- galaxy-dev - lists.galaxyproject.org

Error running workflow
by Branden Timm 01 Oct '10

01 Oct '10

Hello, I seem to be having database-related issues when running my workflow. galaxy.jobs DEBUG 2010-09-09 21:14:48,967 dispatching job 180 to local runner galaxy.jobs INFO 2010-09-09 21:14:49,058 job 180 dispatched galaxy.jobs.runners.local DEBUG 2010-09-09 21:14:49,697 executing: soap -a /home/galaxy/galaxy_dist/database/files/000/dataset_400.dat -D /home/galaxy/galaxy_dist/soap_indices/ecoli_U00096.fasta.index -o /home/galaxy/galaxy_dist/database/files/000/dataset_431.dat -u None -r 1 -n 5 -v 2 -M 4 2>&1 galaxy.jobs ERROR 2010-09-09 21:14:50,209 failure running job 181 Traceback (most recent call last): File "/home/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 185, in __monitor_step self.sa_session.refresh( job ) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 926, in refresh self._validate_persistent(state) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 1234, in _validate_persistent raise sa_exc.InvalidRequestError( InvalidRequestError: Instance '<Job at 0x1a4074d0>' is not persistent within this Session 146.151.211.150 - - [09/Sep/2010:21:14:48 -0500] "POST /workflow/run?id=f597429621d6eb2b HTTP/1.1" 200 - "http://galaxy.glbrc.wisc.edu/workflow/run?id=f597429621d6eb2b" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_4; en-us) AppleWebKit/533.17.8 (KHTML, like Gecko) Version/5.0.1 Safari/533.17.8" galaxy.jobs ERROR 2010-09-09 21:14:51,219 failure running job 182 Traceback (most recent call last): File "/home/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 185, in __monitor_step self.sa_session.refresh( job ) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 926, in refresh self._validate_persistent(state) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 1234, in _validate_persistent raise sa_exc.InvalidRequestError( InvalidRequestError: Instance '<Job at 0x2aaab001acd0>' is not persistent within this Session galaxy.jobs.runners.local DEBUG 2010-09-09 21:14:52,460 execution finished: soap -a /home/galaxy/galaxy_dist/database/files/000/dataset_400.dat -D /home/galaxy/galaxy_dist/soap_indices/ecoli_U00096.fasta.index -o /home/galaxy/galaxy_dist/database/files/000/dataset_431.dat -u None -r 1 -n 5 -v 2 -M 4 2>&1 In Galaxy itself, the SOAP tool returns its results and the rest of the jobs just wait to run. Why am I having these errors? Cheers -- Branden Timm btimm(a)glbrc.wisc.edu

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user interface aspects don't show up right or look right in IE 7
by Leandro Hermida 01 Oct '10

01 Oct '10

Hello, I just had a look and see initially that certain aspects of the Galaxy UI don't show up or don't look right in IE 7, e.g. in the history pane the underlying link on the name of each data object to expand it isn't there. Is IE 7 supported? I dislike IE and don't use it otherwise but am forced to use it in my environment as it's part of there standard client image and it is almost impossible to get another browser like Firefox installed for every user that will use Galaxy. best, Leandro

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Global settings from tool wrapper XML, e.g. threads
by Peter 01 Oct '10

01 Oct '10

Hi all, I'm wondering if there is any mechanism in the XML file format for tool wrappers to access global settings? e.g. something like $environment.temp to access the temp environment variable, or something like this for values in universe_wsgi.ini http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax In particular, I'd like to know if there is a way to know how many threads a wrapped tool can use - is there a policy here? Looking at the existing megablast wrapper, this is hard coded as 8 in the Python script, tools/metag_tools/megablast_wrapper.py For the BLAST+ wrappers I am writting, I want to set the number of threads in the XML file - again currently hard coded as 8. Peter

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Policy on tool defaults
by Peter 01 Oct '10

01 Oct '10

Hi all, Is there an overall policy on default values when wrapping tools? e.g. Should defaults be set explicitly in the wrapper (which we can track in the Galaxy version control under hg), or omitted to let the command line tool set its own defaults? I am thinking about pipeline reproducibility as defaults can change... Peter

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SFF to (Sanger) FASTQ
by Peter 01 Oct '10

01 Oct '10

Hi all, This trivial patch makes it explicit that the sff_extract tool converts from SFF to Sanger FASTQ files: http://bitbucket.org/peterjc/galaxy-central/changeset/1c65fc26f05f I'm assuming here that datatype "fastq" in Galaxy is a legacy entry and/or only used when the FASTQ variant is unknown. Regards, Peter

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Proxy error
by Davide Cittaro 30 Sep '10

30 Sep '10

Hi all, I'm running galaxy behind apache proxy. I was manually changing the data type for some dataset from bed to bedgraph and galaxy was stuck... after that I got this error in the admin frame: Proxy Error The proxy server received an invalid response from an upstream server. The proxy server could not handle the request POST /library_common/ldda_edit_info. Reason: Error reading from remote server Apache/2.2.16 (Unix) Server at host001.instruments.ifom-ieo-campus.it Port 8080 Any hint? d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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Apache authentication for local Galaxy install
by Brian J. Abraham 29 Sep '10

29 Sep '10

Hello developers, I am attempting to install a local production copy of Galaxy on an SLES 11 machine running Apache 2.2.16 and PostgreSQL. It is important that we keep our data protected via password so I am trying to use Apache's standard .htaccess for security. galaxy-dist is installed and running at /home/abrahamb2/galaxy-dist Apache's document root is /usr/local/apache/htdocs I have been successful at protecting both /usr/local/apache/htdocs and /usr/local/apache/cgi-bin using the same .htaccess file in both directory that points to /usr/local/apache/.htpasswd for a password file/ I have attempted to use this working .htaccess in /home/abrahamb2/galaxy-dist with no success. I have also modified /usr/local/apache/conf/httpd.conf to AllowOverride and specifically with the following code: <Directory "/home/abrahamb2/galaxy-dist"> Options Indexes FollowSymLinks AllowOverride AuthConfig Order allow,deny Allow from all AuthType Basic AuthName Galaxy AuthUserFile /usr/local/apache/.htpasswd Require valid-user </Directory> I previously tried to put galaxy-dist within /usr/local/apache/cgi-bin which not only failed but read on the wiki is not a great idea. Do you have any further suggestions for security configuration of this local installation? Thank you, ~Brian J. Abraham Predoctoral Bioinformatics Fellow with Boston University Lab of Molecular Immunology National Heart, Lung and Blood Institute National Institutes of Health 10 Center Drive - Room 7B20A Bethesda, MD 20892

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multiple data types
by Davide Cittaro 29 Sep '10

29 Sep '10

Hi all, I see there's a wig -> bigwig converter that uses the wigToBigWig utility... as it accepts bedgraph files also, it would be great if one can feed the same utility with bdg files too... How can I enable multiple data types here: <param format="wig" name="input1" type="data" label="Convert"> ? d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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How to make the "Display data in browser" works?
by Zhe Chen 29 Sep '10

29 Sep '10

Hi, I implement my own tool. The tool return results as html. But the eye button on the panel, which is "Display data in browser" button, does not work, when I set data format to html. I tried to set it to text, it asks me to download a bin file when clicking on the eye button. I also tried tabular, it shows nothing when I click the eye button. BTW, can you tell me what kind of data format Galaxy supports? Thanks

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Reduce logging on missing tool XML file
by Peter 29 Sep '10

29 Sep '10

Hi all, I've got a patch to reduce the noise in the log output when a tool XML file is missing, e.g. galaxy.tools ERROR 2010-09-29 11:34:43,111 error reading tool from path: ./tools/data_source/hapmapmart.xml Traceback (most recent call last): File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py", line 75, in load_tool tool = self.load_tool( path ) File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py", line 133, in load_tool tree = util.parse_xml( config_file ) File "/Users/xxx/repositories/galaxy-central/lib/galaxy/util/__init__.py", line 102, in parse_xml tree = ElementTree.parse(fname) File "/Users/xxx/repositories/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.5.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/Users/xxx/repositories/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.5.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/hapmapmart.xml' becomes: galaxy.tools ERROR 2010-09-29 11:36:03,982 Tool file missing: ./tools/data_source/hapmapmart.xml Changeset here: http://bitbucket.org/peterjc/galaxy-central/changeset/5c9046c8bb08 Peter

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