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Ghost
@ghost~5772e7e2c2f0db084a206e1b
and are you sure about sam input ? that seems like a huge waste of space
we have a new samtools view that can subsample and works well
galaxybot
@galaxybot
[gronke] yeah
[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
Ghost
@ghost~5772e7e2c2f0db084a206e1b
So the default output of bwa-mem is bam, that's why I'm asking
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
galaxybot
@galaxybot
[gronke] what's the samtools view tool?
[gronke] I think I found it in the toolshed
galaxybot
@galaxybot
[gronke] btw a bit of a "bug" report, but I have a workflow that uses the ">" symbol, and once I edited the name it changed it to ">", but it still ends up showing as an error when I run the workflow. It's just in the workflow editor it shows as ">"
[gronke] s/error/arrow/g
Ghost
@ghost~5772e7e2c2f0db084a206e1b
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
John Chilton
@jmchilton
@mvdbeek are you on board for specify at runtime and specify via connection as two different states for non-data tool inputs?
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
Ghost
@ghost~5772e7e2c2f0db084a206e1b
yes
That sounds intuitively right to me ... based on nothing more than a gut feeling
John Chilton
@jmchilton
me too - though now that I pause to think about it I wonder if the terminology is what causes that. If we changed "Specify at Runtime" to "Make Default Configurable" or something would the behavior in your PR make more sense and be good enough
"Configurable by Default" maybe is what I meant there
Ghost
@ghost~5772e7e2c2f0db084a206e1b
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 ?
galaxybot
@galaxybot
[gronke] Is there a Maxheight option for Bam Track Data in the jbrowse tool? It looks like there is only one for the gff.
Jennifer Hillman-Jackson
@jennaj
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
Ghost
@ghost~5772e7e2c2f0db084a206e1b
maybe useful: https://gist.github.com/mvdbeek/db5724a16606fc19c645be5c6215e8d0 this sets up a galaxy db without migrations
Nicola Soranzo
@nsoranzo
@jennaj That's a "duplicate" of galaxyproject/tools-iuc#2151 , for which I'm working on a fix
Although it should be a galaxy not tools-iuc issue
Jennifer Hillman-Jackson
@jennaj
Great, thanks @nsoranzo, I missed the dup post. Glad this is sorted out
Robert Leach
@hepcat72
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]
Robert Leach
@hepcat72
I'll post an issue.
galaxybot
@galaxybot
[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
galaxybot
@galaxybot
[natefoo] no dice
Robert Leach
@hepcat72
OK, I submitted issue galaxyproject/galaxy#6918
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.
galaxybot
@galaxybot
[dannon] natefoo: I've tried multiple times and I can't get it to happen, still digging.
[dannon] Is anyone else seeing this? From that machine, can you check out that repo w/ normal git, natefoo?
galaxybot
@galaxybot
[dannon] Github is reporting 100% now, too, so it might not be on that side.
[dannon] @natefoo yarnpkg/yarn#4468 ? Anything on that box change lately at all?
[dannon] Someone was saying an old git was the culprit.
galaxybot
@galaxybot
[natefoo] nothing changed but the installer image is based off centos 6
[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`.