Waiting for CI to finish here: BioJulia/BiobakeryUtils.jl@fa35517
Gonna go work on my fence, but back in ~10 min
And I have the log page open so I should catch it
waking up
So it looks like it's seeing you call it
And the request get's sent
But it seems to respond saying 204 - DONE! without actually doing anything
So I probably need to first check the HTTP payloads sent by myself or Ciaran and those sent by you to see if there are any significant parameter differences.
And while you're at it, almost certainly unrelated, but I'd love your thoughts on this: BioJulia/BioJuliaRegistry#53
Anyone else feel free to chime in too
@kescobo So one thing that is interesting... in my json payload when I commented it says:
@BioJuliaBot register... for yours it says @biojuliabot register... Here's my idea what's happening - may be wrong, maybe not: So I think if you or anyone enters @biojuliabot register, whilst GitHub will recognize you're using BioJuliaBot's handle and will capitalize it for you when it renders your comment - Registrator is far more literal, and when the comment data arrives in the HTTP payload, it's like "@biojuliabot? Who's that? I'm listening for @BioJuliaBot!" ... and so it's ignoring you until you capitalize it's name!
I've definitely been putting it in lowercase
Yep ok here's the relevant registrator code:
trigger = Regex(CONFIG["trigger"] * "(.*)")
listener = GitHub.CommentListener(comment_handler, trigger; check_collab=false, auth=auth, secret=CONFIG["github"]["secret"])So the trigger is a regex of the exact trigger phrase (@BioJuliaBot register) followed by any other text, so it's gonna be sniffy about the caps!
Although you know this suggests editing the trigger string in the config might be able to get it to recognize the lowercase from of the name
Hmm - bad news is that now it doesn't seem able to be installed at all https://github.com/BioJulia/BioJuliaRegistry/pull/54/checks?check_run_id=477021230
All my other packages are broken too
If anyone here is using XAM.jl v0.2, there is an issue with versions v0.2.0, v0.2.1, v0.2.2 where the in-place record used during the iteration of SAM records was not emptied between iterations. This occurrence means that for successive iterations, record fields not overwritten would contain values from a previous iteration instead of being empty. The release of XAM.jl v0.2.3 addresses this issue.
BioJulia/BioSequences.jl#110 I thought it was just me but it seems someone else is seeing the same behaviour- reverse_complement mutates sequences. Does anyone have an idea about where to start with this? I kind of need BioSequences to be algorithmically reliable nowish so I am willing to investigate if need be
Doing this in python was pretty time-consuming. So wanted to try the same in Julia with FASTX package.
Can anyone recommend a method or provide an example to loop through each description and substitute with a modified line and writing it back to Fastq in an efficient way?