[galaxy-dev] Two questions
Hello, Just want to clarify two questions: 1) Is there a way to get the absolute path of a dataset directly from the interface? This is sometimes useful to create a local directory of all required files (by using symlink) if we know the full path. 2) How do we create a data library from datasets from multiple saved histories? I could see upload dataset from current history option in Add dataset of DataLibrary, but what is the case if files to be uploaded are distributed in many histories? Do we can another way to accomplish this? Best, Raj This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] MySQL problem at startup
Derar all,
I have recently moved from galaxy-central to galaxy-dist and all seems
to work fine except that everytime I start a new session (ie: I go to my
galaxy with my browser), I get the error below. I just need to reload
the page and all is fine again.
I would mention that while the whole 'dist' is original, the ./database/
directory is a mere copy (and updated) of the one I had in
galaxy-central. Needless to say that the MySQL engine is never down :)
Any help is most than welcome
Thanks a million!
Here's the error I get.
URL: http://galaxy.cbs.dtu.dk/galaxy/
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.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-py2.7.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.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-py2.7.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 111 in __call__
return self.app( environ, start_response )
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.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
134 in __call__
trans = self.transaction_factory( environ )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 187 in lambda
self.set_transaction_factory( lambda e: self.transaction_chooser( e,
galaxy_app, session_cookie ) )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 207 in transaction_chooser
return GalaxyWebUITransaction( environ, galaxy_app, self,
session_cookie )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 870 in __init__
self._ensure_valid_session( session_cookie )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 351 in _ensure_valid_session
self.app.model.GalaxySession.table.c.is_valid==True ) ) \
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py',
line 1300 in first
ret = list(self[0:1])
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py',
line 1221 in __getitem__
return list(res)
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py',
line 1361 in __iter__
return self._execute_and_instances(context)
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py',
line 1364 in _execute_and_instances
result = self.session.execute(querycontext.statement,
params=self._params, mapper=self._mapper_zero_or_none())
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py',
line 755 in execute
clause, params or {})
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py',
line 824 in execute
return Connection.executors[c](self, object, multiparams, params)
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.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-py2.7.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-py2.7.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-py2.7.egg/sqlalchemy/engine/base.py',
line 931 in _handle_dbapi_exception
raise exc.DBAPIError.instance(statement, parameters, e,
connection_invalidated=is_disconnect)
OperationalError: (OperationalError) (2006, 'MySQL server has gone
away') u'SELECT galaxy_session.id AS galaxy_session_id,
galaxy_session.create_time AS galaxy_session_create_time,
galaxy_session.update_time AS galaxy_session_update_time,
galaxy_session.user_id AS galaxy_session_user_id,
galaxy_session.remote_host AS galaxy_session_remote_host,
galaxy_session.remote_addr AS galaxy_session_remote_addr,
galaxy_session.referer AS galaxy_session_referer,
galaxy_session.current_history_id AS galaxy_session_current_history_id,
galaxy_session.session_key AS galaxy_session_session_key,
galaxy_session.is_valid AS galaxy_session_is_valid,
galaxy_session.prev_session_id AS galaxy_session_prev_session_id,
galaxy_session.disk_usage AS galaxy_session_disk_usage
Re: [galaxy-dev] Two questions
On Apr 9, 2012, at 3:04 AM, Praveen Raj Somarajan wrote: Hello, Just want to clarify two questions: 1) Is there a way to get the absolute path of a dataset directly from the interface? This is sometimes useful to create a local directory of all required files (by using symlink) if we know the full path. Hi Raj, I'm not clear on whether you mean programmatically or not. If not, you can see the paths to library datasets from their info page if you're an admin. For history datasets, it's not possible to do from the interface, and you have to use the script galaxy-dist/scripts/helper.py. 2) How do we create a data library from datasets from multiple saved histories? I could see upload dataset from current history option in Add dataset of DataLibrary, but what is the case if files to be uploaded are distributed in many histories? Do we can another way to accomplish this? There's not a way to do this, unfortunately, without switching to the history that you wish to import from. --nate Best, Raj This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Tasks do not start
On Apr 6, 2012, at 2:31 PM, Robert Chase wrote: Hello, On our test instance of galaxy we have set up filesharing with the rest of our cluster. We have also setup LDAP authentication on the server. We are having problems getting data from the tools based on data_source.py. For instance, if we try to run ucsc main then we can click on get output and then send query to galaxy we do not get a green screen saying that our task has started, we are redirected right back to the welcome screen. No tasks appear in our history. Has anyone encountered this before? Hi Rob, If your proxy is using https, be sure to set the X-URL-SCHEME header as described in the documentation. My guess would be that UCSC is POSTing the form back to your http address, which then redirects to https without the path, arguments, or form contents. --nate -Rob ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Same error in multiple tools
On Mar 30, 2012, at 5:53 AM, Alban Lermine wrote: Hi, It seems that PYTHONPATH isn't set when galaxy start.. (according to http://osdir.com/ml/galaxy-development-source-control/2011-11/msg00035.html) Should I search this way ? Hi Alban, Galaxy should be setting PYTHONPATH itself, it's only necessary to set it if you are trying to run some of the tools from outside Galaxy. Could you set cleanup_job = never in your Galaxy config and check the PBS script (the path to it should be output to the log when you run a job). The script should have this at the top: GALAXY_LIB=/path/to/galaxy-dist/lib if [ $GALAXY_LIB != None ]; then if [ -n $PYTHONPATH ]; then export PYTHONPATH=$GALAXY_LIB:$PYTHONPATH else export PYTHONPATH=$GALAXY_LIB fi fi --nate Thanks by advance, Alban Alban Lermine wrote: Hi, I'm running these tools on a cluster.. Alban Emil Bouvier wrote: Alban, Are you running these tools on a cluster, or on a local system? Dave B. On 3/19/12 6:55 AM, Alban Lermine wrote: Hi, I have the same error message for multiple tools (GFFtoBED, BEDtoBIGBED,BAMtoSAM,...): /from galaxy import eggs ImportError: No module named galaxy It's happening only since the last upgrade, do you know what is going wrong? Thanks, Alban / -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Tool Requirement tag and dependency management
I recently ran into a problem where the tool-dependency env.sh file was not getting sourced for a particular tool. I realized that the problem was in how the tool 'requirement' tag was specified. The requirement tag was specified as in the Tool Config Syntax documentation (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crequirement.3E_tag_set): requirements requirement type=binarytaxBuilder/requirement /requirements However, it appears that the type must be set to package in order for the dependency system to source the env.sh file (http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies): requirements requirement type=packagetaxBuilder/requirement /requirements I'm working on getting this working with bedtools, and I'm wondering what the recommended way to do this would be. Since there are various binaries for this package, I'm thinking I could do something like: requirements requirement type=packagebedtools/requirement requirement type=binarygenomeCoverageBed/requirement /requirements Secondly, once this is sorted out, it would be nice to update the Tool Config Syntax documentation. Thanks in advance for any advice. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] samtools BAM to SAM tmp directory
Is there a reason that the samtools BAM to SAM does not respect the new_file_path set in the config file? The tmp directory handling by different tool wrappers seems to be an issue right now on systems with small system tmp directories. -- Matt Shirley Ph.D Candidate - BCMB Pevsner Lab http://pevsnerlab.kennedykrieger.org/ Johns Hopkins Medicine ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Toolshed tribulations--certain types seem unsupported
I am testing galaxy for wide use, and I have legacy text files that call algorithms, sorts, and displays. One such has a tool.xml file with 10 parameters, one select, three integer, and one float, with the rest text for the moment. (some will be type=data later if the runs equate to the runs we do outside galaxy) The tool does not show up. Firefox, emacs and vim all agree that it is well-formed, and galaxy has been properly bounced. I experimented with removing parameters and found with 7 parameters, I did not have the problem, then I noticed that all of them had been changed to text or select in my desperation to make it show up for placement on the workflow. I returned to 10 parameters, but this time all type=select and type=text, and everything worked. But slipping even one integer, even with the (optional) min max and default tags, and the tool would disappear on restart. Am I looking at a bug, or is there something I need to be doing to make this tool visible with numeric parameters? MGM ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] [galaxy-user] permissions on folder created by Galaxy
Hello, I am going to forward your question over to the galaxy-...@bx.psu.edu mailing list so that it can get more visibility in the development community. That list is probably where you will want to post regarding similar topics in the future: http://wiki.g2.bx.psu.edu/Support#Mailing_Lists To get things started, I am wondering if you are asking about datasets in histories or data in libraries? Parts of your question seem to refer to both, or I have misunderstood (my apologies!). If about data in libraries, then you can get around this by not actually moving the data into the Galaxy directory structure at all, and instead just link in data from some other location on the filesystem (where you can control the permissions). See the Copy data into Galaxy? No option described on this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Other data/lib/security related links, mostly admin UI: http://wiki.g2.bx.psu.edu/Learn/Security Features http://wiki.g2.bx.psu.edu/Admin/Data Libraries/Libraries http://wiki.g2.bx.psu.edu/Admin/Data Libraries/Library Security Hopefully this helps or some more discussion on the galaxy-dev list about your question will find a solution, Jen Galaxy team On 4/6/12 2:42 AM, Guilhem Sempéré wrote: Hi, I would like folders created by Galaxy under the location defined by the file_path parameter (which defaults to database/files) to be created with permissions 775 instead of 755. Is this possible? The reason for me asking this question is that I have developed an external tool (running under Tomcat) for feeding Galaxy libraries. And my tomcat user needs to be allowed to write to the mentioned folders. Any ideas? G. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
