Trouble running docker container with example inputs

[lsimmons2]

Hello,

I'm trying to run the docker container with the sample inputs provided in test_data but cannot get the program to run.

I'm trying docker run -v $(pwd):/workspace -w /workspace --user $(id -u):$(id -g) vout/megahit megahit -1 test_data/r1.il.fa.gz -2 test_data/r2.il.fa.bz2 -o test_output but the program doesn't seem to be running and I just get the documentation printed out:

contact: Dinghua Li <voutcn@gmail.com>

Usage:
  megahit [options] {-1 <pe1> -2 <pe2> | --12 <pe12> | -r <se>} [-o <out_dir>]

Any ideas?

[nikhilbhalla94]

same, it wont run when compiled locally, source code, conda installed etc. it just wont run. miraculously it ran once and for the last time on my WSL2

[USMortality]

Same happens for me with the provided docker image, but here's a minimal docker image, that works for me:

FROM alpine:latest

RUN apk update && apk add --no-cache python3 && \
  wget https://github.com/voutcn/megahit/releases/download/v1.2.9/MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz && \
  mkdir /megahit && tar zvxf MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz --strip-components=1 -C /megahit && \ 
  rm MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz
ENV PATH="/megahit/bin:${PATH}"
WORKDIR /data

ENTRYPOINT ["megahit"]

Build: docker build . -t megahit -f ./Dockerfile Run: docker run -v /Users/ben/Downloads/:/data megahit -1 CRR122287_f1.fastq.gz -2 CRR122287_r2.fastq.gz -o out

Hope this helps!