Any Expert in Singularity can help me convert a Docker script ?

[Nidhal Ghanmi]

Hi

I have a tool named Big-Mex that researchers have to use it

I am asked to make it run with singularity

the code is simple as I see .. just can not get the things on my mind

Docker code :

  docker run \
    --volume ${INPUT_DIR}:${CONTAINER_SRC_DIR}:rw \
    --volume ${OUTPUT_DIR}:${CONTAINER_DST_DIR}:rw \
    --detach=false \
    --rm \
    --user $(id -u):$(id -g) \
     epereira/bgc_class_pred:latest \
    --input "${CONTAINER_SRC_DIR}/${INPUT_FILE}" \
    --bgc_models "${CONTAINER_SRC_DIR}/${MODELS}" \
    --outdir "${OUTPUT}" \

So ... the options I have some issues with

Any one please can clarify ? this code is working with docker , but asked for singularity

Thanks

Nidhal

[v]

Generally you can do:

singularity pull docker://epereira/bgc_class_pred:latest

singularity exec <options> <container> <entrypoint> <command-args>  # use your own entrypoint/command

singularity run <options> <container> <command-args>  # use the docker set entrypoint/cmd

and for both you might run into issue if the container expects a working directory (Singularity doesn't honor this, but you can set --pwd for the present working directory) OR there are scripts/assets in roots home, which you couldn't see as your user. So I'd probably first try:

singularity run --bind ${INPUT_DIR}:${CONTAINER_SRC_DIR} --bind ${OUTPUT_DIR}:${CONTAINER_DST_DIR} bgc_class_pred_latest.sif --input "${CONTAINER_SRC_DIR}/${INPUT_FILE}" --bgc_models "${CONTAINER_SRC_DIR}/${MODELS}" --outdir "${OUTPUT}"

and if you need to look around the container and test things first interactively you can use singularity shell <container>/

And then report back here with errors/issues you run into. Sharing the expected entrypoint/cmd would help too.

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[Nidhal Ghanmi]

Hey vanessa

Thanks for that code

I am still cofused ! I did the changes on the bash sscript , but still getting a strange issue !

The full code is in attached

the issue is with some overwrite thing .. I tryed all even creating a new work directory but getting same issue

[kcnedal@kcgebhpc test_dir]$ ./run_bgc_class_pred.bash . . --version
. already exist. Use "--overwrite t" to overwrite.

Regards

Nidhal

[v]

Sounds like you need to debug the script and understand the container entry point, which I can’t help you with unless I did it myself.

[Nidhal Ghanmi]

Thank you VAnessa !

I will try to look upon it

[Paulina Paiz]

Hi Vanessa, 

Thank you for supporting new users to Singularity! I also have a dockerfile and a singularity definition file but I haven't managed to get the container working on my HPC. When I execute `singularity shell image.sif" the container doesn't have it's own filesystem as I have seen in tutorials. It might also be useful to note that the remote builder was able to get to the layer of renv::restore() but then it timed out after 1 hour. 

Here is my dockerfile for reference:

FROM rocker/rstudio:4.1.1

MAINTAINER paudocker02 <paulin...@gladstone.ucsf.edu>

# Install system dependencies for R

RUN apt-get update -qq && \

DEBIAN_FRONTEND=noninteractive apt-get install -y \

apt-transport-https \

build-essential \

gfortran \

libatlas-base-dev \

libbz2-dev \

libcairo2-dev \

libxml2-dev \

libicu-dev \

liblzma-dev \

libpango-1.0-0 \

libpangocairo-1.0-0 \

libpcre3-dev \

libtcl8.6 \

libtiff5 \

libtk8.6 \

libx11-6 \

libxt6 \

libxt-dev \

locales \

tzdata \

libglib2.0-dev \

zlib1g-dev \

meson \

pkg-config \

gtk-doc-tools \

libfreetype6-dev \

libpng-dev \

libtiff5-dev \

libjpeg-dev \

libharfbuzz-dev \

libfribidi-dev \

libbz2-dev \

libgsl0-dev

RUN apt-get update && apt-get install -y --no-install-recommends \

python3-dev \

python3-pip

# Install Python packages

RUN pip3 install MACS2

ENV RENV_VERSION 0.14.0

RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"

RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"

WORKDIR /home/rstudio/myproject/

COPY renv.lock renv.lock

WORKDIR /home/rstudio/

RUN chown -R rstudio .

RUN R -e 'renv::restore()'

and my singularity definition file:

Bootstrap: docker

From: rocker/tidyverse:4.1.1

%post

# Install system dependencies for R

wget -O renv.lock "https://raw.githubusercontent.com/rcorces/ArchR_docker/main/renv.lock?token=AOHUDISVOOHAHDXW7AJBJFLB3XHEM"

apt-get update -qq && \

DEBIAN_FRONTEND=noninteractive apt-get install -y \

apt-transport-https \

build-essential \

gfortran \

libatlas-base-dev \

libbz2-dev \

libcairo2-dev \

libxml2-dev \

libicu-dev \

liblzma-dev \

libpango-1.0-0 \

libpangocairo-1.0-0 \

libpcre3-dev \

libtcl8.6 \

libtiff5 \

libtk8.6 \

libx11-6 \

libxt6 \

libxt-dev \

locales \

tzdata \

libglib2.0-dev \

zlib1g-dev \

meson \

pkg-config \

gtk-doc-tools \

libfreetype6-dev \

libpng-dev \

libtiff5-dev \

libjpeg-dev \

libharfbuzz-dev \

libfribidi-dev \

libbz2-dev \

libgsl0-dev

apt-get update && apt-get install -y --no-install-recommends \

python3-dev \

python3-pip

# Install Python packages

pip3 install MACS2

# Install R packages

R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"

R -e "remotes::install_github('rstudio/re...@0.14.0')"

# pull in an renv manifest file and restore it to load pacakges

R -e 'renv::restore()'

%runscript

exec /bin/bash "$@"

%startscript

exec /bin/bash "$@"

[Dave Dykstra]

Paulina,

Since you are using the remote builder you must be a Sylabs customer.
I suggest you contact them directly through their website.

Dave

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