Jellyfish docker image error with bam files

Question

[enee]

Hi everyone, I'm new on docker and I'm trying to run jellyfish count on .bam samples but I always get this error: Error: SAM/BAM/CRAM not supported (missing htslib). I tried to run it with .fq files and it works perfectly, I downloaded also several docker images from version 2.2.7 onwards (enter link description here) but no way. It seems like an image problem whit htslib, any ideas?

This is my command for the container docker run -it -v $(pwd):/home -w /home --rm quay.io/biocontainers/kmer-jellyfish:2.3.1--h4ac6f70_0 e this is the command runned inside jellyfish count -m 25 -s 100M --out-counter-len 1 --text -t 8 -C --sam file.bam -o file.jf

[bhumm]

It looks like you are right in assuming the issue lies with htslib. Do you have access to the Dockerfile? Can you try installing htslib and see if it resolves the issue?

You could add something like this to the Dockerfile to install when building the image:

RUN wget https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2
  && tar -vxjf htslib-1.20.tar.bz2
  && cd htslib-1.20
  && make