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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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@@ -2,13 +2,13 @@ FROM debian:bullseye | |
LABEL maintainer="<[email protected]>" | ||
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||
# dcm2niix version | ||
ENV DCM2NIIXTAG v1.0.20210317 | ||
ENV DCM2NIIXTAG v1.0.20220720 | ||
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#heudiconv version: | ||
ENV HEUDICONVTAG v0.10.0 | ||
ENV HEUDICONVTAG v0.11.3 | ||
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#bids validator version: | ||
ENV BIDSTAG 1.9.3 | ||
ENV BIDSTAG 1.9.7 | ||
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#pydeface version: | ||
ENV PYDEFACETAG v1.1.0 | ||
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@@ -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/${DCM2NIIXTAG}/dcm2niix_lnx.zip \ | ||
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@@ -44,15 +44,15 @@ RUN apt-get update -qq \ | |
# install BIDS Validator | ||
RUN apt-get update -qq \ | ||
&& apt-get install -y -q --no-install-recommends \ | ||
nodejs=12.22.5~dfsg-2~11u1 \ | ||
npm=7.5.2+ds-2 \ | ||
nodejs \ | ||
npm \ | ||
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* | ||
RUN npm install -g bids-validator@${BIDSTAG} | ||
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# 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 \ | ||
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@@ -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 | ||
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@@ -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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