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we have a new samtools view that can subsample and works well
[gronke] what tool?
[gronke] I am going from bwa-mem --> downsample before going to jbrowse, because they were soooo huge in jbrowse
[gronke] the entire workflow is cutadapt --> bwa-mem --> Downsample (from picard) --> Jbrowse
there's really no advantage to sam output
and yes, try samtools view, this one's robust and up to date
noone really takes much care of the picard wrappers
[gronke] I think I found it in the toolshed
[gronke] s/error/arrow/g
if you think it is a bug please report it at https://github.com/galaxyproject/galaxy/issues including a full description on how to reproduce
I'm working on the tool form piece of that now - but I guess I should check with someone that it is a good idea
That sounds intuitively right to me ... based on nothing more than a gut feeling
"Configurable by Default" maybe is what I meant there
I mean there's still a difference in that a runtime parameter does need to be specified, while a connected parameter doesn't. That sounds like a different state on the surface. I'm thinking here about the workflow run form, for the editor I guess it doesn't matter and 'make configurable' fits both states. Making a distinction here might make things unnecessarily complex ?
Tool devs: Does anyone know the correct way to model this filter? https://biostar.usegalaxy.org/p/29788/ I only found this and it doesn't really apply (or does it?) https://planemo.readthedocs.io/en/latest/writing_advanced.html
maybe useful: https://gist.github.com/mvdbeek/db5724a16606fc19c645be5c6215e8d0 this sets up a galaxy db without migrations
Although it should be a galaxy not tools-iuc issue
So I was editing a workflow and the editor froze up. Now the workflow won't load and every time I try to open it in the editor, the whole galaxy page stops working. The javascript console has the following errors:
Source map error: request failed with status 404
Resource URL: https://galaxy.princeton.edu/static/scripts/bundled/libs.bundled.js?v=1540224765
Source Map URL: libs.bundled.js.map[Learn More]
Synchronous XMLHttpRequest on the main thread is deprecated because of its detrimental effects to the end user’s experience. For more help http://xhr.spec.whatwg.org/ libs.bundled.js:24:63678
[Show/hide message details.] TypeError: n.match is not a function[Learn More] extended.bundled.js:49:38621
Source map error: request failed with status 404
Resource URL: https://galaxy.princeton.edu/static/scripts/bundled/extended.bundled.js?v=1540224765
Source Map URL: extended.bundled.js.map[Learn More]
[natefoo] client building for Test failed just now with: error Couldn't find match for "6a1028fb562f9aa68c451f0901f8cfeb43cad140" in "_c" for "https://github.com/sorich87/bootstrap-tour.git"
[dannon] Hrmm. Let me look.
[dannon] That commit should be there, and that's what we needed to work against. Github outage? Trying locally.
[natefoo] retrying
I isolated the issue to setting post_job_actions in the cut tool. If you set anything there, the editor stops working on that workflow.
[dannon] Is anyone else seeing this? From that machine, can you check out that repo w/ normal git, natefoo?
[dannon] @natefoo yarnpkg/yarn#4468 ? Anything on that box change lately at all?
[dannon] Someone was saying an old git was the culprit.
[natefoo] i can update it to 7 now that we don't have any centos 6 infrastructure left
[dannon] I mean, maybe? The other thing you could do is try a manual 'yarn cache clean' on teh box or something.
[dannon] Can you just manually run 'yarn' from the client dir to see if there's extra output being masked?
[dannon] (or remind me where to go and I'll just tinker)
[natefoo] g2test@cvmfs0-tacc0.galaxyproject.org, run `cvmfs_server transaction test.galaxyproject.org`, the venv's in `/cvmfs/test.galaxyproject.org/venv`.