Container to run ccp4 (Collaborative Computational Project No. 4)
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Please note that the original software licenses still apply
This container allows calling hgen command throught python3 but with a caveut (see below):
Dockerfile
FROM pegi3s/ccp4
# make ccp4 scripts visible (useful only for running with Docker)
#RUN ./ccp4/BINARY.setup\
# && echo "" >> .bashrc\
# && echo ". /ccp4/bin/ccp4.setup-sh" >> ~/.bashrc
# install python3.8
RUN apt-get update \
&& apt-get install -y build-essential checkinstall \
&& apt-get install -y libreadline-gplv2-dev libncursesw5-dev libssl-dev \
libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev libffi-dev zlib1g-dev \
&& cd opt \
&& wget https://www.python.org/ftp/python/3.8.12/Python-3.8.12.tgz \
&& tar xzf Python-3.8.12.tgz \
&& cd Python-3.8.12 \
&& ./configure --enable-optimizations \
&& make altinstall \
&& cd ../ \
&& rm -f Python-3.8.12.tgz
# create symlink to run python3
RUN ln -sf /usr/local/bin/python3.8 /usr/bin/python3
WORKDIR /
Run with docker:
docker run --rm -it --entrypoint bash --platform linux/amd64 francecosta/ccp4:v0.0.5
source /ccp4/bin/ccp4.setup-sh
hgen
Despite having tried to explicit the "/ccp4/bin/ccp4.setup-sh" commands, hgen still does not run from singularity There is a workaround. Create a script "run_hgen.sh" as follows:
#! /bin/bash
source /ccp4/bin/ccp4.setup-sh
hgen "$@"
and run thw script from singularity
chmod +x hgen.sh
singularity pull ccp4.sif docker://francecosta/ccp4:v0.0.5
singularity run ccp4.sif ./run_hgen.sh
or with python3:
singularity run ccp4.sif python3 -c "import os; os.system('./run_hgen.sh')"
Content type
Image
Digest
sha256:76139c335…
Size
4.3 GB
Last updated
about 3 years ago
docker pull francecosta/ccp4:v0.0.5