Comments (3)
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
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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.
from nextneopi.
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.
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Related Issues (20)
- Bwa terminated with an error exit status (137) -- Execution is retried HOT 5
- error message when run a test case HOT 12
- Error executing process > 'gatherMutect2VCFs (sample2)' HOT 11
- Target regions bed file for TESLA patients 4,8,9 HOT 3
- NeoFuse: long running time HOT 4
- pVACSeq chmod error HOT 4
- Process `installVEPcache (installVEPcache)` terminated with an error exit status (104) HOT 4
- nextNEO resources bundle installation issues HOT 4
- Failed to run, issues related to pvacseq , etc HOT 5
- Error executing process > 'pVACseq (sample1)' HOT 4
- including SNV/indel calling on RNA-seq data HOT 1
- HLA-HD silently fails if bowtie2 is not installed/loaded HOT 1
- Error executing process "installVEPcache" HOT 7
- How could I improve this pipeline?
- mkfifo: cannot create fifo : Operation not supported HOT 2
- `pVACseq ` terminated with an error exit status (1) HOT 2
- Process `get_vhla (test)` terminated with an error exit status (1) HOT 32
- amino acids sometimes doesn't match the reference or variant HOT 2
- Is .cram input format supported? HOT 1
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