April 2015 - galaxy-dev - lists.galaxyproject.org

Running jobs as real user and extra_file_path
by Louise-Amélie Schmitt 28 Apr '17

28 Apr '17

Hi everyone, I just wanted to ask how the extra_file_path is handled in case of job running as the real user since the file_path is only writable by the galaxy user. Any clue? Thanks, L-A

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Re: [galaxy-dev] how to create users through Galaxy API?
by Martin Čech 03 Sep '16

03 Sep '16

Hi, you specify username, password and email in the body (payload) of the POST as Key:Value pairs. Code from the API method: ( https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/ga…) username = payload[ 'username' ] email = payload[ 'email' ] password = payload[ 'password' ] There are also other conditions that need to be fulfilled (e.g. user creation has to be turned on in the configuration) - you will find these when you look at the source code of the method (because the documentation is not perfect yet, sorry). M. On Sun, Dec 29, 2013 at 11:22 PM, xlwang <xlwang_0903(a)163.com> wrote: > hi, > I still have some confusion. > post /api/users , when i use postman, it seems like this: > > > No other parameters? How to confirm the new user's information?Such as > user name, password. > Can you give me a example please?Thank you! > > At 2013-12-30 06:04:15,"Martin Čech" <marten(a)bx.psu.edu> wrote: > > Hello, > > to create a user through API you send a POST request to /api/users > > More information about User API here: > > > https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.… > > Martin > > > On Fri, Dec 27, 2013 at 5:11 AM, xlwang <xlwang_0903(a)163.com> wrote: > >> hello, >> I want to create users through Galaxy API.For example, I can get users >> information through url like this(use postman): >> http://localhost:8080/api/users?key=my_key >> But how to create a user? >> >> >> >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > > >

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error loading files into galaxy
by Hakeem Almabrazi 04 Mar '16

04 Mar '16

Hi, I started getting the following error whenever I try to load a file into Galaxy local. Traceback (most recent call last): File "/usr/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 8, in <module> from galaxy import eggs ImportError: cannot import name eggs I will appreciate if someone can tell me what could happen to cause such issue and how to resolve it. Regards,

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Upload issue in local installation
by Batsal Devkota 05 Feb '16

05 Feb '16

I installed galaxy locally in a linux server. However, I cannot upload the files (no matter how small, I have tried few kb size fasta files). When I try to upload, the link to the file shows up in the History and gets a new number (purple box). When I click on the link I get 'Dataset is uploading' forever. In the terminal window where I start galaxy, I get the following error report: 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://redhat:8080/root/tool_menu" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" The last line keeps going for ever... writes new line every 4 secs. I am stuck and don't know where to look. Please help. Batsal.

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Rename output from a repeat
by Ulf Schaefer 27 Aug '15

27 Aug '15

Hi all We frequently use the syntax below to rename outputs of workflows that we run in batch. It is convenient to have sample names from fastqs carried over to sams, bams, vcfs, etc. #{input1 | basename}.bam This does not seem to be working for inputs that are in repeats, e.g. the VelvetOptimiser. Does anybody know if there is a syntax to make this work, maybe #{repeatname[0].input1 | basename}.bam ? Thanks a lot for your help Ulf ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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Object-Store, setting filetypes crashes Galaxy
by bjoern.gruening＠googlemail.com 22 Jul '15

22 Jul '15

Hi, I have configured to use the hierarchical object store but as soon as I try to reset the filetpye of a dataset Galaxy is crashing with: galaxy.objectstore DEBUG 2014-06-12 14:39:21,180 Using preferred backend 'files3' for creation of MetadataFile 5963 132.230.153.57 - - [12/Jun/2014:14:39:20 +0200] "POST /datasets/966f24627ef70c12/edit HTTP/1.1" 500 - " http://galaxy.uni-freiburg.de/datasets/966f24627ef70c12/edit" "Mozilla/5.0 (X11; Linux x86_64; rv:29.0) Gecko/20100101 Fire fox/29.0" Error - <type 'exceptions.OSError'>: [Errno 2] No such file or directory: 'database/tmp/metadata_temp_file_1xnGcE' URL: http://galaxy.uni-freiburg.de/datasets/966f24627ef70c12/edit File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 295 in edit trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':data }, overwrite = False ) #overwrite is False as per existi ng behavior File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/actions/metadata.py', line 18 in execute overwrite, history, job_params ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/actions/metadata.py', line 79 in execute_via_app kwds = { 'overwrite' : overwrite } ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py', line 717 in setup_external_metadata shutil.copy( dataset.metadata.get( meta_key, None ).file_name, metadata_temp.file_name ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py', line 575 in file_name self._filename = abspath( tempfile.NamedTemporaryFile( dir = self.tmp_dir, prefix = "metadata_temp_file_" ).name ) File '/usr/local/python/2.7/lib/python2.7/tempfile.py', line 454 in NamedTemporaryFile (fd, name) = _mkstemp_inner(dir, prefix, suffix, flags) File '/usr/local/python/2.7/lib/python2.7/tempfile.py', line 235 in _mkstemp_inner fd = _os.open(file, flags, 0600) OSError: [Errno 2] No such file or directory: 'database/tmp/metadata_temp_file_1xnGcE' I have attached my object_store_conf.xml file. Thanks, Bjoern

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Parallelism using metadata
by Marco Albuquerque 06 Jul '15

06 Jul '15

Hello Galaxy Dev, I have a question regarding parallelism on a BAM file. I have currently implemented 3 split options for the BAM datatype 1) by_rname -> splits the bam into files based on the chromosome 2) by_interval -> splits the bam into files based on a defined bp length, and does so across the entire genome present in the BAM file 3) by_read -> splits the bam into files based on the number of reads encountered (if multiple files, all other files match the interval as the first) Now, as you can imagine, reading and writing large BAM files is a pain, and I personally think this is not the best solution for Galaxy. What I was hoping to implement (but don't know how) is to create a new metadata option in bam (bam.metadata.bam_interval) which would generate the interval without creating a new file (essentially, I would create a symbolic link to the old large file, and then update the metadata.bam_interval, this would contain some string of the form chrom:start-end which could then be used in a variety of tools which accept an interval as an option (for example samtools view)) This would be far more efficient then my first implementation, but the thing I don't know how to do is specify some kind of metadata at the split level. I was hoping maybe you could direct me to an example that does this? I have added the following to my metadata.py file: class IntervalParameter( MetadataParamter ) def __init__( self, spec ): MetadataParamter.__init__( self, spec ): self.rname = self.spec.get( "rname" ) self.start = self.spec.get( "start" ) self.end = self.spec.get( "end" ) def to_string(self): if self.rname = 'all': return '' else: return ''.join([self.rname, ':', self.start, '-', self.end]) And the following to my binary.py file: ### UNDER THE BAM CLASS MetadataElement( name="bam_interval", desc="BAM Interval", param=metadata.IntervalParameter, rname="all", start="", end="", visible=False, optional=True) I somehow want rname="all" to be the default, but upon parallelism, I want to be able to adjust this parameter in the split functions. So, <parallelism method="multi" split_inputs="normal,tumour" split_mode="by_interval" split_size="50000000" merge_outputs="output"/> Would actually change the metadata of each file, and not create sub-bams. PLEASE HELP!!! Marco

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Strange repository dependency behavior with toolshed-installed naive_variant_caller
by Brian Claywell 20 Jun '15

20 Jun '15

First, I'm at a bit of a loss to even describe what's going on, so I apologize in advance for a rambling bug report. Please bear with me! The naive_variant_caller tool was failing on our instance with "Failed to resolve dependency" errors on numpy, pyBamParser, and pyBamTools, despite the tool dependencies and their respective dependency packages being installed. I attempted to use the "repair repository" action on naive_variant_caller with no success. I then uninstalled naive_variant_caller, package_numpy_1_7, package_pybamparser_0_0_1, and package_pybamtools_0_0_1 and attempted to reinstall naive_variant_caller from scratch, again allowing Galaxy to manage the dependencies. This time, the dependencies resolved (at least as far as the "Building dependency shell command" messages were concerned), but naive_variant_caller still failed, this time with an import error: ImportError: No module named pyBamTools.genotyping.naive Digging around a little I found that the env.sh that was sourced for pyBamTools was looking for an env.sh in another pyBamTools revision directory, but the revision it was looking for didn't exist. Then I looked in the admin interface and saw that package_pybamtools_0_0_1 and package_pybamparser_0_0_1 were each installed twice; each had both the most recent revision and an older revision with the "updates are available" icon. At this point I uninstalled naive_variant_caller and all of its dependency packages again. I then installed naive_variant_caller from the toolshed *without* dependency management, and manually installed the required revisions of numpy, pybamparser, and pybamtools. Finally naive_variant_caller started working. However, naive_variant_caller is now shown in the admin interface as "Installed, missing repository dependencies", and the installed repository page shows that the dependencies are a very strange state (see attached screenshot). That is, the same revision of numpy is listed as installed twice, and the pybamparser and pybamtools dependencies are each listed as simultaneously installed and uninstalled. Can anyone shed some light on what could be happening and what to do about it? Is there some external way to verify the consistency of a tool and its dependencies? Thanks! Cheers, Brian -- Brian Claywell | programmer/analyst Matsen Group | http://matsen.fredhutch.org <http://matsen.fhcrc.org/> Fred Hutchinson Cancer Research Center

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Job submission failed
by Vipin TS 04 May '15

04 May '15

Hi dev-team, I am experiencing an issue with my production instance in dispatching the jobs. When I click on execute button, each tool page shows the popup error message as here: [image: Inline image 1] I am not sure what is happening, not getting any single line of error message in log file. Here is the version I am using: changeset: 17051:28113eeee212 branch: stable date: Mon Mar 16 22:38:27 2015 -0400 summary: Update tag latest_15.03 for changeset 9f40ff3e3fe1 any suggestions, Thank you! Vipin | Rätsch Lab

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use of copied history while original user account deleled (and purged)
by Olivia Doppelt-Azeroual 04 May '15

04 May '15

Dear Developers, We manage a Galaxy instance at Institut Pasteur where there are more than a hundred users. Among them there are postdocs that are meant to leave the institute. Our Galaxy instance is configured with LDAP authentication. The LDAP entry is suppressed shortly after the end of contracts. We are facing the following problem: A user left a few month ago, 1/ before leaving, she shared interesting histories with another colleague of the lab. 2/ before leaving, the colleague created a copy of every shared history in her own Galaxy account. 3/ The colleague made a few tests to check that the data were really transfered, by displaying them or downloading them and everything was ok. 4/ The time passed and the ldap user account of the user who left was suppressed. We deleted then purged her Galaxy account. 5/ The colleague has tried to relaunch some analysis using the copied histories. The data are there as her colleague is able to download the files or display them, but the jobs haven't been launched. They have remained grey in the copied history. The problem is that there are no logs at all on the galaxy side. No command line is generated either. On the reporting side of Galaxy, we see that the jobs have been created but their status remains "NEW' We know that this will be a recurrent problem if we can't resolve it. Have someone already complained about something like that? Best regards, -- Olivia Doppelt-Azeroual, PhD Fabien Mareuil, PhD Bioinformatics Engineer Galaxy Team - CIB/C3BI Institut Pasteur, Paris

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Fwd: Failure to set attributes_type metadata for interval files / error in gff_filter_by_attribute tool
by Marius van den Beek 01 May '15

01 May '15

Hello all, Not sure if the mailing list or trello would be appropriate for this. I had a problem using the gff_filter_by_attribute tool, both locally and on usegalaxy.org. Neither filtering for GTF or GFF were working. The error message was: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 158, in prepare_job job_wrapper.prepare() File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 832, in prepare self.command_line, self.extra_filenames = tool_evaluator.build() File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 408, in build self.__build_command_line( ) File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 424, in __build_command_line command_line = fill_template( command, context=param_dict ) File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 92, in respond NotFound: cannot find 'attribute_types' while searching for 'input.metadata.attribute_types' I could fix it by importing safe_dumps from galaxy.util.json, which apparently was not imported. The next problem occurred because gff_filter_by_attribute expects GTF attribute name-value separators (" ") but allowed GFF input, which uses ("=") as separator. I added a logic to switch between seperators based on the file extension. Everything works smoothly now, the code changes are here: https://github.com/mvdbeek/galaxy Should I create a pull request? -- Marius van den Beek, PhD Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine <http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-e…> 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 01 44 27 34 01

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Configuring galaxy to run on LSF
by Asma Riyaz 30 Apr '15

30 Apr '15

Hi, Configuration of Galaxy for an LSF server led me to this link: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#DRMAA The issue being the /lsf folder under galaxy does not exist. I am sort of stuck at this point and would highly appreciate anybody's help in this regard. Thank you, Asma

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Migrating user account from galaxy specific to LDAP
by Teshome Dagne Mulugeta 30 Apr '15

30 Apr '15

?Hi, We are currently using galaxy specific login using email address. We changed the authentication to LDAP. Most users email address doesn't match with their registered email address in LDAP. Now, users are not able to see their previous works which is expected of course but I have no clue how to fix it. Please help. Cheers, Teshome

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Galaxy for Natural Language Processing
by Keith Suderman 30 Apr '15

30 Apr '15

Hello, Our group is investigating using Galaxy as a workflow engine for NLP (Natural Language Processing) tasks. I have installed a local Galaxy instance and created wrappers for the services we use and so far everything is working great. I do have a few questions and they all fall under the “Advanced Topics” section as defined at the end of the tutorial for creating a Histogram [1] 1. parameter validation: Many of our tools rely on additions made by previous tools in the workflow; for example, a tool that identifies noun phrases may require that the input has been run through a part of speech (POS) tagger, the POS tagger may require that the input has been run through a tokenizer, etc. Our tools can do this validation, I am just looking for a way to wire this into Galaxy so a user can only connect tools in the workflow editor if this validation passes. I have been looking looking at the code for lib/galaxy/tools/parameters/validation.py and I don’t see anything that I can (easily) bend to our use case. What I was hoping for was something like: <input type=“data” format=“our_custom_format” name=“input”> <validator type=“dataset_custom”> <command interpreter=“bash”>validate.sh $input</command> <!— OR —> <tool file=“custom_validator.xml”/> </validator> </input> I also see the tantalizing sentence, "Custom code execution at various time points of the workflow that allows a fine grained control over the execution process", but I can't find any examples of how this is done. 2. data repositories / data collections I need to be able to process collections of data pulled from remote servers. I have been looking at DataManagers and data collections in Galaxy, but everything seems to assume the data is local to the server, or can be copied/uploaded to the server. For practical and legal reasons beyond my pay grade this is not a solution in our case. For example, an organization may be willing to allow our users to query their service for documents, run the documents through our workflow, and store the intermediate results; but they will not allow us to copy their data to another server verbatim. There are possibilities for me to cache data, but the general use case is that I have to call an external service to fetch documents one at a time and then run the same workflow on each document. Any suggestions on how to accomplish this in Galaxy? I can do single documents, I just need to expand this to include collections of documents. A typical workflow might look something like: a) Query Tool -> Server, find all documents that contain the word “cheese” b) Server -> Here is the list of document IDs [ id1, id2, …, idn ] c) WorkFlow -> for each id in the list do c1) Download document c2 ) Work work work work… c3) Persist output I can do all of the above except the most important bit; iterating… 3. format conversion: Is it possible for Galaxy to automatically convert between formats when designing a workflow? I see the <change_format/> tag, but that seems to change the output format of a tool based on the input (or some other condition) in the same tool; I need to be able to change the format based on the input requirements of the next tool in the workflow. For example, if Tool A produces format X, Tool B requires format Y, and a converter from X to Y has been defined in the datatypes_conf.xml; I would like for Galaxy to implicitly insert the converter from X to Y when I drag the output noodle from Tool A to Tool B in the designer. Is this possible? 4. OAuth 2.0 / OpenID Connect: I need to be able to fetch documents from data providers that require an OAuth 2.0 access token. Currently, I use a separate service to go through the OAuth authentication/authorization process and then have the user copy/paste their access token into a text field in Galaxy. Is there a way to perform the OAuth authentication dance required by the remote service inside Galaxy itself? I’ve looked at the Trello site for Galaxy and see that both OAuth 2.0 and OpenID Connect are on the radar, hopefully this use case is being considered as well. I’m sure to have more questions after working through some visualization examples, but this should keep me busy for now. Sincerely, Keith Suderman REFERENCES 1. https://wiki.galaxyproject.org/Admin/Tools/AddingTools ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY

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new tool works correctly but galaxy thinks it failed
by Ryan G 30 Apr '15

30 Apr '15

Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed. I checked the output file the tools create, and it succeeded. How do I tell Galaxy that a tool it ran was successful? Is it something in my XML file? The tool is outputting some info to stderr. Could this be why?

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Re: [galaxy-dev] <code> tagset in tools
by Simon Gladman 30 Apr '15

30 Apr '15

Hi Dan, Thanks for the reply and the suggestions. I think the data libraries would work much better than the get_microbial_data tool as then it would be more easily kept up to date. Cheers, Simon. On 30 April 2015 at 01:01, Daniel Blankenberg <dan(a)bx.psu.edu> wrote: > The <code> tag won’t be going away any time soon, but in many cases there > are other ways to do what this tag does, using the built-in dynamic options > (in particular, currently for tab-delimited files), that are much > preferred. So it is deprecated, and it should be used sparingly, but there > are times when there isn’t a better way for tools to dynamically build > their options without using a code file. > > In the case of the get microbial data tool, if it was working prior to > 15.03, it should still be working, afaik we haven’t changed the handling of > these recently (with the exception of not loading them inside of a ToolShed > application instance). Its been a while since I’ve played with that > specific tool (and we deprecated it ourselves and removed it from main), so > I can’t confirm off-the-cuff whether it should still be working or not. If > something really did break with respect to the code files, we should take a > look though. > > > I think using a Data Library is the perfect replacement for for the > microbial import tool, and would cause less file duplication when used. But > what exactly is no longer working? > > > Thanks for using Galaxy, > > Dan > > On Apr 29, 2015, at 10:38 AM, Peter Cock <p.j.a.cock(a)googlemail.com> > wrote: > > > On Wed, Apr 29, 2015 at 6:33 AM, Simon Gladman > > <simon.gladman(a)unimelb.edu.au> wrote: > >> Hi dev, > >> > >> Now that the <code> tagset is deprecated, how do we replace that > >> functionality. For example the "get microbial data" tool runs the script > >> listed in the <code> tagset to load the list of available microbe data > when > >> the tool is selected. This doesn't seem to work in the latest stable > 15.03.1 > >> or 15.03.2. > >> > >> How do we configure tools like this now? Or is there an updated version > of > >> the microbial_import tool? > >> > >> Cheers, > >> > >> Simon. > > > > Good question Simon. > > > > I am still using <code> for advanced parameter validation, e.g. > > > https://github.com/peterjc/pico_galaxy/blob/64aecfa6041b3b7fe2c70a30236a7aa… > > > > i.e. Validation before the job gets submitted to the cluster or run. > > If the <code> tag suddenly goes away, my tool will still work but > > would be a little less user friendly (some errors would only be > > spotted after the tool starts running). > > > > 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: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > -- Simon Gladman | Bioinformatician Victorian Life Sciences Computation Initiative - LSCC 187 Grattan Street, The University of Melbourne | Victoria 3010 Australia T +61 3 9035 5822 | M 0418 421 077 Mail: simon.gladman(a)unimelb.edu.au Web: http://www.vlsci.org.au

1 0

Data Libraries
by Ryan G 29 Apr '15

29 Apr '15

Hi all - We are trying to use Galaxy as a mechanism for our sequencing lab to create data libraries for data they generate. I noticed in the docs, only Admins are able to create data libraries. Is there a way to change this? I'd like to give specific users in our group this ability without giving them admin rights. Ryan

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Authenticating Against Galaxy from within a tool?
by Ben Bimber 29 Apr '15

29 Apr '15

Hello, I am new to galaxy. I"m trying to write a data input tool wrapper. It will call a script that does a query, produces a list of files, and then the plan is to use the BioBlend API to create datasets/data collections in galaxy. In other words I am making the dataset(s) based on the contents of this file, rather than making a dataset from that file. In my case this file has a pair of columns representing FASTQ files, and I want to create one paired dataset collection in galaxy for each genome. In theory using bioblend to create datasets is easy. However, when I call this as a galaxy tool, I have not found a clean way to pass the credentials to bioblend. BioBlend needs to know the serverURL and either the user's API key or username/password. I think if I poke around $__app__ or $__user__ there's a good change I will find a property with the information I need; however, this has the obvious problem of writing the API key to the log. Is there another way to approach this problem? Thanks in advance for any help, Ben

2 3

optional tool arguments
by Ryan G 29 Apr '15

29 Apr '15

Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2 fastq files as input. If 1 file is specified, then 1 output file is created. If 2 inputs are specified, then 2 output files will be created. How do I specify the optional output parameter? I'm using this as my tool description right now: <tool id="subsample_fastq" name="Random subsample"> <description>a fastq file</description> <command> ### Check for optional input file #if strlen($fq2) > 0: RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o $out2 #else: RandomSubFq -w $readsRequested -i "$fq1" -o $out1 #end if </command> <inputs> <param name="fq1" type="data" format="fastq" label="FASTQ file (1st of Pair)"/> <param name="fq2" type="data" format="fastq" label="FASTQ file (2nd of Pair)" optional="true"/> <param name="readsRequested" type="integer" min="1" value="100000" label="Total number of reads you want from the file"/> </inputs> <outputs> <data format="fastq" name="out1" /> <data format="fastq" name="out2" /> </outputs> <stdio> <exit_code range="-1" level="fatal" description="RandomSubFq failed" /> </stdio>

3 3

Question about automated cleanup scripts
by Van Der Pol William 29 Apr '15

29 Apr '15

Hello, I had a quick question about how one of the cleanup scripts works. I was wondering if admin_cleanup_datasets.py will delete old datasets even if they have been shared or published. Thanks for the help -Liam

1 0

PR 149
by Roberto Alonso CIPF 29 Apr '15

29 Apr '15

Hello, I created a PR https://github.com/galaxyproject/galaxy/pull/149 dome days ago, but I don't have any feedback yet, is there any problem with it? Is it not interesting for the current Galaxy? didn't the authors realized about it? It would be nice to have some feedback, even if it is not a convenient PR. Thanks so much, Best regards -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralonso(a)cipf.es

3 3

<code> tagset in tools
by Simon Gladman 29 Apr '15

29 Apr '15

Hi dev, Now that the <code> tagset is deprecated, how do we replace that functionality. For example the "get microbial data" tool runs the script listed in the <code> tagset to load the list of available microbe data when the tool is selected. This doesn't seem to work in the latest stable 15.03.1 or 15.03.2. How do we configure tools like this now? Or is there an updated version of the microbial_import tool? Cheers, Simon. -- Simon Gladman | Bioinformatician Victorian Life Sciences Computation Initiative - LSCC 187 Grattan Street, The University of Melbourne | Victoria 3010 Australia T +61 3 9035 5822 | M 0418 421 077 Mail: simon.gladman(a)unimelb.edu.au Web: http://www.vlsci.org.au

3 2

UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped
by Peter Cock 29 Apr '15

29 Apr '15

Hi all, I think this is the second time I've have the following error on TravisCI (last time I reran a similar failure, and it worked). I've not yet re-run the test so that you can see the full error log: UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped https://travis-ci.org/peterjc/galaxy_blast/builds/60510547 My hunch is this is a race condition, perhaps with the SQLite database? Should I ask TravisCI to re-run the test and confirm this? Peter -- Except from the full log, ... <snip> ... galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,952 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,957 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,000 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,001 Enabling 'x-forwarded-host' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,002 Enabling 'Request ID' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,046 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.queue_worker INFO 2015-04-29 09:45:14,057 Initalizing Galaxy Queue Worker on sqlalchemy+sqlite:////tmp/tmpGyX8vL/tmpTRGC3O/database/universe.sqlite functional_tests.py DEBUG 2015-04-29 09:45:14,089 Attempting to serve app on randomly chosen port: 9572 Error - <class 'sqlalchemy.orm.exc.UnmappedClassError'>: Class 'kombu.transport.sqlalchemy.Message' is not mapped URL: http://localhost:9572/ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in handle_request trans = self.transaction_factory( environ ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 73 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 104 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 205 in __init__ self._ensure_valid_session( session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 430 in _ensure_valid_session galaxy_session = self.__create_new_session( prev_galaxy_session, user_for_new_session ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 510 in __create_new_session referer=self.request.headers.get( 'Referer', None ) ) File '<string>', line 2 in __init__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 347 in _new_state_if_none File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py', line 747 in __get__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 177 in _state_constructor File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/event/attr.py', line 258 in __call__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2788 in _event_on_first_init File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2684 in configure_mappers File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 1706 in _post_configure_properties File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/interfaces.py', line 183 in init File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/relationships.py', line 1616 in do_init File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/relationships.py', line 1673 in _process_dependent_arguments File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py', line 747 in __get__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/relationships.py', line 1595 in mapper File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/base.py', line 426 in class_mapper UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT_ENCODING: 'identity' HTTP_HOST: 'localhost:9572' PATH_INFO: '/' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '127.0.0.1' SERVER_PORT: '9572' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0xa1a4e10> is_api_request: False paste.cookies: (<SimpleCookie: >, '') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xa1a4a90> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xa720d50> paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: '6f5c7eaaee5411e4bea1473d5f4e3057' wsgi process: 'Multithreaded' ------------------------------------------------------------ Exception in thread Thread-1: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 551, in __bootstrap_inner self.run() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py", line 170, in run for _ in self.consume(limit=None): # pragma: no cover File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py", line 187, in consume with self.consumer_context(**kwargs) as (conn, channel, consumers): File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__ return self.gen.next() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py", line 180, in consumer_context with self.Consumer() as (connection, channel, consumers): File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__ return self.gen.next() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py", line 229, in Consumer with self._consume_from(*self.get_consumers(cls, channel)) as c: File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/queue_worker.py", line 53, in get_consumers callbacks=[self.process_task])] File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py", line 359, in __init__ self.revive(self.channel) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py", line 371, in revive self.declare() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py", line 381, in declare queue.declare() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/entity.py", line 505, in declare self.queue_declare(nowait, passive=False) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/entity.py", line 531, in queue_declare nowait=nowait) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/virtual/__init__.py", line 446, in queue_declare self._new_queue(queue, **kwargs) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/sqlalchemy/__init__.py", line 80, in _new_queue self._get_or_create(queue) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/sqlalchemy/__init__.py", line 68, in _get_or_create obj = self.session.query(self.queue_cls) \ File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1249, in query return self._query_cls(entities, self, **kwargs) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 110, in __init__ self._set_entities(entities) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 120, in _set_entities self._set_entity_selectables(self._entities) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 150, in _set_entity_selectables ent.setup_entity(*d[entity]) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 3184, in setup_entity self._with_polymorphic = ext_info.with_polymorphic_mappers File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py", line 747, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py", line 1889, in _with_polymorphic_mappers configure_mappers() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py", line 2681, in configure_mappers raise e InvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: Class 'kombu.transport.sqlalchemy.Message' is not mapped Error - <class 'sqlalchemy.exc.InvalidRequestError'>: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: Class 'kombu.transport.sqlalchemy.Message' is not mapped URL: http://localhost:9572/ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in handle_request trans = self.transaction_factory( environ ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 73 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 104 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 205 in __init__ self._ensure_valid_session( session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 430 in _ensure_valid_session galaxy_session = self.__create_new_session( prev_galaxy_session, user_for_new_session ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 510 in __create_new_session referer=self.request.headers.get( 'Referer', None ) ) File '<string>', line 2 in __init__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 347 in _new_state_if_none File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py', line 747 in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 177 in _state_constructor File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/event/attr.py', line 258 in __call__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2788 in _event_on_first_init configure_mappers() File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2681 in configure_mappers raise e InvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: Class 'kombu.transport.sqlalchemy.Message' is not mapped CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT_ENCODING: 'identity' HTTP_HOST: 'localhost:9572' PATH_INFO: '/' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '127.0.0.1' SERVER_PORT: '9572' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0xa1a4e10> is_api_request: False paste.cookies: (<SimpleCookie: >, '') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xa1a4a90> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xa720d50> paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: '6f72e654ee5411e490fc473d5f4e3057' wsgi process: 'Multithreaded' ------------------------------------------------------------ Error - <class 'sqlalchemy.exc.InvalidRequestError'>: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: Class 'kombu.transport.sqlalchemy.Message' is not mapped URL: http://localhost:9572/ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in handle_request trans = self.transaction_factory( environ ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 73 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 104 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 205 in __init__ self._ensure_valid_session( session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 430 in _ensure_valid_session galaxy_session = self.__create_new_session( prev_galaxy_session, user_for_new_session ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 510 in __create_new_session referer=self.request.headers.get( 'Referer', None ) ) File '<string>', line 2 in __init__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 347 in _new_state_if_none File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py', line 747 in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 177 in _state_constructor File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/event/attr.py', line 258 in __call__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2788 in _event_on_first_init configure_mappers() File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2681 in configure_mappers raise e InvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: Class 'kombu.transport.sqlalchemy.Message' is not mapped CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT_ENCODING: 'identity' HTTP_HOST: 'localhost:9572' PATH_INFO: '/' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '127.0.0.1' SERVER_PORT: '9572' SERVER_PROTOCOL: 'HTTP/1.1' (etc, repeats this a lot)

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follow up question regarding the 'toolform-upgrade'
by Hans-Rudolf Hotz 29 Apr '15

29 Apr '15

Hi all We just need some confirmation before we fix our tools: We have several local tools, where the input is a list of (gene)names with the following xml syntax: <param name="genenames" type="text" area="true" size="5x20" label="gene names" help="(one per line)"/> so far this, assuming you enterred: foo bar produced a string like: foo__cr____cn__bar__cr____cn__ Now, with "toolform-upgrade=True", we get: foo__cn__bar__cn__ (using firefox, with linux, Mac, and Windows) Can anybody confirm this (before we fix all affected tools) Thank you very much for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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Fwd: History panel error
by Jose Juan Almagro Armenteros 28 Apr '15

28 Apr '15

Hello Dannon, This is the log when a job is executed: galaxy.jobs DEBUG 2015-04-24 17:25:27,266 (9568) Working directory for job is: /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568 galaxy.jobs.handler DEBUG 2015-04-24 17:25:27,313 (9568) Dispatching to local runner galaxy.jobs DEBUG 2015-04-24 17:25:27,600 (9568) Persisting job destination (destination id: local) galaxy.jobs.handler INFO 2015-04-24 17:25:27,686 (9568) Job dispatched galaxy.jobs.runners DEBUG 2015-04-24 17:25:28,465 (9568) command is: python /steno-internal/projects/galaxy/galaxy-dist/tools/table_gen/generator.py "/steno-internal/projects/galaxy/galaxy-dist/database/files/021/dataset_21041.dat" "1"; return_code=$?; python /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/set_metadata_MH6prK.py /steno-internal/projects/galaxy/galaxy-dist/database/tmp/tmpw80FFi /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/galaxy.json /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_in_HistoryDatasetAssociation_14967_7w0ALE,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_kwds_HistoryDatasetAssociation_14967_uH3ZBP,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_out_HistoryDatasetAssociation_14967_5iEavP,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_results_HistoryDatasetAssociation_14967_6FT2qV,/steno-internal/projects/galaxy/galaxy-dist/database/files/021/dataset_21041.dat,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_override_HistoryDatasetAssociation_14967_iOPJoQ; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2015-04-24 17:25:28,475 (9568) executing job script: /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/galaxy_9568.sh galaxy.jobs DEBUG 2015-04-24 17:25:28,617 (9568) Persisting job destination (destination id: local) galaxy.jobs.runners.local DEBUG 2015-04-24 17:25:31,960 execution finished: /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/galaxy_9568.sh galaxy.datatypes.metadata DEBUG 2015-04-24 17:25:32,207 loading metadata from file for: HistoryDatasetAssociation 14967 galaxy.jobs INFO 2015-04-24 17:25:34,775 Collecting job metrics for <galaxy.model.Job object at 0x7f3154cacad0> galaxy.jobs DEBUG 2015-04-24 17:25:34,799 job 9568 ended galaxy.datatypes.metadata DEBUG 2015-04-24 17:25:34,800 Cleaning up external metadata files I am not sure at all but I think this is the internal error that I got with the history panel problem: 130.225.125.174 - - [24/Apr/2015:15:22:19 +0200] "GET /api/histories/32c70b5011288952/contents HTTP/1.1" 500 - " http://galaxy.bric.dk/history/view_multiple" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/37.0.2062.120 Safari/537.36" galaxy.web.framework.decorators ERROR 2015-04-24 15:22:20,033 Uncaught exception in exposed API method: Traceback (most recent call last): File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py", line 251, in decorator rval = func( self, trans, *args, **kwargs) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/history_contents.py", line 105, in index hda_dict = self.hda_serializer.serialize_to_view( trans, content, view=view ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/base.py", line 621, in serialize_to_view return self.serialize( trans, item, all_keys ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/hdas.py", line 453, in serialize serialized = super( HDASerializer, self ).serialize( trans, hda, keys ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/base.py", line 566, in serialize returned[ key ] = self.serializers[ key ]( trans, item, key ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/hdas.py", line 403, in <lambda> 'resubmitted' : lambda t, i, k: i._state == t.app.model.Dataset.states.RESUBMITTED, AttributeError: 'Bunch' object has no attribute 'RESUBMITTED' Thanks a lot for your help! Regards, Jose 2015-04-24 17:16 GMT+02:00 Dannon Baker <dannon.baker(a)gmail.com>: > Hi Jose, > > Can you review (and share, maybe) the relevant part of the logs from when > you attempt to execute a job? It'd be worth it, if you still have the > logs, to know what the "Internal Server Error" indicated in your first > message was, as well. > > -Dannon > > On Fri, Apr 24, 2015 at 11:00 AM Jose Juan Almagro Armenteros < > jjalmagro(a)gmail.com> wrote: > >> Hi again, >> >> Now it is working, I just went back to the previous version and updated >> it again. All is okay except that the job table in the postgresql database >> is empty and is not being updated with new jobs (the problem is only with >> this table). I run manage_db.sh upgrade but nothing happened. >> >> Do you know what could be causing this? >> >> Thank you again! >> >> Best regards, >> >> Jose >> >> 2015-04-24 14:22 GMT+02:00 Jose Juan Almagro Armenteros < >> jjalmagro(a)gmail.com>: >> >>> Hello all, >>> >>> I have updated my Galaxy distribution today to the latest version 15.03 >>> and the history panel is not being shown. The history seems to be there but >>> Galaxy can't display the datasets. Even if I create a new history and I >>> run a tool the dataset is not shown. It is just displayed an error which >>> says: "An error occurred while getting updates from the server..." and the >>> details shows this: >>> >>> { >>> "agent": "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/37.0.2062.120 Safari/537.36", >>> "url": "http://galaxy.bric.ku.dk/history/view_multipl/api/histories/782c6cc7ec4cfd9…", >>> "data": "", >>> "options": { >>> "data": {}, >>> "silent": true, >>> "parse": true, >>> "emulateHTTP": false, >>> "emulateJSON": false >>> }, >>> "xhr": { >>> "readyState": 4, >>> "responseText": "{\"err_msg\": \"Uncaught exception in exposed API method:\", \"err_code\": 0}", >>> "responseJSON": { >>> "err_msg": "Uncaught exception in exposed API method:", >>> "err_code": 0 >>> }, >>> "status": 500, >>> "statusText": "Internal Server Error", >>> "responseHeaders": { >>> "Date": "Fri, 24 Apr 2015 12:09:40 GMT\r", >>> "cache-control": "max-age=0,no-cache,no-store\r", >>> "Transfer-Encoding": "chunked\r", >>> "Server": "PasteWSGIServer/0.5 Python/2.7.3\r", >>> "Connection": "close\r", >>> "x-frame-options": "SAMEORIGIN\r", >>> "content-type": "application/json\r" >>> } >>> }, >>> "source": [], >>> "user": { >>> "username": "jose", >>> "quota_percent": 0, >>> "total_disk_usage": 101352147, >>> "nice_total_disk_usage": "96.7 MB", >>> "email": "jjalmagro(a)gmail.com", >>> "is_admin": true, >>> "tags_used": [], >>> "model_class": "User", >>> "id": "72ad249754f05d26" >>> } >>> } >>> >>> Do you have any idea what could go wrong? >>> >>> Thank you and best regards, >>> >>> Jose >>> >> >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > >

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