Move Docker container to alpine and update dependencies

cavenel · Feb 17, 2023 · 1e853ef · 1e853ef
1 parent 6b367ab
commit 1e853ef
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Showing 4 changed files with 59 additions and 10 deletions.
diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,6 @@
+examples
+plugins
+plugins_repo
+standalone
+build
+.git
diff --git a/container/Dockerfile b/container/Dockerfile
@@ -1,12 +1,42 @@
-FROM python:3.8
-
-# Install libvips and openslide
-RUN apt-get update && apt-get upgrade -y && apt-get install bash nano openslide-tools libvips -y
+FROM python:3.10-alpine
 
 COPY ./container/requirements.txt /requirements.txt
 COPY ./container/tissuumaps.cfg /tissuumaps.cfg
 
-RUN pip3 install -r /requirements.txt
+# Install libvips
+
+RUN apk update \
+	&& apk upgrade
+RUN apk add vips hdf5 hdf5-dev
+
+RUN pip3 install --upgrade pip setuptools wheel && \
+    apk add --no-cache --virtual .build-deps gfortran openblas-dev gcc g++ zlib-dev make python3-dev jpeg-dev && \
+    pip3 install -r /requirements.txt && \
+    apk del .build-deps
+
+# Install openslide
+
+WORKDIR /usr/local/src
+
+ARG OPENSLIDE_VERSION=3.4.1
+ARG OPENSLIDE_URL=https://github.com/openslide/openslide/releases/download
+
+COPY container/openslide-init.patch /usr/local/src
+
+RUN apk add --no-cache --virtual .build-deps2 build-base \
+	autoconf automake libtool bc zlib-dev libxml2-dev jpeg-dev \
+	openjpeg-dev tiff-dev glib-dev gdk-pixbuf-dev sqlite-dev libjpeg-turbo-dev \
+	libexif-dev lcms2-dev fftw-dev giflib-dev libpng-dev libwebp-dev orc-dev \
+	poppler-dev librsvg-dev libgsf-dev openexr-dev gtk-doc \
+    && wget ${OPENSLIDE_URL}/v${OPENSLIDE_VERSION}/openslide-${OPENSLIDE_VERSION}.tar.gz \
+	&& tar xf openslide-${OPENSLIDE_VERSION}.tar.gz \
+	&& patch -p0 <openslide-init.patch \
+    && cd openslide-${OPENSLIDE_VERSION} \
+	&& ./configure \
+	&& make \
+	&& make install \
+    && apk del .build-deps2
+
 RUN pip3 install gunicorn gevent
 
 COPY ./tissuumaps/ /app/tissuumaps

diff --git a/container/openslide-init.patch b/container/openslide-init.patch
@@ -0,0 +1,13 @@
+diff -Naur openslide-3.4.1-orig/src/openslide.c openslide-3.4.1/src/openslide.c
+--- openslide-3.4.1-orig/src/openslide.c	2015-04-20 20:32:12.000000000 +0100
++++ openslide-3.4.1/src/openslide.c	2018-03-23 16:47:13.788824940 +0000
+@@ -61,7 +61,9 @@
+     g_thread_init(NULL);
+   }
+   // initialize GObject
++#if !GLIB_CHECK_VERSION(2, 36, 0)
+   g_type_init();
++#endif
+   // init libxml2
+   xmlInitParser();
+   // parse debug options
diff --git a/container/requirements.txt b/container/requirements.txt
@@ -1,8 +1,8 @@
-Flask==2.0.0
-openslide-python==1.1.2
+scipy<1.9.0
+Flask>=2.0.0
+openslide-python>=1.1.2
 Pillow>=8.2.0
-pyvips==2.1.14
-matplotlib==3.2.2
+pyvips>=2.1.14
+matplotlib>=3.2.2
 pyyaml>=6.0
 h5py>=3.6.0
-scipy>=1.7.2