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Update Dockerfile
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had issues solving apt dependencies, since seems like all the dependencies were pinned. I've relaxed these to make things more forward compatible
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akhanf authored Aug 19, 2022
1 parent 77bae7f commit fd898c0
Showing 1 changed file with 16 additions and 16 deletions.
32 changes: 16 additions & 16 deletions Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,13 @@ FROM debian:bullseye
LABEL maintainer="<[email protected]>"

# dcm2niix version
ENV DCM2NIIXTAG v1.0.20210317
ENV DCM2NIIXTAG v1.0.20220720

#heudiconv version:
ENV HEUDICONVTAG v0.10.0
ENV HEUDICONVTAG v0.11.3

#bids validator version:
ENV BIDSTAG 1.9.3
ENV BIDSTAG 1.9.7

#pydeface version:
ENV PYDEFACETAG v1.1.0
Expand All @@ -18,12 +18,12 @@ ARG DEBIAN_FRONTEND="noninteractive"
# install dcm2niix
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
apt-utils=2.2.4 \
ca-certificates=20210119 \
locales=2.31-13+deb11u3 \
pigz=2.6-1 \
unzip=6.0-26 \
wget=1.21-1+deb11u1 \
apt-utils \
ca-certificates \
locales \
pigz \
unzip \
wget \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& mkdir /opt/dcm2niix \
&& wget -q -O /opt/dcm2niix/dcm2niix.zip https://github.com/rordenlab/dcm2niix/releases/download/${DCM2NIIXTAG}/dcm2niix_lnx.zip \
Expand All @@ -44,15 +44,15 @@ RUN apt-get update -qq \
# install BIDS Validator
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
nodejs=12.22.5~dfsg-2~11u1 \
npm=7.5.2+ds-2 \
nodejs \
npm \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN npm install -g bids-validator@${BIDSTAG}

# install GNU parallel
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
parallel=20161222-1.1 \
parallel \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
&& echo "LANG=en_US.UTF-8" > /etc/locale.conf \
Expand All @@ -62,8 +62,8 @@ RUN apt-get update -qq \
# install FSL flirt and fslorient
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
libxml2-dev=2.9.10+dfsg-6.7+deb11u1 \
libopenblas-dev=0.3.13+ds-3 \
libxml2-dev \
libopenblas-dev \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN pip install --no-cache-dir pytest===3.6.0 networkx==2.0
ENV FSLDIR /opt/fsl
Expand All @@ -77,8 +77,8 @@ ENV PATH $FSLDIR/bin:$PATH
# install pydeface
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
git=1:2.30.2-1 \
python3-setuptools=52.0.0-4 \
git \
python3-setuptools \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& git clone https://github.com/poldracklab/pydeface /src/pydeface \
&& git -C /src/pydeface checkout ${PYDEFACETAG}
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