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ShixiangWang / sigflow

Sigflow: Streamline Analysis Workflows for Mutational Signatures, https://github.com/ShixiangWang/sigflow/pkgs/container/sigflow
https://hub.docker.com/r/shixiangwang/sigflow
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Cannot set hg38 for genome in container model #34

Closed jpcartailler closed 5 months ago

jpcartailler commented 5 months ago

Greetings,

I'm trying to set the genome via -g hg38 on version 2.2, from the Docker container. However, I get:

Try parsing VCF files...
Reading file(s): /data/cds_group/Processed-Data/2023-275-Jan_T-WGS-Cutaneous-Squamous-Cell-Carcinoma/results/130-mut-sig/GSQ062-DM/input/GSQ062-DM.vcf
Annotating Variant Type...
Downloading https://zenodo.org/record/4771552/files/human_hg38_gene_info.rds to /usr/local/lib/R/site-library/sigminer/extdata/human_hg38_gene_info.rds
Error in gzfile(file, "rb") : cannot open the connection
Calls: <Anonymous> -> readRDS -> gzfile
In addition: Warning messages:
1: In download.file(url = x_url, destfile = x_dest) :
  URL https://zenodo.org/record/4771552/files/human_hg38_gene_info.rds: cannot open destfile '/usr/local/lib/R/site-library/sigminer/extdata/human_hg38_gene_info.rds', reason 'Read-only file system'
2: In download.file(url = x_url, destfile = x_dest) :
  download had nonzero exit status
3: In gzfile(file, "rb") :
  cannot open compressed file '/usr/local/lib/R/site-library/sigminer/extdata/human_hg38_gene_info.rds', probable reason 'No such file or directory'
Execution halted

Please note that this is actually run from a Singularity image (from your Docker image, TY). The image is not writeable, which explains the cannot open connection error. We use Singularity on our HPC since Docker isn't allowed.

Would it be possible for the human_hg38_gene_info.rds to be downloaded to the host machine, vs the guest (container)? That would bypass such permission problems.

I couldn't find the code reference to https://zenodo.org/record/4771552/files/human_hg38_gene_info.rds in sigflow or sigminer.. happy to help recode this, but unclear where the code actually is. Thanks!

ShixiangWang commented 5 months ago

@jpcartailler Thanks for your report. It seems a permission issue in the docker container, I will take a check.

ShixiangWang commented 5 months ago

@jpcartailler Could you run with the master tag of docker image again? I have added the data into the latest build container.

https://github.com/ShixiangWang/sigflow/actions/runs/8504003290/job/23290297823#step:8:33294

jpcartailler commented 5 months ago

@ShixiangWang Thank you for updating this. I tested the master tag of the docker image - hg38 option works now.

ShixiangWang commented 5 months ago

Great to hear that.