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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
author goeckslab
date Tue, 06 Sep 2022 21:15:56 +0000
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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1 FROM python:3.7.12
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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3 ENV OPS_VERSION=3.4.1
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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5 ENV PALOM_VERSION=2022.8.2
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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7 RUN apt update -y && apt install -y openslide-tools python3-opencv
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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9 RUN cd /opt && \
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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10 wget https://github.com/openslide/openslide/releases/download/v$OPS_VERSION/openslide-$OPS_VERSION.tar.gz && \
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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11 tar -zxvf openslide-$OPS_VERSION.tar.gz && \
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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12 cd openslide-$OPS_VERSION
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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14 RUN /opt/openslide-$OPS_VERSION/configure && \
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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15 make && \
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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16 make install
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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18 RUN pip install zarr==2.10.3 pandas palom==$PALOM_VERSION