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I am unable to retrieve <raw.githubusercontent.com...
# nostupidquestions
n
I am unable to retrieve raw.githubusercontent.com/nf-core/…/genomeassembler.config (400 bad request) but e.g. raw.githubusercontent.com/nf-core/…/rnaseq.config is fine. Is this a problem on my end, or on githubs end?
G 1
🚫 1
m
Let me verify the repo
n
But the genomeassembler one also does not work for you?
m
nope
n
ok
m
weird
n
so it is not something I can fix 🤷
m
only reason I can think of is something on the github side
nothing we can do to fix this particular url I am afraid
n
ok
m
but it's not a problem
there are ways
https://raw.githubusercontent.com/nf-core/configs/master would be the constructed default value, because we append master to the raw...configs url path, so switching to the full url including the refs/heads should do the trick properly
☝️ 1
n
Thanks, that seems to work.
While doing that, I noticed that my nextflow.config contains these two lines:
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includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
and
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includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/genomeassembler.config" : "/dev/null"
I had to comment out the first one, for this to work, but with the previous (now broken) url it seemed ok, but to be honest, I dont understand why?
m
so basically the first line points towards the institutional configs we have in https://github.com/nf-core/configs the second one points towards the pipeline specific institutional configs from the same repo. So they both share the same base custom_config_params, and shouldn't really need to be commented out or anything
a
n
aha
m
But I do notice the same issues that Daniel is reporting, and I was about to point that issue out
thanks Arthur
n
m
oh
n
but with the old link it was ok
m
and in this case without the refs/heads it works
n
exactly
m
GITHUB shakefist
shakefist 1
n
Well, thanks for you help, I guess I have to wait until this resolves
m
no worries, there also another solution
Do you need institutional configs?
n
yes
well, currently not at the pipeline level, but nf-core, yes
m
ok, so the one from your institute?
n
I mean, I do not need them, since I have a local one, but the pipeline should support them
m
yeah, but for now what you could do is setup the ENV NXF_OFFLINE to true, that should disable getting the configs from github, and you can just point to the one you want via -c
n
yeah, good idea, but I am only trying to regenerate test snapshots, so I am assume that once this goes into CI it will anyway break again
but at least I can generate the snapshot that way 😄
m
CI is probably not working at the moment anyway, cf issue reported on #CJRH30T6V by Daniel
n
github breaking kinda regularily is a bit annoying, and maybe also concerning
m
I agree
I'll raise this issue, because we do rely on it quite a lot for everything more or less
n
which was fine, while it was a reliable service
a
Personally I would say configs being pulled from the raw GitHub was a mistake anyway, should be in S3 and synced to S3 when there are PRs to master
But that comes with a cost to nf-core, so it's not trivial
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