[galaxy-dev] 8-bit bytestrings
Hi, I am new to Galaxy and have not found a solution on dev-list to this 8-bit bytestrings error. That occurs on my local installation but not on Galaxy main server. Cheers Dataset generation errors *Dataset 22: Neighbor Joining Tree on data 20* The Galaxy framework encountered the following error while attempting to run the tool: Traceback (most recent call last): File /data/APPLIS/GALAXY/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 123, in run_job job_wrapper.finish( stdout, stderr ) File /data/APPLIS/GALAXY/galaxy-dist/lib/galaxy/jobs/__init__.py, line 573, in finish self.sa_session.flush() File /data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py, line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File /data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py, line 1356, in flush self._flush(objects) File /data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py, line 1434, in _flush flush_context.execute() File /data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 261, in execute UOWExecutor().execute(self, tasks) File /data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 753, in execute self.execute_save_steps(trans, task) File /data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 773, in execute_save_steps self.execute_cyclical_dependencies(trans, task, False) File /data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 789, in execute_cyclical_dependencies self.execute(trans, [t], isdelete) File /data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 753, in execute self.execute_save_steps(trans, task) File /data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 768, in execute_save_steps self.save_objects(trans, task) File /data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py, line 759, in save_objects task.mapper._save_obj(task.polymorphic_tosave_objects, trans) File /data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py, line 1413, in _save_obj c = connection.execute(statement.values(value_params), params) File /data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py, line 824, in execute return Connection.executors[c](self, object, multiparams, params) File /data/APPLIS/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 /data/APPLIS/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 /data/APPLIS/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 /data/APPLIS/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) ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings. u'UPDATE history_dataset_association SET update_time=?, info=?, blurb=?, peek=? WHERE history_dataset_association.id = ?' ['2012-09-04 06:23:08.928377', 'Single Alignment Analyses\nsh: /data/APPLIS/GALAXY/galaxy-dist/tool-data/HYPHY/HYPHY: Aucun fichier ou r\xc3\xa9pertoire de ce type\n', 'error', 'no peek', 55] -- Gauthier Jean-Pierre. Bio-informatique. INRA. UMR IGEPP. Domaine de la Motte. BP. 35327. 35653 LE RHEU CEDEX. tel : 33(0)2.23.48.51.68 fax : 33(0)2.23.48.51.50 mail : jean-pierre.gauth...@rennes.inra.fr ___ 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] Filter options for type=select based on former selection
Hi all! I am facing a simple problem but can?t find a solution to solve it. Before I start describing my problem here is the code from my tool: conditional name=sReference param name=reference type=select label=Select a reference genome help= option value=mm9_64mm9_64/option option value=hg19hg19/option option value=customcustom (from history, fasta)/option /param when value=mm9_64 param name=ref type=hidden value=7596a73211022433 / /when when value=hg19 param name=ref type=hidden value=f73725d4339c9140 / /when when value=custom param name=ref type=hidden value=b5d0b09143f99c68 / param name=cReference format=fasta type=data label=Select the reference genome / /when /conditional conditional name=sCuffcompare param name=cuffcompare type=boolean truevalue=yes falsevalue=no label=Run Cuffcompare? help= / when value=yes conditional name=sRefannotation param name=refannotation type=select label=Will you select a reference annotation from your history or use a GATC supported one? help= option value=no_refNo reference annotation/option option value=supportedSupported/option option value=historyHistory/option /param when value=supported param name=index type=select label=Select reference annotation help= options from_file=gatc_transcriptome_annotations.loc column name=name index=2 / column name=value index=3 / filter type=sort_by column=2 / filter type=param_value ref=sReference.reference column=0/ validator type=no_options message=No annotations are available for the selected reference genome/ /options /param /when when value=history param name=cAnnotation format=gtf type=data label=Select the reference annotation / /when when value=no_ref / /conditional /when when value=no / /conditional As you might see from the code above I am trying to filter the contents for param name=index type=select label=Select reference annotation help= based on the selected value in param name=reference type=select label=Select a reference genome help= (filter type=param_value ref=sReference.reference column=0/). As soon as I try to load this configuration I get the error KeyError: ?sReference.reference?. So it seems, that the tool cannot access the key sReference.reference. I figured out that the tool can access only the top key from the conditional, i.e. I can use filter type=param_value ref=sReference column=0/ and no error appears while reloading the tools config. But this is not useful because sReference does not contain any value for filtering. Does anybody know how the tool can access variables/keys under a conditonal tag without being within the conditional tag itself? Thanks for any help/hints/advice! Cheers, Sascha ___ 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] Toolsheds and job runners
I've inherited a galaxy setup from someone (details: a contractor set it up but left it unfinished so I'm completing the job while discovering and documenting what was done). The catch: it's setup as a twin galaxy instance with one as a front-end web-server and the other as the job runner. Admittedly the documentation is lighter on this sort of setup, but I've been able to puzzle it out until getting to the issue of toolsheds. We have a large number of custom tools we want to install from our own toolshed and the main Galaxy one. The problem: I'm not clear on how this supposed to work. Once I started installing tools, of course they all appeared in the front-end toolshed and are running on the front-end. Understandable - but not what I wanted. Does this mean that for every custom tool I install, I have to go to every Galaxy instance (frontend and job-runners) and install the tools into their toolshed? It would seem so, but this seems ... awkward. tl;dr: Toolsheds and job-ruuners - how is that supposed to work? Is there a convenient way to handle this? Any pointers to documentation or experience? -- Paul Agapow (p...@agapow.net) ___ 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] Tool shed empty
Ahh.. Just realized that the installation to local galaxy is done from the web runner interface...under search and browse toolsheds...forgotten about that one! :) On Tue, Sep 4, 2012 at 2:13 PM, Ivan Lovric i...@genome.edu.au wrote: Hi there, I've been having some trouble with the Tool Shed recently. This image from the ToolShed wiki http://wiki.g2.bx.psu.edu/Tool%20Shed?action=AttachFiledo=gettarget=user_register.png Suggests that there is a Browse all repositories link on the side panel in the non-admin interface, however the link seems to only appear on the admin interface. After some digging around, I've realized that the link really is formed only for the admin interface (see: templates/webapps/community/admin/index.mako). I guess it's been removed at some stage (however looking at the hg logs for this file didn't help me figure out when). But back to the real problemclicking on Browse by category yields nothing - everything is empty. A bit about the configurations I tested... galaxy-central AND galaxy-dist - minimal configuration (setting database_file in community_wsgi.ini and unsetting it (same outcome)). One thing that has led me to believe that there is something quite wrong in my configuration is that there is no hgweb.config file created (apparently it should be created once the toolshed starts). Right now I'm looking around the hg/mercurial related code in the community/ dirs but I'm not getting very far...the HgController class is loaded but none of its methods ever get called (nor can I find out from the code where they're supposed to be called from). Has anyone else had this problem? I remember a few weeks ago on a clean galaxy-dist I had (lost now), I was able to see the repositories as per the user_register.png image above. Since then I've made new VM images and lost the original galaxy-dist so I can't go back and figure out what was different on that configuration...I'd very much appreciate any thoughts on this. Thanks! Ivan ___ 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] Filter options for type=select based on former selection
Hi Sascha I don't quite understand your question... $sReference.ref is the variable you are looking for, isn't-it? Regards, Hans On 09/04/2012 11:40 AM, Sascha Kastens wrote: Hi all! I am facing a simple problem but can’t find a solution to solve it. Before I start describing my problem here is the code from my tool: conditional name=sReference param name=reference type=select label=Select a reference genome help= option value=mm9_64mm9_64/option option value=hg19hg19/option option value=customcustom (from history, fasta)/option /param when value=mm9_64 param name=ref type=hidden value=7596a73211022433 / /when when value=hg19 param name=ref type=hidden value=f73725d4339c9140 / /when when value=custom param name=ref type=hidden value=b5d0b09143f99c68 / param name=cReference format=fasta type=data label=Select the reference genome / /when /conditional conditional name=sCuffcompare param name=cuffcompare type=boolean truevalue=yes falsevalue=no label=Run Cuffcompare? help= / when value=yes conditional name=sRefannotation param name=refannotation type=select label=Will you select a reference annotation from your history or use a GATC supported one? help= option value=no_refNo reference annotation/option option value=supportedSupported/option option value=historyHistory/option /param when value=supported param name=index type=select label=Select reference annotation help= options from_file=gatc_transcriptome_annotations.loc column name=name index=2 / column name=value index=3 / filter type=sort_by column=2 / filter type=param_value ref=sReference.reference column=0/ validator type=no_options message=No annotations are available for the selected reference genome/ /options /param /when when value=history param name=cAnnotation format=gtf type=data label=Select the reference annotation / /when when value=no_ref / /conditional /when when value=no / /conditional As you might see from the code above I am trying to filter the contents for param name=index type=select label=Select reference annotation help= based on the selected value in param name=reference type=select label=Select a reference genome help= (filter type=param_value ref=sReference.reference column=0/). As soon as I try to load this configuration I get the error KeyError: ’sReference.reference’. So it seems, that the tool cannot access the key sReference.reference. I figured out that the tool can access only the top key from the conditional, i.e. I can use filter type=param_value ref=sReference column=0/ and no error appears while reloading the tools config. But this is not useful because sReference does not contain any value for filtering. Does anybody know how the tool can access variables/keys under a conditonal tag without being within the conditional tag itself? Thanks for any help/hints/advice! Cheers, Sascha ___ 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] Filter options for type=select based on former selection
Hi Hans! I try to clarify my problem: The user selects a reference genome from param name=reference type=select label=Select a reference genome help=. So in my scenario the value for $sReference.reference will be either mm9_64 or hg19. This value is needed to filter the supported reference annotations in case the user wants cuffcompare to be run. That?s why I need filter type=param_value ref=sReference.reference column=0/ I hope this brings some light in my problem ;-) Cheers, Sascha Original Message processed by CONSOLIDATE Subject: Re: [galaxy-dev] Filter options for type=select based on former selection Sent: Dienstag, 4. September 2012 12:56 From: Hans-Rudolf Hotz (h...@fmi.ch) Hi Sascha I don?t quite understand your question... $sReference.ref is the variable you are looking for, isn?t-it? Regards, Hans On 09/04/2012 11:40 AM, Sascha Kastens wrote: Hi all! I am facing a simple problem but can t find a solution to solve it. Before I start describing my problem here is the code from my tool: falsevalue=no label=Run Cuffcompare? help= / help= column=0/ label=Select the reference annotation / As you might see from the code above I am trying to filter the contents for based on the selected value in label=Select a reference genome help= (). As soon as I try to load this configuration I get the error KeyError: sReference.reference . So it seems, that the tool cannot access the key sReference.reference. I figured out that the tool can access only the top key from the conditional, i.e. I can use ref=sReference column=0/ and no error appears while reloading the tools config. But this is not useful because sReference does not contain any value for filtering. Does anybody know how the tool can access variables/keys under a conditonal tag without being within the conditional tag itself? Thanks for any help/hints/advice! Cheers, Sascha ___ 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] Toolsheds and job runners
Hi Paul, In case you are not aware of it, the Galaxy tool shed wiki explains the tool shed: http://wiki.g2.bx.psu.edu/Tool%20Shed On Sep 4, 2012, at 6:25 AM, Paul-Michael Agapow wrote: I've inherited a galaxy setup from someone (details: a contractor set it up but left it unfinished so I'm completing the job while discovering and documenting what was done). The catch: it's setup as a twin galaxy instance with one as a front-end web-server and the other as the job runner. Just to confirm, you have set up a single Galaxy instance (with a single database on the back-end) with multiple web front-ends - is this correct? Admittedly the documentation is lighter on this sort of setup, but I've been able to puzzle it out until getting to the issue of toolsheds. We have a large number of custom tools we want to install from our own toolshed and the main Galaxy one. The problem: I'm not clear on how this supposed to work. Once I started installing tools, of course they all appeared in the front-end toolshed and are running on the front-end. Understandable - but not what I wanted. Does this mean that for every custom tool I install, I have to go to every Galaxy instance (frontend and job-runners) and install the tools into their toolshed? It would seem so, but this seems ... awkward. The Galaxy tool shed is a separate application that has no dependencies on a Galaxy instance (and vice-versa), although a Galaxy instance and a tool shed instance can each communicate with the other, so your question is a bit confusing. A single Galaxy tool shed can be used by any number of Galaxy instances, so if you create a repository in a tool shed instance and upload tools to it, any number of Galaxy instances will be able to access that tool shed and install the repositories from it. Keep in mind that if you are, in fact, running a single Galaxy instance with multiple web front-ends, automatically installing a tool into that galaxy instance from the tool shed will result in displaying the tool only in the web front-end in which it was installed. Your Galaxy server will need to be stopped and restarted in order for the installed tools to be available in all of the web front-ends you've configured in your Galaxy instance. Again, this has nothing to do with any tool shed instances that you may have configured in your Galaxy instance. tl;dr: Toolsheds and job-ruuners - how is that supposed to work? Is there a convenient way to handle this? Any pointers to documentation or experience? -- Paul Agapow (p...@agapow.net) ___ 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] Programmatically deleting data sets from data libraries?
Hi, Galaxy Developers,
I apologize for resurrecting another old thread
(http://dev.list.galaxyproject.org/delete-data-library-via-API-td4553000.html),
and for this long-winded email...
First things first, I am trying to confirm what is suggested in the thread
cited above (that data sets cannot be deleted from a Galaxy data library via
the API). I am trying to confirm this because I have a vested interested in
performing this operation to the extent that I've started investigating
modifying the PostgreSQL tables directly if it can't be done via the API (more
about this later).
The gist of why I am trying to programmatically delete data from a data library
is because I am trying to write/implement some custom python code that
maintains consistency between a folder on the local filesystem and a
corresponding Galaxy data library (i.e bi-directional synchronization). I need
do do this in an automated fashion to account for the following two conditions;
1) The file on the filesystem gets deleted (i.e. the path that is referenced in
the data library is no longer valid).
2) The MD5 of the file on the filesystem changes (i.e. the file was replaced or
modified, and needs to be re-imported such that the correct metadata (i.e. file
size) is reported via the Galaxy UI).
Based on the limited amount of testing I have done, it doesn't appear to be
possible to delete an actual data set from the data library via the API. Here
is a test that leads me to believe that this is not possible;
1) I can delete a data library successfully without issue; Here is the output
of me doing so:
--(galaxy@crigalaxy)-(/group/galaxy/galaxy-dist/scripts/api)--
./delete.py 11f3cb91acb2ab1677f8265b
http://localhost:8081/api/libraries/e85a3be143d5905b
Response
{'synopsis': 'dansully', 'description': 'dansully', 'name': 'dansully'}
--(galaxy@crigalaxy)-(/group/galaxy/galaxy-dist/scripts/api)--
2) Whenever I try to delete an item in the data library, I get a 404, with the
response no action found for ...
--(galaxy@crigalaxy)-(/group/galaxy/galaxy-dist/scripts/api)--
./display.py 11f3cb91acb2ab1677f8265b
http://localhost:8081/api/libraries/e85a3be143d5905b/contents/62e564808c5368d4
Member Information
--
ldda_id: 62e564808c5368d4
misc_blurb: 2 lines
name: whatever.txt
data_type: txt
file_name: /group/galaxy/galaxy-dist/database/files/008/dataset_8938.dat
uploaded_by: dansu...@uchicago.edu
template_data: {}
genome_build: ?
model_class: LibraryDataset
misc_info: uploaded txt file
file_size: 329
metadata_data_lines: 2
message:
id: 62e564808c5368d4
date_uploaded: 2012-08-29T15:48:38.335445
metadata_dbkey: ?
--(galaxy@crigalaxy)-(/group/galaxy/galaxy-dist/scripts/api)--
./delete.py 11f3cb91acb2ab1677f8265b
http://localhost:8081/api/libraries/e85a3be143d5905b/contents/62e564808c5368d4
HTTP Error 404: Not Found
404 Not Found
The resource could not be found.
No action for /api/libraries/e85a3be143d5905b/contents/62e564808c5368d4
--(galaxy@crigalaxy)-(/group/galaxy/galaxy-dist/scripts/api)--
My hope of being able to actually use the API for a delete is that I am either
not forming the URL string to correctly delete the data set, or the data{} dict
implements a key that I am not aware of (it is my understanding that the Galaxy
API is still under active development; so far I have not been able to locate
any documentation that suggests any keys or attributes (other than the example
code distributed)) that will make a delete operation for an individual data set
feasible. Would it be possible for somebody with specific knowledge of the
Galaxy API to comment on whether or not this functionality is implemented?
All of this being said, if it is *not* possible to delete an individual data
set from the Galaxy API, I am prepared to make a 'reasonable' effort to try and
do this by modifying the galaxy back-end SQL tables directly. Based on the
research I have done (I have enabled mod logging on the PostgreSQL database),
here is what a delete operation from the Galaxy UI looks like in terms of
database changes:
2012-08-29 08:44:20.361
CDT,galaxy_,galaxy,7952,127.0.0.1:46174,503e1a8d.1f10,41,idle in
transaction,2012-08-29 ent: UPDATE library_dataset SET
update_time='2012-08-29T13:44:20.361070', deleted=true WHERE library_dataset.id
= 6013,$
So, at this point (assuming that I cannot delete the data set from the Galaxy
API), I'm trying to work backwards from information I know (i.e. file_name or
ldda_id) to discern the library_dataset.id (I'm still digging through database
query logs to try to determine how this is done (it appears that there are more
than one query executed when a data library is rendered via the Galaxy UI).
Determining the id of the dataset in question continues to be an ongoing
challenge.
Which leads me to one final last question. Could anybody tell me how the ID's
(the ldda_id) that get returned by the Galaxy API are
[galaxy-dev] password param type
Hi, Kind of feature request: parameter of type 'password' so that an entered password is not shown in the html form nor in the logs. Or is there already a way to achieve this that I missed out ? Cheers, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] using data_ref to refer to column names?
So, sounds like maybe this feature does not existI'd like to request it (given a dataset, I'd like to be able to show the column headers of that dataset in a select box). Thanks, Dan On Wed, Aug 29, 2012 at 11:09 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hi, I have some code that makes a plot and creates a legend from a given column name in the user's input data, which may have arbitrary column names. I'd like to create a dropdown list that has all the column names in it, but I don't know the names beforehand; I won't know them until the user uploads their data file. So all I can do is have a freeform text box where I ask the user to type a column name, which seems error-prone and ugly. I notice that the XY plotting tool has something sort of like this, where it can tell how many columns are in your dataset and lets you choose them, but it calls the columns c1, c2, etc. My datasets have a header line with column names and I want to show the actual column name, not reference them by column number. Is this possible? Is there a solution to this? I have a number of use cases like this, so it would be great if there was. Thanks, Dan ___ 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] Getting syntax error on Join + environment_setup_file not read
On Jul 28, 2012, at 8:09 PM, Peter Schmitt wrote: New galaxy install. Running the tutorial Galaxy 101 and trying to do the join. Get the following error in the stderr of the job: Traceback (most recent call last): File /opt/galaxy/galaxy-dist/tools/new_operations/gops_join.py, line 20, in ? from galaxy.tools.util.galaxyops import * File /opt/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py, line 15, in ? from galaxy import util, jobs, model File /opt/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 15, in ? from galaxy import util, model File /opt/galaxy/galaxy-dist/lib/galaxy/model/__init__.py, line 13, in ? import galaxy.datatypes.registry File /opt/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line 146 finally: ^ SyntaxError: invalid syntax Traceback (most recent call last): File ./scripts/set_metadata.py, line 24, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File /opt/galaxy/galaxy-dist/lib/galaxy/model/__init__.py, line 13, in ? import galaxy.datatypes.registry File /opt/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line 146 finally: ^ SyntaxError: invalid syntax Hi Pete, It looks like the version of Python your tools are running is 2.4. Please make sure that `python` as executed on the cluster is = 2.5. Also I believe the line, environment_setup_file = scripts/galaxy.sh, is not being used any longer. When I put the line: export DRMAA_LIBRARY_PATH=/opt/drmaa/1.0.12/lib/libdrmaa.so.1.0.12, in there the server didn't see it. When I added that line to the top of run.sh, it does. environment_setup_file is not applied to the Galaxy server, it's sourced in the environment in which tools are run. Anything that needs to be set in the environment for Galaxy itself to run should be done elsewhere, such as run.sh, ~/.profile, etc. --nate -- Pete Schmitt Technical Director: Discovery Cluster NH INBRE Grid Computational Genetics Lab Dartmouth College, HB 6223 L24 Berry/Baker Library Hanover, NH 03755 Phone: 603-646-8109 http://discovery.dartmouth.edu http://columbia.dartmouth.edu/grid http://www.epistasis.org Mail Attachment.jpeg ___ 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] Automatic installation of third party dependancies
I've put together a tool wrapper for the htseq-count script that is part of the HTSeq python package and uploaded that to the tool shed. However, I have discovered that the tool dependancies do not install properly. There are a couple of issues that I've run into. 1) The biggest issue is the inability to set both the PYTHONPATH and PATH environment variables as part of installation. If I put two separate action type=set_environment tags, then the second overwrites the first in the env.sh file. If instead, I put two environment_variable tags within the action, only one (the second) gets executed during installation. 2) Another issue is the inability to install Numpy as a dependancy to HTSeq. I can get Numpy to install, but it won't be in the PYTHONPATH when HTSeq is installed (or executed). Any thoughts on how to address these issues would be appreciated. -- 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] Migrate Galaxy database from MySQL to Postgres
Dear list members, Did anyone migrate the Galaxy database from MySQL to Postgres lately? Any verified script available? Simple solution by adding a postgres flag in mysqldump (http://dev.list.galaxyproject.org/MySQL-2-Postgres-td4139570.html) didn't work for me. It throws lots of syntax errors on int(), double quote, etc. My mysql version: 14.14, distribution 5.5.25a My postgres version: 9.1 I am now on a quest following the suggested list at: http://wiki.postgresql.org/wiki/Converting_from_other_Databases_to_PostgreSQL#Scripts.2C_programs I appreciate if someone can share his or her experience on this. Thanks a lot, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nl Skype: leon_meiMobile: +31 6 41709231 ___ 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] Automatic installation of third party dependancies
Hi Lance, Thanks for reporting these issues - the tool dependencies component is fairly new, so you may have uncovered some problems that need correction. I'll take a look at these. make corrections if necessary, and get back to you when all is functional. Thanks! Greg Von Kuster On Sep 4, 2012, at 3:15 PM, Lance Parsons wrote: I've put together a tool wrapper for the htseq-count script that is part of the HTSeq python package and uploaded that to the tool shed. However, I have discovered that the tool dependancies do not install properly. There are a couple of issues that I've run into. 1) The biggest issue is the inability to set both the PYTHONPATH and PATH environment variables as part of installation. If I put two separate action type=set_environment tags, then the second overwrites the first in the env.sh file. If instead, I put two environment_variable tags within the action, only one (the second) gets executed during installation. 2) Another issue is the inability to install Numpy as a dependancy to HTSeq. I can get Numpy to install, but it won't be in the PYTHONPATH when HTSeq is installed (or executed). Any thoughts on how to address these issues would be appreciated. -- 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/ ___ 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] using data_ref to refer to column names?
On Tue, Sep 4, 2012 at 4:54 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: So, sounds like maybe this feature does not existI'd like to request it (given a dataset, I'd like to be able to show the column headers of that dataset in a select box). Thanks, Dan No, it doesn't, but I'd like it too: https://bitbucket.org/galaxy/galaxy-central/issue/554/show-column-names-headers-or-first-entry Peter ___ 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] using data_ref to refer to column names?
On Tue, Sep 4, 2012 at 4:57 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Sep 4, 2012 at 4:54 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: So, sounds like maybe this feature does not existI'd like to request it (given a dataset, I'd like to be able to show the column headers of that dataset in a select box). Thanks, Dan No, it doesn't, but I'd like it too: https://bitbucket.org/galaxy/galaxy-central/issue/554/show-column-names-headers-or-first-entry Thanks much. Strong +1 from me. Dan Peter ___ 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/
