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> Op 22 mei 2015 om 18:01 heeft "galaxy-dev-requ...@lists.galaxyproject.org" > <galaxy-dev-requ...@lists.galaxyproject.org> het volgende geschreven: > > Send galaxy-dev mailing list submissions to > galaxy-dev@lists.galaxyproject.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.galaxyproject.org/listinfo/galaxy-dev > or, via email, send a message with subject or body 'help' to > galaxy-dev-requ...@lists.galaxyproject.org > > You can reach the person managing the list at > galaxy-dev-ow...@lists.galaxyproject.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-dev digest..." > > > HEY! This is important! If you reply to a thread in a digest, please > 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to > the original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread you > are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from > the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search > queries, but that aren't actually informative. > > Today's Topics: > > 1. Re: connecting composite data elements to a display > application (Brian Haas) > 2. Re: connecting composite data elements to a display > application (Daniel Blankenberg) > 3. Re: connecting composite data elements to a display > application (Brian Haas) > 4. Re: samtools index tool (Eleanor Morgan) > 5. Re: samtools index tool (Peter Cock) > 6. Re: Web processes and SSL (John Chilton) > 7. Re: error executing test (John Chilton) > 8. Re: error executing test (Roberto Alonso CIPF) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 May 2015 13:48:11 -0400 > From: Brian Haas <bh...@broadinstitute.org> > To: galaxy-dev@lists.galaxyproject.org > Subject: Re: [galaxy-dev] connecting composite data elements to a > display application > Message-ID: > <cajcu8qobpm71ht1qynmlvczb966vp26cq8of4fxmxf7xq2u...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > The following slides show how my 'hack' works: > > ftp://ftp.broadinstitute.org/pub/users/bhaas/tmp/FI-web.pptx > > It's definitely suboptimal, but at the very least, I've got something that > works and meets my immediate needs. > > I'm still *very* interested in following up with an alternative that > somehow leverages a galaxy API or well-supported mechanism for doing this. > > best, > > ~brian > > > On Thu, May 21, 2015 at 7:18 AM, Brian Haas <bh...@broadinstitute.org> > wrote: > >> Hi Bjoern, >> >> My galaxy/database/files/000/dataset_1_files/ directory contains a bunch >> of files that I want to load into a genome viewer, including the target >> fasta file, .fai, several bam and .bam.bai files, and some bed files among >> a few others. I'm looking to wire up an IGV-web application (a pure >> javascript version of IGV) to access and display these files. The IGV-web >> app just needs the URLs to access these files. I have a tool built into >> galaxy that generates these files and stores them as the composite data >> type, and I'm trying to add in the visualization capability such that one >> can click on a hyperlink provided in the finished job panel in order to >> access the igv-web view. >> >> Again, the general issue is just - how to best enable an external >> application to access the extra_files of a composite data set? >> >> Ideally, it would involve configuration of some >> >> galaxy/display_applications/display.xml >> >> file to indicate how the URL should be constructed. The final url could >> be simply: >> >> http://MyWebServer/my_web_app.cgi?data_base_url=http://galaxyURL >> >> where data_base_url just gives the base URL to where my files would exist >> on galaxy, and since I know ahead of time the names of the files to expect >> in that directory, my web app can just reconstruct the URLs to the various >> files (fa, bam, bed, etc.). >> >> Alternatively, the url could provide a list of urls to all of the required >> resources - with the requirement that the .bam.bai files can be accessed by >> simply putting a .bai on the end of the bam url for each bam, and likewise >> for .fai for fasta files. >> >> >> many thx, >> >> ~brian >> >> >> >> >> On Thu, May 21, 2015 at 4:56 AM, Bjoern Gruening < >> bjoern.gruen...@gmail.com> wrote: >> >>> Hi Brian, >>> >>> sorry to be so late to this adventure ... >>> Can you give me a few more details about your web-application? >>> >>> Have you considered to use the VIS framework from Galaxy or the >>> interactive environment framework? >>> This will give you more control over your datasets, because it's build-in >>> into Galaxy and would open up your webapp also for other servers. >>> >>> Cheers, >>> Bjoern >> -- >> -- >> Brian J. Haas >> The Broad Institute >> http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> > > > > -- > -- > Brian J. Haas > The Broad Institute > http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20150521/c81b1d70/attachment-0001.html> > > ------------------------------ > > Message: 2 > Date: Thu, 21 May 2015 14:41:04 -0400 > From: Daniel Blankenberg <d...@bx.psu.edu> > To: Brian Haas <bh...@broadinstitute.org> > Cc: galaxy-dev@lists.galaxyproject.org > Subject: Re: [galaxy-dev] connecting composite data elements to a > display application > Message-ID: <f236623c-685c-4af7-baad-552fae849...@bx.psu.edu> > Content-Type: text/plain; charset="windows-1252" > > Hi brian, > > I’ve enhanced Galaxy’s external display application framework to support > accessing files in the extra files path in a pull request here: > https://github.com/galaxyproject/galaxy/pull/284 > > To enable access you need to set allow_extra_files_access="True" for the > display parameter. To access the files, you append the relative path of the > extra file to the end of the URL generated for the parameter. > > If you want to try this feature before it is merged into the codebase, you > can apply it as a patch > (https://github.com/galaxyproject/galaxy/pull/284.patch). > > Please let us know if you encounter any issues using this new feature. > > > Thanks for using Galaxy, > > Dan > > >> On May 20, 2015, at 11:10 PM, Brian Haas <bh...@broadinstitute.org> wrote: >> >> Here's a quick update on my adventure in galaxy-dev. First - a quick >> review. I have a composite data type where files are stored as: >> primary data set: >> galaxy/database/files/000/dataset_1.dat >> and extra associated files: >> galaxy/database/files/000/dataset_1_files/* >> >> I want to link this up to a display application (web app running on the same >> server via apache) such that galaxy provides a URL that will enable read >> access to these files. >> >> From what I could gather, there's no straightforward way to get a stable URL >> from galaxy that points to the extra_files in the composite data set, such >> as getting links to a bunch of bam files and indexes placed there. >> >> Assigning each of the extra files as metadata items (ie. similar to a >> bam.bai file as a metadata file for a single bam file) could have been an >> option, but I couldn't get that to work. >> >> For now, since my Galaxy instance and my web app are running on the same >> machine with access to the same file system, I'll just have my web app read >> the files directly from the galaxy database directory via symlinks set up by >> my galaxy tool during the run. It's a clunky way of doing things but should >> suffice for now given my setup. >> >> If others have better solutions, I'm definitely interested in hearing them. >> >> many thanks, >> >> ~brian >> >> >> ___________________________________________________________ >> 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/ > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20150521/b657e5e8/attachment-0001.html> > > ------------------------------ > > Message: 3 > Date: Thu, 21 May 2015 14:48:41 -0400 > From: Brian Haas <bh...@broadinstitute.org> > To: Daniel Blankenberg <d...@bx.psu.edu> > Cc: galaxy-dev@lists.galaxyproject.org > Subject: Re: [galaxy-dev] connecting composite data elements to a > display application > Message-ID: > <cajcu8qmjbvycydywezzwcinorxkjo+txkeq1cser4bqs-xl...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Thanks, Dan! This will be a huge help. :) > > yours truly, > > ~brian > > >> On Thu, May 21, 2015 at 2:41 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote: >> >> Hi brian, >> >> I’ve enhanced Galaxy’s external display application framework to support >> accessing files in the extra files path in a pull request here: >> https://github.com/galaxyproject/galaxy/pull/284 >> >> To enable access you need to set allow_extra_files_access="True" for the >> display parameter. To access the files, you append the relative path of the >> extra file to the end of the URL generated for the parameter. >> >> If you want to try this feature before it is merged into the codebase, you >> can apply it as a patch ( >> https://github.com/galaxyproject/galaxy/pull/284.patch). >> >> Please let us know if you encounter any issues using this new feature. >> >> >> Thanks for using Galaxy, >> >> Dan >> >> >> On May 20, 2015, at 11:10 PM, Brian Haas <bh...@broadinstitute.org> wrote: >> >> Here's a quick update on my adventure in galaxy-dev. First - a quick >> review. I have a composite data type where files are stored as: >> primary data set: >> galaxy/database/files/000/dataset_1.dat >> and extra associated files: >> galaxy/database/files/000/dataset_1_files/* >> >> I want to link this up to a display application (web app running on the >> same server via apache) such that galaxy provides a URL that will enable >> read access to these files. >> >> From what I could gather, there's no straightforward way to get a stable >> URL from galaxy that points to the extra_files in the composite data set, >> such as getting links to a bunch of bam files and indexes placed there. >> >> Assigning each of the extra files as metadata items (ie. similar to a >> bam.bai file as a metadata file for a single bam file) could have been an >> option, but I couldn't get that to work. >> >> For now, since my Galaxy instance and my web app are running on the same >> machine with access to the same file system, I'll just have my web app read >> the files directly from the galaxy database directory via symlinks set up >> by my galaxy tool during the run. It's a clunky way of doing things but >> should suffice for now given my setup. >> >> If others have better solutions, I'm definitely interested in hearing them. >> >> many thanks, >> >> ~brian >> >> >> ___________________________________________________________ >> 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/ > > > -- > -- > Brian J. Haas > The Broad Institute > http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20150521/16ecbc3e/attachment-0001.html> > > ------------------------------ > > Message: 4 > Date: Fri, 22 May 2015 02:16:33 +0000 > From: Eleanor Morgan <e.mor...@curtin.edu.au> > To: "galaxy-dev@lists.galaxyproject.org" > <galaxy-dev@lists.galaxyproject.org> > Subject: Re: [galaxy-dev] samtools index tool > Message-ID: <d184af28.13a6f%e.mor...@curtin.edu.au> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > Excuse me for the newbie question. I am developing a local instance of > galaxy to use primarily for teaching purposes. > I would like to index bam files produced in galaxy in order to view them in > IGV. I can't seem to find the samtools index tool in the toolshed. I can > run samtools on the command line and generate indexes, but can find no way to > add this functionality to the tool panel so that I can do it in Galaxy. I > also can't find this functionality in the tool panel (under Samtools or BAM > tools) on usegalaxy.org. Am I missing something? Do I need to write my own > tool? > > Regards, > Eleanor > > Eleanor Morgan > Senior Scientific Officer | School of Biomedical Sciences | Faculty of Health > Sciences > > Curtin University > Tel | +61 8 9266 7516 > Mob | +61 408 004 369 > Fax | +61 8 9266 2342 > Email | e.mor...@curtin.edu.au<mailto:e.mor...@curtin.edu.au> > Web | biomed.curtin.edu.au > > [cid:ED62B336-732F-4D99-ABF8-AFACA1E1C7E3] > > Curtin University is a trademark of Curtin University of Technology. > CRICOS Provider Code 00301J (WA), 02637B (NSW) > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20150522/26eb90de/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: 91CCC686-9541-451E-B585-2948E3C297CD[43].png > Type: image/png > Size: 5216 bytes > Desc: 91CCC686-9541-451E-B585-2948E3C297CD[43].png > URL: > <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20150522/26eb90de/attachment-0001.png> > > ------------------------------ > > Message: 5 > Date: Fri, 22 May 2015 09:46:59 +0100 > From: Peter Cock <p.j.a.c...@googlemail.com> > To: Eleanor Morgan <e.mor...@curtin.edu.au> > Cc: "galaxy-dev@lists.galaxyproject.org" > <galaxy-dev@lists.galaxyproject.org> > Subject: Re: [galaxy-dev] samtools index tool > Message-ID: > <CAKVJ-_4J6wY=nw-xthv0tvqryeznrzyzpwjv5w7rzocq+da...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Galaxy itself will call "samtools index" on BAM files, so > they should be there on disk already, See for example: > > https://github.com/peterjc/pico_galaxy/blob/master/tools/samtools_idxstats/samtools_idxstats.xml > > https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/samtools/samtools_idxstats/samtools_idxstats.xml > > These demonstrate some different ways to find the BAI file. > > Peter > > > On Fri, May 22, 2015 at 3:16 AM, Eleanor Morgan <e.mor...@curtin.edu.au> > wrote: > >> Hi all, >> >> Excuse me for the newbie question. I am developing a local instance of >> galaxy to use primarily for teaching purposes. >> I would like to index bam files produced in galaxy in order to view them >> in IGV. I can’t seem to find the samtools index tool in the toolshed. I >> can run samtools on the command line and generate indexes, but can find no >> way to add this functionality to the tool panel so that I can do it in >> Galaxy. I also can’t find this functionality in the tool panel (under >> Samtools or BAM tools) on usegalaxy.org. Am I missing something? Do I >> need to write my own tool? >> >> Regards, >> Eleanor >> >> Eleanor Morgan >> Senior Scientific Officer | School of Biomedical Sciences | Faculty of >> Health Sciences >> >> >> Curtin University >> Tel | +61 8 9266 7516 >> >> Mob | +61 408 004 369 >> Fax | +61 8 9266 2342 >> Email | e.mor...@curtin.edu.au >> Web | biomed.curtin.edu.au >> >> >> >> Curtin University is a trademark of Curtin University of Technology. >> CRICOS Provider Code 00301J (WA), 02637B (NSW) >> >> >> >> >> ___________________________________________________________ >> 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/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20150522/2e4f4b85/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: 91CCC686-9541-451E-B585-2948E3C297CD[43].png > Type: image/png > Size: 5216 bytes > Desc: not available > URL: > <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20150522/2e4f4b85/attachment-0001.png> > > ------------------------------ > > Message: 6 > Date: Fri, 22 May 2015 09:59:53 -0400 > From: John Chilton <jmchil...@gmail.com> > To: Scott Szakonyi <scott.b.szakony...@nd.edu> > Cc: Galaxy Dev Mailing List <galaxy-dev@lists.galaxyproject.org> > Subject: Re: [galaxy-dev] Web processes and SSL > Message-ID: > <CANwbokeVO+kXq0i2w3KMqMka+5=xetdsfux0gxlzjz1lqqp...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Just to clarify - you cannot serve Galaxy only to localhost over http > and configure Apache to do the SSL and load balancing? I am having a > hard time conceiving of a scenario where I would encourage someone to > have paste deal with the SSL instead of Apache - configuring that in > paste is not going to be as robust, well documented, or secure IMO. > > If you really do need to serve paste via SSL - I am not sure what to > do next. I have no experience in configuring Apache to do this and I > have not heard of anyone else doing it (one can imagine it is a lot > harder to act as a proxy for a process when the traffic to and from > that process is encrypted). > > -John > > On Wed, May 20, 2015 at 10:15 AM, Scott Szakonyi > <scott.b.szakony...@nd.edu> wrote: >> Hello all, >> >> In our situation we're required to serve Galaxy via SSL. I encountered >> problems trying to do this with Paste processes. It appears that when Apache >> load balancing sends an incoming request to one of the load balanced >> processes, it's no longer under SSL. >> >> Running uWSGI is not a preferred option, as our computing infrastructure is >> not set up to support RedHat 7. >> >> Thus, I either need to understand how to configure SSL to work with the load >> balanced Paste processes, or run with another setup. >> >> So, if anyone in the community has experience with getting SSL to work with >> the Paste processes, or with setting up some other sort of SSL friendly >> configuration, I'd appreciate it if you would share your experience. >> >> -- >> Scott B. Szakonyi >> Research Programmer >> >> Center for Research Computing >> 107 Information Technology Center >> Notre Dame, IN 46556 >> http://crc.nd.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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > > ------------------------------ > > Message: 7 > Date: Fri, 22 May 2015 10:11:07 -0400 > From: John Chilton <jmchil...@gmail.com> > To: Roberto Alonso CIPF <ralo...@cipf.es> > Cc: "galaxy-dev@lists.galaxyproject.org" > <galaxy-dev@lists.galaxyproject.org> > Subject: Re: [galaxy-dev] error executing test > Message-ID: > <CANwbokfX0azspaLrhy1d1kWdyYtCu7F=gd5qrvtmkvup47c...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Roberto - > > Sorry for consistently taking so long to respond to these parallelism > inquires - you are doing awesome work but I am just constantly swamped > - I'll try to do more testing today. > > I can confirm both of those tests fail - it has nothing to do with your setup. > > compare_bam_as_sam was added here: > > https://github.com/galaxyproject/galaxy/commit/a38bae5cca98177eacaa3cdbeb74d3722263f377 > > It looks like I added a failing test to demonstrate metadata > generation was broken - and I was going to follow up on it and never > did. > > parallelism_bam_filter_reads only ever existed in my fork on github > right? I am not sure why it failed - but you had some clues and I was > going to try to follow up. Once it is working I will open a pull > request for it. > > If you are working on tests that is great - but I would focus on the > tests that work as examples. Some relevant ones may be: > > test/functional/tools/parallelism_optional.xml > test/functional/tools/parallelism.xml > test/functional/tools/metadata_bam.xml > test/functional/tools/metadata_bcf.xml > > These can be executed one at a time with: > > ./run_tests.sh -framework -id <tool_id> > > ... where tool id is the id in the tool XML file (which for these > tools usually match the basename of the file without the .xml > extension). > > Will try to get to the pull requests today. > > Thanks a bunch for your patience. > -John > >> On Mon, May 11, 2015 at 6:51 AM, Roberto Alonso CIPF <ralo...@cipf.es> wrote: >> Hello, >> >> I am designing some test and I have a problem, it works under the Galaxy web >> environment, but it doesn't work when I try to use it as a test case. Indeed >> I am trying other tests and they fail as well. >> >> My test ./run_tests.sh -framework -id parallelism_bam_filter_reads says the >> next: >> >> ====================================================================== >> ERROR: filter reads ( parallelism_bam_filter_reads ) > Test-1 >> ---------------------------------------------------------------------- >> Traceback (most recent call last): >> File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 268, in >> test_tool >> self.do_it( td ) >> File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 55, in >> do_it >> raise e >> RunToolException: Error creating a job for these tool inputs - {u'type': >> u'error', u'data': {u'input': u'History does not include a dataset of the >> required format / build'}} >> >> >> >> >> And the other test ./run_tests.sh -framework -id compare_bam_as_sam >> >> ====================================================================== >> ERROR: compare_bam_as_sam ( compare_bam_as_sam ) > Test-1 >> ---------------------------------------------------------------------- >> Traceback (most recent call last): >> File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 268, in >> test_tool >> self.do_it( td ) >> File "/home/ralonso/galaxy/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 "/home/ralonso/galaxy/test/base/interactor.py", line 38, in >> stage_data_in_history >> upload_wait() >> File "/home/ralonso/galaxy/test/base/interactor.py", line 279, in wait >> while not self.__history_ready( history_id ): >> File "/home/ralonso/galaxy/test/base/interactor.py", line 297, in >> __history_ready >> return self._state_ready( state, error_msg="History in error state." ) >> File "/home/ralonso/galaxy/test/base/interactor.py", line 356, in >> _state_ready >> raise Exception( error_msg ) >> Exception: History in error state. >> -------------------- >> begin captured logging << -------------------- >> >> Besides than it tries to migrate the database each time I try a test case >> and it takes too long. I have seen that you can use --db postgres but it >> doesn't work, I think this option should be user with --dockerize (that is >> not my case). >> >> would you have any idea of what is going on? >> >> 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: ralo...@cipf.es >> >> ___________________________________________________________ >> 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/ > > > ------------------------------ > > Message: 8 > Date: Fri, 22 May 2015 16:41:11 +0200 > From: Roberto Alonso CIPF <ralo...@cipf.es> > To: John Chilton <jmchil...@gmail.com> > Cc: "galaxy-dev@lists.galaxyproject.org" > <galaxy-dev@lists.galaxyproject.org> > Subject: Re: [galaxy-dev] error executing test > Message-ID: > <caceagz3ffatmfycyugr-xq5d+3jb9tuebak9ro74h+bzz-n...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > don't worry John, I understand that there are plenty of things before this > and also there is the Galaxy conference, so I can wait, no problem. > I will go through the things that you suggest. > > Best regards > >> On 22 May 2015 at 16:11, John Chilton <jmchil...@gmail.com> wrote: >> >> Roberto - >> >> Sorry for consistently taking so long to respond to these parallelism >> inquires - you are doing awesome work but I am just constantly swamped >> - I'll try to do more testing today. >> >> I can confirm both of those tests fail - it has nothing to do with your >> setup. >> >> compare_bam_as_sam was added here: >> >> >> https://github.com/galaxyproject/galaxy/commit/a38bae5cca98177eacaa3cdbeb74d3722263f377 >> >> It looks like I added a failing test to demonstrate metadata >> generation was broken - and I was going to follow up on it and never >> did. >> >> parallelism_bam_filter_reads only ever existed in my fork on github >> right? I am not sure why it failed - but you had some clues and I was >> going to try to follow up. Once it is working I will open a pull >> request for it. >> >> If you are working on tests that is great - but I would focus on the >> tests that work as examples. Some relevant ones may be: >> >> test/functional/tools/parallelism_optional.xml >> test/functional/tools/parallelism.xml >> test/functional/tools/metadata_bam.xml >> test/functional/tools/metadata_bcf.xml >> >> These can be executed one at a time with: >> >> ./run_tests.sh -framework -id <tool_id> >> >> ... where tool id is the id in the tool XML file (which for these >> tools usually match the basename of the file without the .xml >> extension). >> >> Will try to get to the pull requests today. >> >> Thanks a bunch for your patience. >> -John >> >> On Mon, May 11, 2015 at 6:51 AM, Roberto Alonso CIPF <ralo...@cipf.es> >> wrote: >>> Hello, >>> >>> I am designing some test and I have a problem, it works under the Galaxy >> web >>> environment, but it doesn't work when I try to use it as a test case. >> Indeed >>> I am trying other tests and they fail as well. >>> >>> My test ./run_tests.sh -framework -id parallelism_bam_filter_reads says >> the >>> next: >>> >>> ====================================================================== >>> ERROR: filter reads ( parallelism_bam_filter_reads ) > Test-1 >>> ---------------------------------------------------------------------- >>> Traceback (most recent call last): >>> File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 268, >> in >>> test_tool >>> self.do_it( td ) >>> File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 55, >> in >>> do_it >>> raise e >>> RunToolException: Error creating a job for these tool inputs - {u'type': >>> u'error', u'data': {u'input': u'History does not include a dataset of the >>> required format / build'}} >>> >>> >>> >>> >>> And the other test ./run_tests.sh -framework -id compare_bam_as_sam >>> >>> ====================================================================== >>> ERROR: compare_bam_as_sam ( compare_bam_as_sam ) > Test-1 >>> ---------------------------------------------------------------------- >>> Traceback (most recent call last): >>> File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 268, >> in >>> test_tool >>> self.do_it( td ) >>> File "/home/ralonso/galaxy/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 "/home/ralonso/galaxy/test/base/interactor.py", line 38, in >>> stage_data_in_history >>> upload_wait() >>> File "/home/ralonso/galaxy/test/base/interactor.py", line 279, in wait >>> while not self.__history_ready( history_id ): >>> File "/home/ralonso/galaxy/test/base/interactor.py", line 297, in >>> __history_ready >>> return self._state_ready( state, error_msg="History in error state." >> ) >>> File "/home/ralonso/galaxy/test/base/interactor.py", line 356, in >>> _state_ready >>> raise Exception( error_msg ) >>> Exception: History in error state. >>> -------------------- >> begin captured logging << -------------------- >>> >>> Besides than it tries to migrate the database each time I try a test case >>> and it takes too long. I have seen that you can use --db postgres but it >>> doesn't work, I think this option should be user with --dockerize (that >> is >>> not my case). >>> >>> would you have any idea of what is going on? >>> >>> 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: ralo...@cipf.es >>> >>> ___________________________________________________________ >>> 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/ > > > > -- > 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: ralo...@cipf.es > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20150522/ae47b6b1/attachment-0001.html> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > galaxy-dev mailing list > galaxy-dev@lists.galaxyproject.org > https://lists.galaxyproject.org/listinfo/galaxy-dev > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > ------------------------------ > > End of galaxy-dev Digest, Vol 107, Issue 22 > ******************************************* ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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