container for micro-sam (#588)

* container for micro-sam * added Metadata * added label version * installing from specific commit * update micro-sam installation * Update micro-sam/1.1.1/Dockerfile --------- Co-authored-by: mboudet <[email protected]>
BioContainers · Jan 14, 2025 · 3c852c7 · 3c852c7
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diff --git a/micro-sam/1.1.1/Dockerfile b/micro-sam/1.1.1/Dockerfile
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+# Base Image
+FROM mambaorg/micromamba:1.5.10-noble
+
+# Matadata
+LABEL base.image="mambaorg/micromamba:1.5.10-noble"
+LABEL version="1"
+LABEL software="micro-sam"
+LABEL software.version="1.1.1"
+LABEL about.summary="Tools for segmentation and tracking in microscopy build on top of Segment Anything."
+LABEL about.home="https://github.com/computational-cell-analytics/micro-sam"
+LABEL about.documentation="https://computational-cell-analytics.github.io/micro-sam/micro_sam.html"
+LABEL about.license="MIT"
+LABEL about.license_file="https://github.com/computational-cell-analytics/micro-sam/blob/master/LICENSE"
+LABEL about.tags="Bioinformatics, Image Analysis, Microscopy, Segmentation"
+
+# Maintainer
+LABEL maintainer="Anwai Archit <[email protected]>"
+LABEL maintainer="Carolin Schwitalla <[email protected]>"
+
+
+# Copy conda.yml and install dependencies
+COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
+
+RUN micromamba install -y -n base -f /tmp/conda.yml \
+    && micromamba install -y -n base conda-forge::procps-ng \
+    && micromamba env export --name base --explicit > environment.lock \
+    && echo ">> CONDA_LOCK_START" \
+    && cat environment.lock \
+    && echo "<< CONDA_LOCK_END" \
+    && micromamba clean -a -y
+
+# Set the environment path
+ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
+
+USER root
+
+# clone the repository and install the package
+RUN pip install git+https://github.com/computational-cell-analytics/micro-sam.git@9b055c3
+
+
+
+
+
+
diff --git a/micro-sam/1.1.1/conda.yml b/micro-sam/1.1.1/conda.yml
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+name: sam
+channels:
+    - pytorch
+    - conda-forge
+dependencies:
+    - cpuonly
+    # This pin is necessary because later nifty versions have import errors on windows.
+    - nifty =1.2.1=*_4
+    - imagecodecs
+    - natsort
+    - pip
+    - zarr
+    - pooch
+    - protobuf <5
+    - python-xxhash
+    - python-elf >=0.4.8
+    - pytorch >=2.4
+    - segment-anything
+    - torchvision
+    - torch_em >=0.7.0
+    - tqdm
+    - timm
+    - git
+    - pip:
+        - git+https://github.com/ChaoningZhang/MobileSAM.git