Permission denied error from Docker container in Snakemake

Question

I had built a Docker container from this Dockerfile previously and it worked fine:

FROM perl:5.32

MAINTAINER Matthew Jordan Oldach, moldach686@gmail.com

WORKDIR /usr/local/bin

# Install cpan modules
RUN cpanm install --force Cwd Getopt::Long POSIX File::Basename List::Util Bio::DB::Fasta Bio::Seq Bio::SeqUtils Bio::SeqIO Set::IntervalTree Set::IntSpan

RUN apt-get install tar

# Download CooVar-v0.07
RUN wget http://genome.sfu.ca/projects/coovar/CooVar-0.07.tar.gz
RUN tar xvf CooVar-0.07.tar.gz
RUN cd coovar-0.07; chmod +x scripts/* coovar.pl

# Set WORKDIR to /data -- predefined mount location.
RUN mkdir /data
WORKDIR /data

# Set Entrypoint
ENTRYPOINT ["perl", "/usr/local/bin/coovar-0.07/coovar.pl"]

The only issue was that I found there was a slight difference between what is on the repo and the coovar-0.07 which is on our server (there was slight difference in the extract-cdna.pl script).

In order to reproduce our pipeline I'll need to COPY CooVar locally into the container (rather than wget ).

I've therefore tried the following Dockerfile :

FROM perl:5.32

MAINTAINER Matthew Jordan Oldach, moldach686@gmail.com

WORKDIR /usr/local/bin

# Install cpan modules
RUN cpanm install --force Cwd Getopt::Long POSIX File::Basename List::Util Bio::DB::Fasta Bio::Seq Bio::SeqUtils Bio::SeqIO Set::IntervalTree Set::IntSpan

# Download CooVar-v0.07
COPY coovar-0.07 /usr/local/bin/coovar-0.07
RUN cd coovar-0.07; chmod +x scripts/* coovar.pl

# Set WORKDIR to /data -- predefined mount location.
RUN mkdir /data
WORKDIR /data

# Set Entrypoint
ENTRYPOINT ["perl", "/usr/local/bin/coovar-0.07/coovar.pl"]

It appears I could run the main script ( coovar.pl ) from Docker (no Permission Denied error):

# pull the container
$ sudo docker pull moldach686/coovar-v0.07:latest

# force entry point of `moldach686/coovar-v0.07` to /bin/bash
## in order to investigate file system
$ sudo docker run -it --entrypoint /bin/bash moldach686/coovar-v0.07

root@c7459dbe216a:/data# perl /usr/local/bin/coovar-0.07/coovar.pl 
USAGE: ./coovar.pl -e EXONS_GFF -r REFERENCE_FASTA (-t GVS_TAB_FORMAT | -v GVS_VCF_FORMAT) [-o OUTPUT_DIRECTORY] [--circos] [--feature_source] [--feature_type]
Program parameter details provided in file README.

However, when I tried to incorporate this into my Snakemake workflow I get the following Permission Denied error:

Workflow defines that rule get_vep_cache is eligible for caching between workflows (use the --cache argument to enable this).
Building DAG of jobs...
Using shell: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        1       coovar
        1
[Tue Nov  3 21:56:51 2020]
rule coovar:
    input: variant_calling/varscan/MTG470.vcf, refs/c_elegans.PRJNA13758.WS265.genomic.fa
    output: annotation/coovar/varscan/MTG470/categorized-gvs.gvf, annotation/coovar/varscan/MTG470.annotated.vcf, annotation/coovar/varscan/filtration/MTG470_keep.tsv, annotation/coovar/varscan/filtration/MTG470_exclude.tsv
    jobid: 0
    wildcards: sample=MTG470
    resources: mem=4000, time=10
Activating singularity image /scratch/moldach/COOVAR/cbc22e3a26af1c31fb0e4fcae240baf8.simg
Can't open perl script "/usr/local/bin/coovar-0.07/coovar.pl": Permission denied

Answer 1

The solution I found to work was adding the following line to the Dockerfile :

RUN echo "user ALL=NOPASSWD: ALL" >> /etc/sudoers

This adds the user to the sudoers file giving permissions:

FROM perl:5.32

MAINTAINER Matthew Jordan Oldach, moldach686@gmail.com

USER root
WORKDIR /usr/local/bin

# Install cpan modules
RUN cpanm install --force Cwd Getopt::Long POSIX File::Basename List::Util Bio::DB::Fasta Bio::Seq Bio::SeqUtils Bio::SeqIO Set::IntervalTree Set::IntSpan
RUN echo "user ALL=NOPASSWD: ALL" >> /etc/sudoers

# Download CooVar-v0.07
COPY coovar-0.07 /usr/local/bin/coovar-0.07
RUN cd coovar-0.07; chmod a+rwx scripts/* coovar.pl
# Download Bedtools 2.27.1
ENV VERSION 2.27.1
ENV NAME bedtools2
ENV URL "https://github.com/arq5x/bedtools2/releases/download/v${VERSION}/bedtools-${VERSION}.tar.gz"
WORKDIR /tmp
RUN wget -q -O - $URL | tar -zxv && \
cd ${NAME} && \
make -j 4 && \
cd .. && \
cp ./${NAME}/bin/bedtools /usr/local/bin/ && \
strip /usr/local/bin/*; true && \
rm -rf ./${NAME}/


# Set WORKDIR to /data -- predefined mount location.
RUN mkdir /data
WORKDIR /data

# Set Entrypoint
ENTRYPOINT ["perl", "/usr/local/bin/coovar-0.07/coovar.pl"]