimm(a)glbrc.wisc.edu

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Error: Unable to cleanup job
by Peter Cock 19 Nov '10

19 Nov '10

Hi all, In some workflow testing I was getting errors "Unable to cleanup job" which was due to the cleanup method trying to remove non-existent directories. The following patch appears to solve this particular error (although I am still looking into why my workflow was failing). Peter Example error (before the patch): galaxy.jobs ERROR 2010-11-19 13:58:04,806 Unable to cleanup job 150 Traceback (most recent call last): File "/home/pjcock/repositories/galaxy-central/lib/galaxy/jobs/__init__.py", line 614, in cleanup shutil.rmtree( self.working_directory ) File "/usr/local/lib/python2.6/shutil.py", line 204, in rmtree onerror(os.listdir, path, sys.exc_info()) File "/usr/local/lib/python2.6/shutil.py", line 202, in rmtree names = os.listdir(path) OSError: [Errno 2] No such file or directory: './database/job_working_directory/150' Proposed patch: diff -r 730b89c4da26 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Wed Nov 17 18:26:33 2010 +0000 +++ b/lib/galaxy/jobs/__init__.py Fri Nov 19 14:13:45 2010 +0000 @@ -610,7 +610,7 @@ try: for fname in self.extra_filenames: os.remove( fname ) - if self.working_directory is not None: + if self.working_directory and os.path.isdir( self.working_directory ): shutil.rmtree( self.working_directory ) if self.app.config.set_metadata_externally: self.external_output_metadata.cleanup_external_metadata( self.sa_session )

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Reports error
by SHAUN WEBB 18 Nov '10

18 Nov '10

Hi, I am having a few issues when developing reports. If I click on jobs per month I get an error OperationalError: (OperationalError) (1305, 'FUNCTION galaxy_test.date_trunc does not exist') Full traceback is below. There are similar errors when I click on links for a specific user or tool. Any idea what the issue is. Thanks in advance for any help. Shaun Webb URL: http://bifx3.bio.ed.ac.uk:9001/jobs/per_month_all File '/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy_dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy_dist/lib/galaxy/webapps/reports/controllers/jobs.py', line 251 in per_month_all for row in q.execute(): File '/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/expression.py', line 1121 in execute return e._execute_clauseelement(self, multiparams, params) File '/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py', line 1209 in _execute_clauseelement return connection._execute_clauseelement(elem, multiparams, params) File '/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py', line 874 in _execute_clauseelement return self.__execute_context(context) File '/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py', line 896 in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File '/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py', line 950 in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File '/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py', line 931 in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) (1305, 'FUNCTION galaxy_test.date_trunc does not exist') u'SELECT date_trunc(%s, date(job.create_time)) AS date, sum(CASE WHEN (galaxy_user.email = %s) THEN %s ELSE %s END) AS monitor_jobs, count(job.id) AS total_jobs \nFROM job LEFT OUTER JOIN galaxy_user ON galaxy_user.id = job.user_id GROUP BY date_trunc(%s, date(job.create_time)) ORDER BY date DESC' ['month', 'monitor(a)bx.psu.edu', 1, 0, 'month'] -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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