From 924fa22f5d75124af80b729e60761e8cdb8fd089 Mon Sep 17 00:00:00 2001 From: Dan Levitas Date: Mon, 12 Aug 2024 16:26:07 +0000 Subject: [PATCH] [ENH] update how pet2bids is installed --- handler/Dockerfile | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/handler/Dockerfile b/handler/Dockerfile index a1b38fe..f86d043 100755 --- a/handler/Dockerfile +++ b/handler/Dockerfile @@ -9,12 +9,17 @@ RUN apt update && \ RUN apt install -y parallel python3 python3-pip tree curl unzip git jq python libgl-dev python-numpy -RUN pip3 install numpy==1.23.0 nibabel==4.0.0 pandas==1.0.1 matplotlib pyyaml==5.4.1 pydicom==2.3.1 natsort pydeface && \ - pip3 install quickshear pypet2bids==1.3.9 mne mne-bids +RUN pip3 install numpy==1.23.0 nibabel==4.0.0 pandas matplotlib pyyaml==5.4.1 pydicom==2.3.1 natsort pydeface && \ + pip3 install quickshear mne mne-bids + +# Install pypet2bids +RUN git clone https://github.com/openneuropet/PET2BIDS && \ + cd PET2BIDS && make installpoetry buildpackage installpackage RUN apt-get install -y build-essential pkg-config cmake git pigz rename zstd libopenjp2-7 libgdcm-tools wget libopenblas-dev && \ apt-get clean -y && apt-get autoclean -y && apt-get autoremove -y + RUN touch /.pet2bidsconfig && chown 1001:1001 /.pet2bidsconfig RUN echo "DEFAULT_METADATA_JSON=/usr/local/lib/python3.8/dist-packages/pypet2bids/template_json.json" > /.pet2bidsconfig