diff --git a/Dockerfile b/Dockerfile index 82ea6d6..ba06feb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.6.8-slim +FROM python:3.7.4-slim ENV DEBIAN_FRONTEND=noninteractive RUN BUILDPKGS="build-essential apt-utils \ @@ -9,7 +9,7 @@ RUN BUILDPKGS="build-essential apt-utils \ apt-get install -y debconf locales && dpkg-reconfigure locales && \ apt-get install -y $BUILDPKGS && \ ### run time: - apt-get install -y zlib1g hdf5-tools gfortran libgcc1 libstdc++ musl \ + apt-get install -y zlib1g hdf5-tools gfortran libgcc1 libstdc++6 musl \ libopenblas-base tcl tk libxml2 libffi6 less procps # install dependencies: @@ -18,9 +18,9 @@ RUN pip install --no-cache-dir --upgrade pip && \ pip install --no-cache-dir -r /tmp/requirements_docker.txt # use version from argument (--build-arg version=0.9.7), or a default: -ARG version="0.9.15" +ARG version="0.9.16" RUN pip install --no-cache-dir pyscenic==$version && \ - pip install --no-cache-dir scanpy==1.4.4 + pip install --no-cache-dir scanpy==1.4.4.post1 RUN apt-get remove --purge -y $BUILDPKGS && \ rm -rf /var/lib/apt/lists/* diff --git a/Singularity b/Singularity index 9713404..f766699 100644 --- a/Singularity +++ b/Singularity @@ -1,5 +1,5 @@ BootStrap: docker -From: python:3.6.8-slim +From: python:3.7.4-slim %files ./requirements_docker.txt /tmp/ @@ -11,13 +11,13 @@ From: python:3.6.8-slim tcl-dev tk-dev libxml2-dev zlib1g-dev libffi-dev cmake" apt-get update apt-get install -y debconf locales && dpkg-reconfigure locales - apt-get install -y zlib1g hdf5-tools gfortran libgcc1 libstdc++ musl \ + apt-get install -y zlib1g hdf5-tools gfortran libgcc1 libstdc++6 musl \ libopenblas-base tcl tk libxml2 libffi6 less procps apt-get install -y $BUILDPKGS pip install --no-cache-dir -r /tmp/requirements_docker.txt - pip install --no-cache-dir --upgrade pyscenic==0.9.15 - pip install --no-cache-dir scanpy==1.4.4 + pip install --no-cache-dir --upgrade pyscenic==0.9.16 + pip install --no-cache-dir scanpy==1.4.4.post1 apt-get remove --purge -y $BUILDPKGS && \ rm -rf /var/lib/apt/lists/* diff --git a/Singularity.0.9.16 b/Singularity.0.9.16 new file mode 100644 index 0000000..f766699 --- /dev/null +++ b/Singularity.0.9.16 @@ -0,0 +1,24 @@ +BootStrap: docker +From: python:3.7.4-slim + +%files + ./requirements_docker.txt /tmp/ + +%post + BUILDPKGS="build-essential apt-utils \ + python3-dev libhdf5-dev libfreetype6-dev libtool \ + m4 autoconf automake patch bison flex libpng-dev libopenblas-dev \ + tcl-dev tk-dev libxml2-dev zlib1g-dev libffi-dev cmake" + apt-get update + apt-get install -y debconf locales && dpkg-reconfigure locales + apt-get install -y zlib1g hdf5-tools gfortran libgcc1 libstdc++6 musl \ + libopenblas-base tcl tk libxml2 libffi6 less procps + apt-get install -y $BUILDPKGS + + pip install --no-cache-dir -r /tmp/requirements_docker.txt + pip install --no-cache-dir --upgrade pyscenic==0.9.16 + pip install --no-cache-dir scanpy==1.4.4.post1 + + apt-get remove --purge -y $BUILDPKGS && \ + rm -rf /var/lib/apt/lists/* + diff --git a/requirements_docker.txt b/requirements_docker.txt index 0bb01f1..15a11a3 100644 --- a/requirements_docker.txt +++ b/requirements_docker.txt @@ -28,7 +28,7 @@ kiwisolver==1.1.0 llvmlite==0.29.0 loompy==2.0.17 louvain==0.6.1 -matplotlib==3.0.2 +matplotlib==3.1.1 mock==3.0.5 msgpack==0.6.1 MulticoreTSNE==0.1