Comments (8)
@apeltzer Really appreciate you taking the time to check Alex. The conversion to DSL2 is going pretty smoothly, it's just the containers that are holding up the show (and linting, probably 🤖 ). Trying my best to have it ready for review next week
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Hi @apeltzer, I was away at a conference last week but have got around to creating PRs to add tools to bioconda. Have you permission to review and merge the above PRs?
Two areas of concern are detailed above, any guidance here would be greatly appreciated
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I have
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Hi @BarryDigby - just checked (sorry, super busy time right now at work): It looks quite good at the moment to me, e.g. targetscan biocontainer is here: https://quay.io/repository/biocontainers/targetscan
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After x-checking, it seems not to have been uploaded - we should maybe ask in their Support Channel. I also opened an issue on bioconda to ask if something was odd there.
See here: bioconda/bioconda-recipes#38099
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@apeltzer Hey Alex, the workflow has been successfully converted to DSL2, the only catch being I am still waiting on those bioconda containers, and for a reason I cannot pin down, singularity fails to pull this image from quay despite it working perfectly fine for Docker. Irritating to say the least 😁
Given the deadline for the response to authors for BMC is December 5th... what's the gameplan here?
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Just asked on the bioconda chat to unhide these & also asked whats going on with Singularity.
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Singularity there in << 24hours, the quay.io should already be there. So "just" in time :-D
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Related Issues (20)
- Implement psirc for isoform detection
- Implement miRNA sponging analysis
- Implement circRNA database annotation functionalities HOT 1
- Implement circbase HOT 1
- Implement circatlas HOT 1
- Implement circbank HOT 1
- Implement circRNADisease HOT 1
- Implement polyA-Benchmarking
- Decide how to proceed with the differential expression subworkflow
- Deprecate the `module` parameter
- Add `psirc quant` output to MulitQC via `kallisto` module
- Problems with empty annotation intersection HOT 12
- GTF entries on sequence which is not present in FASTA HOT 11
- GTF file not found with CIRIquant HOT 4
- SOLUTION: re-run with at least --limitSjdbInsertNsj HOT 11
- FATAL: the requested image was not found HOT 1
- ERROR ~ Invalid method invocation `call` with arguments using DCC HOT 1
- pandas.errors.EmptyDataError: No columns to parse from file
- Error executing process > 'NFCORE_CIRCRNA:CIRCRNA:MIRNA_PREDICTION:TARGETSCAN
- How can I accelerate the TARGETSCAN process when dealing with an excessive number of sequences that takes a long time? HOT 4
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