sina not working within a docker container #107
Description
If I run sina within a docker container (I've tried quay.io/biocontainers/sina:1.7.1--h9aa86b4_0 and creating my own container; see below), I get the error:
02:38:59 [SINA] This is SINA 1.7.2.
02:38:59 [SINA] Unable to open ARB database "SILVA_138.1_SSURef_NR99_12_06_20_opt.arb".
02:38:59 [SINA] The ARB database you were trying to use is likely corrupted.
My job:
sina --threads 4 --turn \
--fasta-write-dna --lowercase none \
--intype fasta --outtype fasta \
--in $fasta \
--db SILVA_138.1_SSURef_NR99_12_06_20_opt.arb \
-o align.fna
If I run the same job outside of the container image:
wget https://github.com/epruesse/SINA/releases/download/v1.7.2/sina-1.7.2-linux.tar.gz
tar -pzxvf sina-1.7.2-linux.tar.gz
./sina-1.7.2-linux/sina --threads ${task.cpus} --turn \
--fasta-write-dna --lowercase none \
--intype fasta --outtype fasta \
--in $fasta \
--db $sina_db_arb \
-o align.fna
...the job completes successfully.
There seems to be something about running sina within a docker container that causes it to fail with the error: [SINA] Unable to open ARB database
Maybe it has something to do with ownership/permissions?
The dockerfile for my own sina image:
FROM ubuntu:22.04
USER root
RUN apt-get update && \
apt-get install -y wget python3.9 && \
ln -sf /usr/bin/python3 /usr/bin/python && \
apt-get clean && \
apt-get purge && \
rm -rf /var/lib/apt/lists/* /tmp/*
RUN wget https://github.com/epruesse/SINA/releases/download/v1.7.2/sina-1.7.2-linux.tar.gz && \
tar -pzxvf sina-1.7.2-linux.tar.gz && \
mv sina-1.7.2-linux /bin/sina-1.7.2-linux/ && \
ln -sf /bin/sina-1.7.2-linux/bin/sina /bin/sina && \
rm -f sina-1.7.2-linux.tar.gz
WORKDIR /data
Switching to ubuntu:20.04 does not fix the issue.