- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] STACKS error
by Ralf Weber 24 May '16

24 May '16

Hi Yvan, Thanks for including me in this conversation. I'll keep an eye on this and will make the necessary changes in our next commit/version. Best wishes, Ralf On 20 May 2016 at 23:28, Yvan Le Bras <yvan.le_bras(a)irisa.fr> wrote: > Thank you John for the rapid answer and the PR! > > I have had the same issue trying installing and use a Galaxy-M instance ( > <https://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0115-8> > https://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0115-8) > . I cc Ralf concerning this. > > Cheers, > > Yvan > > ------------------------------ > > *De: *"John Chilton" <jmchilton(a)gmail.com> > *À: *"Yvan Le Bras" <yvan.le_bras(a)irisa.fr> > *Cc: *"Amogelang Raphenya" <raphenar(a)mcmaster.ca>, > galaxy-dev(a)lists.galaxyproject.org > *Envoyé: *Vendredi 20 Mai 2016 17:15:19 > *Objet: *Re: [galaxy-dev] STACKS error > > This is one the reasons (though not the only one) I generally > discourage putting datatypes in the tool shed - Galaxy isn't very > clear about what interface it provides to datatypes and it would seem > very difficult from my perspective to maintain that interface and grow > Galaxy at the same time. > > This checkers module though is clearly useful to datatypes and it is > quite trivial to provide backward compatibility so I've opened a PR to > the new 16.04 release to restore this module - > https://github.com/galaxyproject/galaxy/pull/2389. > > Sorry for the inconvenience. > > -John > > > On Fri, May 20, 2016 at 10:45 AM, Yvan Le Bras <yvan.le_bras(a)irisa.fr> > wrote: > > Hi Amos, > > > > Thanks to use Stacks on Galaxy! I already seen this error. This is due, I > > think, to newest Galaxy versions who don't have the checkers.py anymore > on > > the datatypes folder.... Thios can be fixed using an older Galaxy > version... > > Otherwise, we are working on a new version of the Stacks Galaxy tools... > who > > will be usable in the upcoming days.... or not ;) > > > > Cheers, > > > > Yvan > > > > > > ________________________________ > > > > De: "Amogelang Raphenya" <raphenar(a)mcmaster.ca> > > À: galaxy-dev(a)lists.galaxyproject.org > > Envoyé: Vendredi 20 Mai 2016 16:37:04 > > Objet: [galaxy-dev] STACKS error > > > > > > Anyone encountered this error? > > > > Fatal error: Exit code 1 (Error in Stacks Process radtag execution) > > Traceback (most recent call last): > > File > > "/galaxylab/production/new/shed_tools/ > toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/STACKS_pro… > ", > > line 16, in <module> > > from stacks import * > > File > > "/galaxylab/production/new/shed_tools/ > toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/stacks.py > ", > > line 19, in <module> > > from galaxy.datatypes.checkers import * > > ImportError: No module named checkers > > > > > > Cheers. > > > > > > Amos Raphenya, B.Eng > > Bioinformatics Software Developer > > Department of Biochemistry & Biomedical Sciences > > McMaster University, MDCL 2317 > > p: (905) 525-9140 > > a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1 > > e: raphenar(a)mcmaster.ca > > skype: amos_raphenya > > > > > > ___________________________________________________________ > > 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/ > > > > > > > > > > -- > > > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > Yvan Le Bras, PhD > > @Yvan2935 > > <°))))>< > > e-Biogenouest project > > http://www.e-biogenouest.org > > CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, > 35042 > > Rennes Cedex > > tél.: +33 (0) 2 99 84 71 79 / > +33 > > (0) 6.10.43.96.51 > > > > yvan.le_bras(a)irisa.fr > > > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > > -- > > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > Yvan Le Bras, PhD > > @Yvan2935 > > <°))))>< > e-Biogenouest project > http://www.e-biogenouest.org > CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, > 35042 Rennes Cedex > tél.: +33 (0) 2 99 84 71 79 / +33 > (0) 6.10.43.96.51 > > yvan.le_bras(a)irisa.fr > >

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Refresh of screens in Galaxy Docker environment
by George Weingart 23 May '16

23 May '16

Hello, We are installing Galaxy in a Docker environment and we are encountering an issue where we need to refresh the screen (For Example, using F5) in order to see the status of the job. We see that using chrome as browser. If we don't refresh the screen, it stays (The job might have completed long ago but it still shows executing in yellow) Any suggestions how to resolve the problem? Thanks! George Weingart

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galaxy does not get kill signal from drmaa (sge6)
by Nick 23 May '16

23 May '16

Hi, it looks like bug. When job is terminated by exceeded wallclock Galaxy assumes that job finished normaly and has green status in history. What confuses user while there are no results or results are broken. Report from SGE: 05/22/2016 20:16:26| main|o3|W|job 1643894.1 exceeded hard wallclock time - initiate terminate method 05/22/2016 20:16:28|worker|ooo|W|job 1643894.1 failed on host o3 qmaster enforced h_rt, h_cpu, or h_vmem limit because: job 1643894.1 died through signal KILL (9) Logs from Galaxy: galaxy.jobs.runners.drmaa DEBUG 2016-05-22 20:16:29,425 (502/1643894) state change: job finished normally Job was submited with following native parameters: galaxy.jobs.runners.drmaa DEBUG 2016-05-22 20:11:19,837 (502) native specification is: -cwd -l h_rt=300 Tested on Galaxy 15.11, 16.01, 16.04 -- Nick

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Galaxy Interactive Environments: node 0.10.X - 0.11.X vintage necessary?
by Tamir,Ido 23 May '16

23 May '16

Hi, are the GIE still tied to an outdated node version? http://galaxy.readthedocs.io/en/master/admin/interactive_environments.html says: 0.10.X - 0.11.X vintage (https://github.com/erasche/galaxy/blob/gie-docs/doc/source/admin/interactiv…) but also: "We’re working on solutions in this space to provide a better deployment mechanism here and fewer dependencies." I now have galaxy 15.10 and node v5.11.1 and don’t really want to downgrade my node installation. best, ido

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Hits2 2.0.3 missing environment
by Nick 22 May '16

22 May '16

HI, Bug in latest Hisat2 tool. Hisat2 tool version 2.0.3 revision 2d449a1bb5ab does not attempt to setup the environment in tool_script.sh and job stops with error: Fatal error: Exit code 127 () /home/galaxy/database/jobs_directory/000/497/tool_script.sh: line 9: hisat2-build: command not found tool_script.sh: PACKAGE_BASE=/home/galaxy/tools/dependencies/samtools/1.2/iuc/hisat2/ 2d449a1bb5ab; export PACKAGE_BASE; . /home/galaxy/tools/dependencies/samtools/1.2/iuc/hisat2/2d449a1bb5ab/e nv.sh; hisat2 --version > /home/galaxy/database/tmp/GALAXY_VERSION_STRING_500 2>&1; ln -s "/home/genomes/caenorhabditis_elegans/release-84/Caenorhabditis_elega ns.WBcel235.dna.toplevel.fa" genome.fa && hisat2-build genome.fa genome && hisat2 -p ${GALAXY_SLOTS:-1} -x "genome" -U "/home/galaxy/database/files/001/dataset_1034.dat" -k 5 | samtools sort - - @ ${GALAXY_SLOTS:-2} -l 6 -o hsbam > "/home/galaxy/database/files/001/dataset_1674.dat" Hisat2 tool version 2.0 revision b1e25f9b5eab works okay and create next tool_script.sh: PACKAGE_BASE=/home/galaxy/tools/dependencies/hisat/2.0/iuc/hisat2/b1e 25f9b5eab; export PACKAGE_BASE; . /home/galaxy/tools/dependencies/hisat/2.0/iuc/hisat2/b1e25f9b5eab/env.s h; PACKAGE_BASE=/home/galaxy/tools/dependencies/samtools/1.2/iuc/hisat2/ b1e25f9b5eab; export PACKAGE_BASE; . /home/galaxy/tools/dependencies/samtools/1.2/iuc/hisat2/b1e25f9b5eab/e nv.sh; hisat2 --version > /home/galaxy/database/tmp/GALAXY_VERSION_STRING_501 2>&1; ln -s "/home/genomes/caenorhabditis_elegans/release-84/Caenorhabditis_elega ns.WBcel235.dna.toplevel.fa" genome.fa && hisat2-build genome.fa genome && hisat2 -p ${GALAXY_SLOTS:-1} -x "genome" -U "/home/galaxy/database/files/001/dataset_1034.dat" -k 5 | samtools sort - - @ ${GALAXY_SLOTS:-2} -l 6 -o hsbam > "/home/galaxy/database/files/001/dataset_1675.dat" Galaxy is: Merge branch 'release_16.04' Probably it can be solve quickly by correction of config files. Does someone know where to look to solve such kind of problems? Thanx, Nick

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Installing a Jupyter Kernel
by Suderman Keith 21 May '16

21 May '16

How do I make my custom kernel the default when starting a Jupyter interactive environment? I have written a native Jupyter kernel for Groovy, that is, a Jupyter kernel written in Groovy that listens to, and responds on, the appropriate ZMQ sockets. I have also extended the bgruening/docker-jupyter-notebook docker image to add my kernel and modified the jupyter.ini file to use my Docker image. This all works. I can launch a Jupyter Notebook (or use 'jupyter console --kernel groovy' from the command line) and interact with Galaxy. I can launch an interactive Jupyter environment in Galaxy and select 'Kernels -> Change kernel -> Groovy' and all of the above works fine; I just want my kernel to be the default. ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY

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Problem upgrading
by Scott Szakonyi 20 May '16

20 May '16

Hello, I'm currently running Galaxy 16.01, and I'd like to upgrade to 16.04. However, when I attempt to do so, I get an error, and git log shows I'm still on 16.01. $ sudo git checkout master && pull --ff-only origin master M tool-data/all_fasta.loc.sample Already on 'master' -bash: pull: command not found I also tried updating to the exact version: sudo git checkout v16.04 error: pathspec 'v16.04' did not match any file(s) known to git. For the record, I'm using Git 1.7.1. I took my commands directory from the announcement page at https://docs.galaxyproject.org/en/master/releases/16.04_announce.html Any suggestions for ways to get the 16.04 code are greatly appreciated! Best, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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STACKS error
by Raphenya, Amogelang 20 May '16

20 May '16

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Error when executing cleanup scripts
by Scott Szakonyi 20 May '16

20 May '16

Hi all, I'm getting an error when executing the cleanup scripts in Galaxy 16.01. It appears the script is unable to import sqlalchemy, but my understanding is that Galaxy can't function without it, so I'm at a loss to explain. Here's the error I'm getting: $ sh scripts/cleanup_datasets/delete_userless_histories.sh Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 13, in <module> import sqlalchemy as sa ImportError: No module named sqlalchemy We have relatively limited space on our storage server, so it's imperative that I be able to execute these scripts and be able to clean up deleted material. I welcome any suggestions. Best regards, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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tool error on TopHat test during metadata manipulations
by Nick 19 May '16

19 May '16

Hi, All our workflows with TopHat finished with status: "tool error" & "Unable to finish job". We tested them on Galaxy 15.11 and 16.01 (latest works with python 2.6). Our batch system is SGE. TopHat is v2.0.14 revision 4eb3c3beb9c7 TopHat calculations on the cluster are fine and finished without any errors but during the running set_metadata_XYZ.py script (which is also called from submited script) job fails and reports above mentioned error status. Logs are: galaxy.jobs.runners.drmaa DEBUG 2016-05-19 13:53:18,054 (481/1533559) state change: job finished normally galaxy.jobs.output_checker INFO 2016-05-19 13:53:19,389 Job 481: Log: tool progress galaxy.jobs.output_checker INFO 2016-05-19 13:53:19,389 Job 481: Log: tool progress galaxy.datatypes.metadata DEBUG 2016-05-19 13:53:21,759 setting metadata externally failed for HistoryDatasetAssociation 1965: [Errno2] No such file or directory galaxy.jobs.runners ERROR 2016-05-19 13:53:24,367 (481/1533559) Job wrapper finish method failed Traceback (most recent call last): File "/ptmp/galaxy1/galaxy/lib/galaxy/jobs/runners/__init__.py", line 590, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/ptmp/galaxy1/galaxy/lib/galaxy/jobs/__init__.py", line 1221, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/ptmp/galaxy1/galaxy/lib/galaxy/datatypes/binary.py", line 314, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib64/python2.6/subprocess.py", line 470, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.6/subprocess.py", line 623, in __init__ errread, errwrite) File "/usr/lib64/python2.6/subprocess.py", line 1141, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory As I understand Galaxy operates with pickle data ( which were saved before submiting job in file with id 1965: metadata_in_HistoryDatasetAssociation_1965_sPyPfZ ) during running function set_metadata() and does not find some files and exit with error message [false, "[Errno 2] No such file or directory"] writen to the file metadata_results_HistoryDatasetAssociation_1965_k5I9PM and kill job. What causes this error and how to fix this behavior? Thanx in advance, Nick

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