Closed davidmasp closed 6 years ago
Umm, this is suspect:
Aug-28 14:25:17.758 [main] DEBUG nextflow.scm.AssetManager - Too bad! Can't find any provider from git config. Check file `/home/dmas/.nextflow/assets/dmas/hello/.git/config`
Does that file exist ?
Yep,
$ more /home/dmas/.nextflow/assets/dmas/hello/.git/config
[core]
repositoryformatversion = 0
filemode = true
logallrefupdates = true
[remote "origin"]
url = <GIT_REPO_URL>
fetch = +refs/heads/*:refs/remotes/origin/*
[branch "master"]
remote = origin
merge = refs/heads/master
You removed the most important info ie the url :) Use a fake host name but provide the complete url structure.
okay sorry
$ more /home/dmas/.nextflow/assets/dmas/hello/.git/config
[core]
repositoryformatversion = 0
filemode = true
logallrefupdates = true
[remote "origin"]
url = http://server.name.es/gitlab/dmas/hello.git
fetch = +refs/heads/*:refs/remotes/origin/*
[branch "master"]
remote = origin
merge = refs/heads/master
I think the problem is that you haven't provided a valid scm
configuration file.
I see now it could be the endpoint that is wrong, let me check it and let you know
Any update on this ?
Hi, tried to change the API endpoint
with http://server.name.es/gitlab/api/v4
but then everything breaks and I cannot even pull the pipeline.
I am unsure what should go in the endpoint
field, is the only one I didn't set up in the scm
file
If this isn't the problem I don't know what I am ding wrong with the scm
file.
Have you specified the server
attribute ?
https://www.nextflow.io/docs/latest/sharing.html#private-server-configuration
yes, server
is http://server.name.es/gitlab
I guess it should be http://server.name.es
mmm I think it doesn't work because gitlab is running under a relative url. See this.
with server = 'http://server.name.es'
$ nextflow pull dmas/hello -hub agendas
Checking dmas/hello ...
Cannot find `dmas/hello` -- Make sure exists a GitLab repository at this address http://server.name.es/dmas/hello
and how is the endpoint
value ?
What I mean you need to specify both server
and endpoint
attributes.
Ah okay, I misunderstood the endpoint field. It works flawlessly now. For whatever reason I didn't though to be a configuration problem because it was downloading the repo fine. Thanks a lot for the help
for my future me, proper way to set up a scm file with gitlab private server configured with relative path.
server = 'http://server.name.es'
endpoint = 'http://server.name.es/gitlab'
I've also realised that the reported error is misleading. I'll modify to provide a more detailed message.
great
Bug report
Hi
As suggested in the gitter I open a issue for this.
Expected behavior and actual behavior
After configuring a instance of my private server in the
$HOME/.nextflow/scm
I can pull private repositories from the server withnextflow pull
but can't run them afterwards. I can also run hem the first time withnextflow run
but can't when I try to re-run them.In order to test it I have cloned this and pushed to a repo in my private git server named
hello
.Program output
The first time I run it I get
The second time though
And this is the
.nextflow.log
when I runnextflow -trace nextflow run dmas/hello
.Steps to reproduce the problem
Can't provide a full reproducible example because this is a local machine but basically I think these steps should reproduce the error.
$HOME/.nextflow/scm
nextflow pull username/hello -hub yourserver
ornextflow run username/hello -hub yourserver
, this works finenextflow run username/hello
this gives the error.Environment