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deng-lab / viroprofiler

A containerized bioinformatics pipeline for viral metagenomic data analysis
https://deng-lab.github.io/viroprofiler
MIT License
23 stars 12 forks source link

Issue in Getting https://sandbox.zenodo.org/record/1098375/files/mmseqs_vrefseq.tar.gz #8

Open nitinShukla1912 opened 1 year ago

nitinShukla1912 commented 1 year ago

Description of the bug

  1. In your configuration script setup_db.nf, the line 131, wget is used to retrive mmseqs_vrefseq.tar.gz, but it is not getting into the system, i tried it manually but, the website itself is showing internal server error
  2. I want to change the default directory of database which is configured in my home environment as it is not having sufficent space, (I have moved the downloded database but now while running nextflow run deng-lab/viroprofiler -r main -profile singularity,test)

Caused by: Process VIROPROFILER:TAXONOMY_MMSEQS terminated with an error exit status (1)

/home/user/viroprofiler/taxonomy/mmseqs_vrefseq/refseq_viral does not exist

Even I have not configured the optional 3 databses,

Can we install this pipeline in local machine instead of running on docker + singularity

Command used and terminal output

nextflow run deng-lab/viroprofiler -r main -profile singularity,test

Relevant files

No response

System information

No response

rujinlong commented 1 year ago

Hi @nitinShukla1912, thanks for reporting the bug.

  1. The link has been updated. Could you please update the pipeline using nextflow pull deng-lab/viroprofiler, and run it again?
  2. You can set the database path by adding the --db /path/to/database when setting up and running the pipeline. One potential problem of changing database path is that if the new path is in a different hard disk, you need to bind that disk to singularity using the -B /path/to/another/disk parameter in the config file, as show in the custom config file.

Installing the pipeline using only conda should be possible, but I need some time to test it. In addition, this approach is not encouraged by nf-core due to poorer reproducibility. Please try singularity first, if still fails, let's figure out other approach.

nitinShukla1912 commented 1 year ago

Hi @rujinlong Also please update the https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-06-01.zip, in your setup_db.nf script.

Thanks in advance