From 303fefc0b39d65957080032d632e7b6b9c2a5e14 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Wed, 6 Nov 2024 14:25:08 +0100 Subject: [PATCH 1/5] container for micro-sam --- micro-sam/1.1.1/Dockerfile | 22 ++++++++++++++++++++++ micro-sam/1.1.1/conda.yml | 25 +++++++++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 micro-sam/1.1.1/Dockerfile create mode 100644 micro-sam/1.1.1/conda.yml diff --git a/micro-sam/1.1.1/Dockerfile b/micro-sam/1.1.1/Dockerfile new file mode 100644 index 00000000..81feb632 --- /dev/null +++ b/micro-sam/1.1.1/Dockerfile @@ -0,0 +1,22 @@ +FROM mambaorg/micromamba:1.5.10-noble + +# 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 git clone https://github.com/computational-cell-analytics/micro-sam.git \ + && cd micro-sam \ + && pip install -e . \ No newline at end of file diff --git a/micro-sam/1.1.1/conda.yml b/micro-sam/1.1.1/conda.yml new file mode 100644 index 00000000..604548d2 --- /dev/null +++ b/micro-sam/1.1.1/conda.yml @@ -0,0 +1,25 @@ +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 \ No newline at end of file From 0043141b306fb06ef1408a19acec0b50ce0878e2 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Thu, 7 Nov 2024 10:58:18 +0100 Subject: [PATCH 2/5] added Metadata --- micro-sam/1.1.1/Dockerfile | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/micro-sam/1.1.1/Dockerfile b/micro-sam/1.1.1/Dockerfile index 81feb632..a2e68806 100644 --- a/micro-sam/1.1.1/Dockerfile +++ b/micro-sam/1.1.1/Dockerfile @@ -1,5 +1,22 @@ +# Base Image FROM mambaorg/micromamba:1.5.10-noble +# Matadata +LABEL base.image="mambaorg/micromamba:1.5.10-noble" +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 License" +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 " +LABEL maintainer="Carolin Schwitalla " + + # Copy conda.yml and install dependencies COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml From 294826fe5e78fd210d5ca5b21240d4a7ad742969 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Thu, 7 Nov 2024 11:02:35 +0100 Subject: [PATCH 3/5] added label version --- micro-sam/1.1.1/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/micro-sam/1.1.1/Dockerfile b/micro-sam/1.1.1/Dockerfile index a2e68806..fc4fe501 100644 --- a/micro-sam/1.1.1/Dockerfile +++ b/micro-sam/1.1.1/Dockerfile @@ -3,6 +3,7 @@ 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." From a113f3ba6e4bf1baa4d0b61ae794912600e9d67b Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Tue, 3 Dec 2024 13:10:56 +0100 Subject: [PATCH 4/5] installing from specific commit --- micro-sam/1.1.1/Dockerfile | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/micro-sam/1.1.1/Dockerfile b/micro-sam/1.1.1/Dockerfile index fc4fe501..8e10e6f8 100644 --- a/micro-sam/1.1.1/Dockerfile +++ b/micro-sam/1.1.1/Dockerfile @@ -37,4 +37,10 @@ USER root # clone the repository and install the package RUN git clone https://github.com/computational-cell-analytics/micro-sam.git \ && cd micro-sam \ - && pip install -e . \ No newline at end of file + && git checkout 9b055c3 \ + && pip install -e . + + + + + \ No newline at end of file From 345f7726a7d35bf8d648f3133f467ec5ae95eccc Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Mon, 30 Dec 2024 17:23:42 +0100 Subject: [PATCH 5/5] update micro-sam installation --- micro-sam/1.1.1/Dockerfile | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/micro-sam/1.1.1/Dockerfile b/micro-sam/1.1.1/Dockerfile index 8e10e6f8..431eb470 100644 --- a/micro-sam/1.1.1/Dockerfile +++ b/micro-sam/1.1.1/Dockerfile @@ -35,10 +35,8 @@ ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH" USER root # clone the repository and install the package -RUN git clone https://github.com/computational-cell-analytics/micro-sam.git \ - && cd micro-sam \ - && git checkout 9b055c3 \ - && pip install -e . +RUN pip install git+https://github.com/computational-cell-analytics/micro-sam.git@9b055c3 +