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phac-nml / snvphyl-galaxy

SNVPhyl whole genome phylogenomics pipeline.
Apache License 2.0
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Streaming Module? #33

Open PHemarajata opened 4 years ago

PHemarajata commented 4 years ago

Hi, I've been trying to run the workflow on Galaxy installed on MacOS Big Sur and ran into this error:

Can't locate Streaming.pm in @INC (you may need to install the Streaming module) (@INC contains: /Users/phemarajata/galaxy/database/dependencies/_conda/bin /Users/phemarajata/galaxy/database/dependencies/_conda/bin/../lib/5.30.3/darwin-thread-multi-2level /Users/phemarajata/galaxy/database/dependencies/_conda/bin/../lib/5.30.3 /Users/phemarajata/galaxy/database/dependencies/_conda/bin/../lib /usr/local/Library/Perl/5.28 /Users/phemarajata/galaxy/database/dependencies/_conda/lib/site_perl/5.30.3/darwin-thread-multi-2level /Users/phemarajata/galaxy/database/dependencies/_conda/lib/site_perl/5.30.3 /Users/phemarajata/galaxy/database/dependencies/_conda/lib/5.30.3/darwin-thread-multi-2level /Users/phemarajata/galaxy/database/dependencies/_conda/lib/5.30.3 .) at /Users/phemarajata/galaxy/database/dependencies/_conda/bin/vcf2snv_alignment.pl line 16. BEGIN failed--compilation aborted at /Users/phemarajata/galaxy/database/dependencies/_conda/bin/vcf2snv_alignment.pl line 16.

I can't seem to find Streaming module anywhere. How do I install it? Thank you!

PHemarajata commented 4 years ago

I thought I fixed this but I didn't. @apetkau could you please help? Thank you so much!

apetkau commented 4 years ago

As per my response in https://github.com/phac-nml/snvphyl-tools/issues/11 the SNVPhyl pipeline is only available for Linux right now. It may be possible to get some of the dependencies installed and working on MacOS, but I cannot make any guarantees.

apetkau commented 4 years ago

Also note that you can try running the Galaxy Docker image on a Mac and then installing the SNVPhyl pipeline. There's currently a version with the SNVPhyl tools already installed (among other tools) on Docker hub which you can run like:

docker run -d -p 48888:80 phacnml/galaxy-irida-20.05

Then go to http://localhost:48888 and login with username admin@galaxy.org and password password. This https://github.com/phac-nml/irida/blob/development/src/main/resources/ca/corefacility/bioinformatics/irida/model/workflow/analysis/type/workflows/SNVPhyl/1.2.2/irida_workflow_structure.ga would be the latest SNVPhyl workflow.

PHemarajata commented 4 years ago

@apetkau I'm trying the Docker container now. Am I allowed to install new tools inside this container if I'm running Docker with an export option? I tried to install Trimmomatic and when I started the job I got an error saying "This tool was disabled before the job completed. Please contact your Galaxy administrator."

Thank you!

apetkau commented 4 years ago

You can install new tools. For any errors though you may need to look at the Galaxy logs (run docker logs -f [container id]) to see what's going on.

PHemarajata commented 4 years ago

@apetkau I think per this log somehow the tool got removed. It installed properly and was listed in the menu.

==> /home/galaxy/logs/handler0.log <== galaxy.jobs.handler WARNING 2020-09-17 15:24:23,595 (8) Tool 'toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1' removed from tool config, unable to run job galaxy.jobs DEBUG 2020-09-17 15:24:23,599 (8) fail(): Job destination raised JobMappingException('Can't map job to destination, tool 'toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1' is unavailable'), caching fake 'fail' destination for completion of fail method galaxy.tools.error_reports DEBUG 2020-09-17 15:24:23,784 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7f79e0300f98> generated response None galaxy.tools.error_reports DEBUG 2020-09-17 15:24:23,785 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7f79e0300f98> generated response None galaxy.tools.error_reports DEBUG 2020-09-17 15:24:23,785 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7f79e0300f98> generated response None galaxy.tools.error_reports DEBUG 2020-09-17 15:24:23,785 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7f79e0300f98> generated response None

apetkau commented 4 years ago

If you still have docker running you can try restarting Galaxy in Docker (without restarting the Docker container) like:

docker exec -it [container id] supervisorctl restart galaxy:

Beyond that though I may have to redirect you to the Galaxy Docker project https://github.com/bgruening/docker-galaxy-stable for more details on how to customize (e.g., install new tools) in the Galaxy Docker container.