environment.yml #206
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nextflow run nf-core/chipseq -profile test,conda |
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changed the
Still 2 warnings: |
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remaining warnings are related to this error or preseq: |
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I wanted to echo that I also have the same issue running on Ubuntu20.04 with the latest anaconda3. |
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Sorry, guys.... 😏 I have been meaning to update this pipeline for the longest time but have been distracted by implementing other stuff on nf-core. The problem we have currently is that the Are you able to use Docker / Singularity because those should work? The error with Conda is known and is one of the big downsides with using it i.e. the environment resolution can change over time and so strictly speaking isn't reproducible. I suspect a bunch of lower-level dependencies have been changed with respect to R that is now breaking the environment. |
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Hi, we're using this workflow in this tutorial https://biocompute-objects.github.io/bco-ro-crate/tutorial/running.html and used Conda as a way to avoid having to teach installing Docker/Singularity; but this now again breaks for us on Ubuntu 20.04. Also R should try to actually follow Semantic Versioning ;) Is it possible to add the environment.yml.lock as saved from |
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Perhaps as the other changes on |
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Hi @stain ! Hope you are well. Awesome that you are using the pipeline in the tutorial you linked to :) I did actually add a line to the standard nf-core Dockerfile that saves the output of Line 13 in 0f487ed I have copied this out of a Singularity container and attached it below but had to change the extension to But when I try to create the environment it still errors: $ conda env create -f nf-core-chipseq-1.2.1.yml
Collecting package metadata (repodata.json): done
Solving environment: failed
ResolvePackageNotFound:
- gfortran_impl_linux-64==7.5.0=hdf63c60_6
- gcc_impl_linux-64==7.5.0=hd420e75_6
- gxx_impl_linux-64==7.5.0=hdf63c60_6When are you hosting the tutorial? I suspect things won't be as straightforward as just doing a patch release because the linting etc we have is always done relative to the latest tools release and so will fail. But can try and give it a go. |
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thanks, @drpatelh, I did not seem to have it recorded in previous run - only the desired I would not want to muddle the tutorial with "First patch the Conda environment" but perhaps it could work to pre-load the environment for this workflow? Nextflow seem however to make temporary conda environments so not sure how to inject it in advance. The tutorial is announced for 12. May, so still time to fix it. But would need to rewrite a fair bit if I need to do another nf-core workflow or require them to install Docker first. |
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Ok. Try this @stain: nextflow pull nf-core/chipseq
nextflow run nf-core/chipseq -profile test,conda -r 1.2.1_envfixThis is just a separate branch with the env fix that can be run directly without having to do anything beforehand. It won't be completely reproducbile unless we have an official release but if you have a look at the ❌ on #208 you will see what I meant about broken tests. I will keep this branch there until we release the next version. If not, it can always be re-instated quite easily. Is that a good enough compromise? |
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Thanks @drpatelh, this works great! I see the broken tests in #208 are with the linting requirements having changed since previous release. I also get this error in PRESEQ which I guess is same as what @kullrich points out. Except for that the workflow itself otherwise runs well, and in a way showing how to report error could be an important part of the tutorial. Will use More on PRESEQ below: from log: Perhaps this is just sample-related. |
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No worries. I released 1.2.2 yesterday so I have deleted the nextflow pull nf-core/chipseq
nextflow run nf-core/chipseq -profile test,conda -r 1.2.2Yup, you can literally just "ignore" the PRESEQ error. It doesn't like the test data we use for the CI because it isn't sufficiently deep enough. This will require changing the standard test data for the pipeline which is another beast. |
Dear nf-core team,
could you please update the
environment.ymlfile from the chipseq pipeline so that it can run on the latest Ubuntu version?The test data is just not running out of the box which might be related to the following error (Ubuntu20.04; latest anaconda3 from today).
Might be related that the default R which is installed by Ubuntu20.04 is already 3.6.3 and not 3.6.2 as in the
environment.ymlfileThank you in anticipation
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