Re: [galaxy-dev] galaxy-dev Digest, Vol 108, Issue 8
errors and questions with run_tests.sh and install_and_test_tool_shed_repositories.sh
在 2015年6月8日，17:00，galaxy-dev-request@lists.galaxyproject.org 写道：
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Today's Topics:
1. Re: Multi-level datatype conversions (Keith Suderman) 2. Re: Bismark doesn't end and blocks the server (Björn Grüning) 3. Re: errors and questions with run_tests.sh and install_and_test_tool_shed_repositories.sh (Loraine Guéguen)
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Message: 1 Date: Sun, 7 Jun 2015 16:37:08 -0400 From: Keith Suderman <suderman@cs.vassar.edu> To: David Kelly <davidkelly@uchicago.edu> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Multi-level datatype conversions Message-ID: <12AB4920-B9A0-4993-B320-B225394C237E@cs.vassar.edu> Content-Type: text/plain; charset="utf-8"
Hi David,
On Jun 5, 2015, at 2:10 PM, David Kelly <davidkelly@uchicago.edu> wrote:
Hi Keith,
I am able to manually convert from a->b and then separately b->c, but not directly from a->c. I'm still thinking about how to approach this as well, but I'll share my thoughts so far.
Does Galaxy automatically do the conversions for you in the workflow editor? For example, if you have a tool A that produces format 'a' and another tool B that consumes format 'b' you should be able to drag the "noodle" from A to B and Galaxy will do an implicit format conversion. If this is working for you then someone from the Galaxy team will have to jump in. If Galaxy is not doing implicit format conversions then it likely means your datatype(s) are not fully defined. I didn't get the implicit format conversion working properly until I implemented the format sniffers.
In our use case, we have a collection of climate tools we'd like to use. The tools are written by different groups, so most use their own file formats. Ideally we would like users to be able to upload their data in any of these file formats and use all tools without having to explicitly convert their data.
Let's say there are 10 climate datatypes. My understanding is that in order to achieve this kind of interoperability, I'd have to write 90 converters.
If Galaxy could chain converters together, I could write 1 converter per datatype and chain them together like this: a -> b -> c -> d -> e -> f -> g -> h -> i -> j -> a
Another scenario I've been thinking about is picking one data type to be the 'standard'. Let's say it's 'a' in this example. You could write 18 converters: a->b, a->c, a->d,... b->a, c->a, d->a,...
This is what we do. We have a standard "pivot format" then converters from the other formats to/from the pivot format.
Cheers, Keith
Then suppose you wanted to plug a 'd' file into a 'c' tool. You could first manually convert d->a, then use the automatic conversion for a->c. Not fully automatic, but not too bad.
On Thu, Jun 4, 2015 at 5:20 PM, Keith Suderman <suderman@anc.org> wrote: Hi David,
We just got it working for the single conversions, that is, getting Galaxy to automatically convert from a -> b when needed. Are you able to do the conversion, i.e a -> b and b -> c individually?
We are just coming to a similar use case and I'm definitely interested in how you make out, even if I can't be much help.
Cheers, Keith
On Jun 3, 2015, at 4:15 PM, David Kelly <davidkelly@uchicago.edu> wrote:
Hello,
Suppose I have three custom datatypes defined: a, b, and c
I have a datatype converter that converts from a -> b I have a datatype converter that converts from b -> c
Can I then send 'a' files as input into tools that accept type 'c'?
This doesn't seem to work in my test case, but I thought it might be worth asking to see if anyone has tried this before. Thanks!
Regards, David ___________________________________________________________ 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/
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------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
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Message: 2 Date: Mon, 08 Jun 2015 11:22:44 +0200 From: Björn Grüning <bjoern.gruening@gmail.com> To: "C. Ch." <tuto345@hotmail.com>, "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] Bismark doesn't end and blocks the server Message-ID: <55755EE4.1080902@gmail.com> Content-Type: text/plain; charset=utf-8
Hi,
I think this is a general problem you encountered here with unsorted BAM files. We can reproduce it locally. Will let you know if I find a workaround.
Cheers, Bjoer
Am 05.06.2015 um 14:23 schrieb C. Ch.: Hi all, I have a clean local install of galaxy from git (commit: 40b69cb948eed2cece82a32dfc5c6116414ab97c).I've installed bismark and I get an error message (see below) if I do not choose the 'sort' option.I have the impression that this might be related more to galaxy than to bismark itself. The result is that the server gets blocked and the only solution is to restart galaxy. Any help is appreciated!Cristian The error message:galaxy.datatypes.metadata DEBUG 2015-06-05 11:14:12,514 setting metadata externally failed for HistoryDatasetAssociation 1305: External set_meta() not called[bam_index_core] the alignment is not sorted (HWI-ST278R:398:C1WUTACXX:3:1101:9378:2574): 2-th chr > 1-th chr[bam_index_build2] fail to index the BAM file.
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Message: 3 Date: Mon, 08 Jun 2015 12:30:29 +0200 From: Loraine Guéguen <loraine.gueguen@sb-roscoff.fr> To: John Chilton <jmchilton@gmail.com> Cc: Galaxy Dev List <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] errors and questions with run_tests.sh and install_and_test_tool_shed_repositories.sh Message-ID: <55756EC5.70303@sb-roscoff.fr> Content-Type: text/plain; charset=utf-8; format=flowed
Thanks for your answers !
I will try "./run_tests.sh -installed" and see if it can solve the 2 first points. By the way, I didn't know this option (not displayed with run_tests.sh --help) or documented on the wiki if I'm not mistaken.
For point 3, I'll try the new "planemo shed_test" subcommand. The subcommand "planemo test" uses the run_tests.sh script, isn't it ? Does the "planemo shed_test" subcommand use all or any part of the Tool Shed Install and Test Framework (https://wiki.galaxyproject.org/AutomatedToolTests) or is it completely different ?
Is there any way to launch the tool tests against an external server (point 4) with Planemo ?
Loraine
Le 02/06/2015 15:16, John Chilton a écrit :
On Tue, Jun 2, 2015 at 4:14 AM, Loraine Guéguen <loraine.gueguen@sb-roscoff.fr> wrote:
Hi,
I have investigated the testing possibilities within a Galaxy local instance and within a toolshed. I met some difficulties and I have 4 questions listed below.
1- Tests on tools installed in a local Galaxy instance (with run_tests.sh) : It seems that it is only possible to test the tools that have been manually installed (run_test.sh -id ...), not the tools that have been installed through a toolshed. Is that true ? When I try to launch the tests of a toolshed installed tool, I have the following error message :
#########
Failure: ValueError (No such test TestForTool_sartools_edger) ... ERROR ====================================================================== ERROR: Failure: ValueError (No such test TestForTool_sartools_edger) ---------------------------------------------------------------------- Traceback (most recent call last): File "/projet/htdocs/galaxy-dev/galaxy-dist/eggs/nose-0.11.1-py2.7.egg/nose/failure.py", line 39, in runTest raise self.exc_class(self.exc_val) ValueError: No such test TestForTool_sartools_edger
---------------------------------------------------------------------- Ran 1 test in 0.002s FAILED (errors=1) ./run_tests.sh -installed runs the tests of all installed tool shed tools. It might be possible to combine that with -id - for a specific tool but I am not sure. It may be possible to construct that test even if -id doesn't work - but it is probably pretty hacky. Let me know if -installed works for you but not when combined with -id and we can work out the details. #########
2- Tests on tools installed in a local Galaxy instance (with run_tests.sh) : Is it possible to test tools which have repository or tool dependencies ? I have a tool (manually installed in galaxy-dist/tools/) with a dependence to a datatype installed from a toolshed. The datatype (no_unzip.zip) is defined in the <param> input tag (in <test>) with attribute "ftype". When running run_tests.sh, it seems that the dataype is not known :
#########
====================================================================== ERROR: test_tool_000001 (functional.test_toolbox.TestForTool_sartools_edger) SARTools edgeR ( sartools_edger ) > Test-2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py", line 268, in test_tool self.do_it( td ) File "/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py", line 37, in do_it stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) File "/w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py", line 36, in stage_data_in_history upload_waits.append( galaxy_interactor.stage_data_async( test_data, history, shed_tool_id ) ) File "/w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py", line 182, in stage_data_async raise Exception(submit_response) Exception: {u'message': {u'type': u'error', u'data': {u'file_type': u"An invalid option was selected for file_type, u'no_unzip.zip', please verify.", u'files_metadata': [u"An invalid option was selected for file_type, u'no_unzip.zip', please verify."]}}}
######### It is possible it is the case that tool shed datatypes are not loaded unless running with the -installed flag. I would either setup the tests to run locally (manually add datatypes and tools) or run installed tools with -installed.
3- Toolshed Install and Test framework ( install_and_test_tool_shed_repositories.sh) : For my tool, the test fails if I don't explicitely defined the dbkey attribute to "unknown" (dbkey="?") in the <param> input tag (in <test>). The default dbkey value seems to be "hg17" (whereas hg17 is not defined on the server running my toolshed). So I have the following error message if I don't add dbkey="?" in <test> :
#########
====================================================================== ERROR: test_tool_000001 (functional.test_toolbox.TestForTool_galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209) SARTools edgeR ( galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209 )
Test-2
Traceback (most recent call last): File "/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py", line 268, in test_tool self.do_it( td ) File "/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py", line 37, in do_it stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) File "/w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py", line 36, in stage_data_in_history upload_waits.append( galaxy_interactor.stage_data_async( test_data, history, shed_tool_id ) ) File "/w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py", line 182, in stage_data_async raise Exception(submit_response) Exception: {u'message': {u'type': u'error', u'data': {u'dbkey': u"An invalid option was selected for dbkey, u'hg17', please verify."}}}
#########
Well that is frustrating. I am not aware of the internals of that script or why that is happening - but my personal recommendation would be not to use the install and test framework at this point - it seems rather un-maintained. I recently added a subcommnd to planemo called shed_test (http://planemo.readthedocs.org/en/master/commands.html#shed-test-command) - that will install and test a tool shed repository. It probably requires modifying your tool shed development process to use planemo (http://planemo.readthedocs.org/en/latest/publishing.html#shed).
4- Is it possible to launch the tests against an external server ? That would be very useful to be able run the tests on a production Galaxy instance in order to test the tools in real condition, within the whole environment.
This would be great - but as I understand it - it is not possible at this time. The test framework needs local access to some aspects of the Galaxy app. Last year I outlined a Trello card to add this option back to Galaxy (https://trello.com/c/8K86l4Qk) - it was available years ago.
Thanks in advance for your answers.
Loraine
-- Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Service Informatique et Bioinformatique Station Biologique de Roscoff FR 2424 CNRS UPMC Place Georges Teissier CS 90074 29688 Roscoff cedex tel: ++33 (0)2 98 29 56 46 (interne : 415) http://abims.sb-roscoff.fr/ http://www.sb-roscoff.fr/
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-- Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Service Informatique et Bioinformatique Station Biologique de Roscoff FR 2424 CNRS UPMC Place Georges Teissier 29680 Roscoff tel: ++33 (0)2 98 29 25 50 http://abims.sb-roscoff.fr/ http://www.sb-roscoff.fr/
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