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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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Nextflow installation error #51

Closed bbmorris1 closed 1 year ago

bbmorris1 commented 1 year ago

Hi,

I'm attempting to install & run the nextNEOpi pipeline on my institution's HPC.

I'm receiving the following error message:

"$ nextflow run icbi-lab/nextNEOpi --help

N E X T F L O W ~ version 22.10.8 Pulling icbi-lab/nextNEOpi ... WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/icbi-lab/nextNEOpi/contents/nextflow.config Remote resource not found: https://api.github.com/repos/icbi-lab/nextNEOpi/contents/main.nf"

How do I address this?

Thanks in advance!

riederd commented 1 year ago

Hi thanks for your interest in nextNEOpi. You need to download the release package and unpack it locally and then run it from there according to the README

bbmorris1 commented 1 year ago

Hi,

When attempting to install and run the nextNEO pipeline, I'm finding that a number of the required resources aren't included in the https://apps-01.i-med.ac.at/resources/nextneopi/nextNEOpi_1.4_resources.tar.gz bundle.

Specifically, the GRCh38d1.vd1/fasta folder is missing (containing needed reference files GRCh38.d1.vd1.fa, GRCh38.d1.vd1.fa.fai, GRCh38.d1.vd1.dict, hg38.len, and chromosomes). Additionally, the GRCh38.d1.vd1/index/bwa/ folder is missing.

I've also noticed that the databases/iedb, databases/mhcflurry_data, and databases/vep_cache are all empty following unpacking of the resource bundle.

For reference, the installation was done on a permissive server (i.e. no firewall restrictions) and did not time out.

Is there a step that I am missing? Or an updated resources bundle that I should use? I've attempted to download & unpack the resources bundle twice now. At present, it looks like I have to pull all of these files in by hand.

riederd commented 1 year ago

Hi, thanks for your interest in nextNEOpi The resources bundle includes all resources that are required. Maybe your download has failed.

iedb, mhcflurry, ans vep databases will be installed automatically during the first run of the pipeline and are not distributed via the resources bundle.