From 797a767d777ae61d291788f2c986d25b09601564 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kre=C5=A1imir=20Be=C5=A1tak?= <kbestak@gmail.com>
Date: Sun, 3 Nov 2024 01:23:35 +0000
Subject: [PATCH] added cellpose 3.1.0 dockerfile

---
 cellpose/3.1.0/Dockerfile | 66 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 66 insertions(+)
 create mode 100644 cellpose/3.1.0/Dockerfile

diff --git a/cellpose/3.1.0/Dockerfile b/cellpose/3.1.0/Dockerfile
new file mode 100644
index 00000000..f8a0f783
--- /dev/null
+++ b/cellpose/3.1.0/Dockerfile
@@ -0,0 +1,66 @@
+FROM python:3.11
+
+LABEL base_image="python:3.11"
+LABEL version="1"
+LABEL software="cellpose"
+LABEL software.version="3.1.0"
+LABEL about.summary="A generalist algorithm for cell and nucleus segmentation."
+LABEL about.home="https://github.com/MouseLand/cellpose"
+LABEL about.license="BSD-3-Clause"
+LABEL about.license_file="https://github.com/MouseLand/cellpose/blob/main/LICENSE"
+LABEL about.documentation="https://cellpose.readthedocs.io/en/latest/"
+LABEL extra.identifiers.biotools=cellpose
+
+MAINTAINER Yi Sun <sunyi000@gmail.com>
+MAINTAINER Florian Wuennemann <flowuenne@gmail.com>
+
+ARG DEBIAN_FRONTEND="noninteractive"
+ARG CELLPOSE_VERSION="3.1.0"
+
+ENV LANG en_US.UTF-8 \
+    LC_ALL en_US.UTF-8 \
+    LANGUAGE en_US:en
+
+ENV MPLCONFIGDIR=/tmp/mpl_cache
+ENV NUMBA_CACHE_DIR=/tmp/numba_cache
+ENV CELLPOSE_LOCAL_MODELS_PATH=/tmp/cellpose_models
+
+RUN apt-get update -qq && \
+    apt-get install -y -q --no-install-recommends \
+            gcc \
+            python3-dev \
+            python3-pip \
+            python3-wheel \
+            libblas-dev \
+            liblapack-dev \
+            libatlas-base-dev \
+            gfortran \
+            apt-utils \
+            bzip2 \
+            ca-certificates \
+            curl \
+            locales \
+            unzip && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* 
+
+RUN sed -i '/en_US.UTF-8/s/^# //g' /etc/locale.gen && \
+    locale-gen
+
+RUN pip install --no-cache-dir  -U pip \
+    numpy \
+    numba>=0.43.1 \
+    wheel \
+    scipy \
+    PyQt5 \
+    PyQt5.sip \
+    torch>=1.6 \
+    opencv-python-headless \
+    pyqtgraph>=0.11.0rc0 \
+    natsort \
+    scikit-image matplotlib \
+    scikit-learn \
+    tqdm \
+    tifffile \
+    fastremap \
+    cellpose==$CELLPOSE_VERSION
\ No newline at end of file