run with docker

Dockerfile

@@ -1,44 +1,31 @@
-# From ubuntu:18.04
-#FROM debian:10
-FROM continuumio/miniconda3
-
-ENV DEBIAN_FRONTEND=noninteractive
+FROM alpine:latest AS builder
 
 WORKDIR /workspaces
-
-RUN apt-get update \
-    # Install C++ tools
-    && apt-get -y install build-essential cmake cppcheck valgrind \
-            libglpk-dev libgsl-dev libgmp-dev libltdl-dev libmpfr-dev pkg-config \
-    # Clean up
-    && rm -f *.deb \
-    && apt-get autoremove -y \
-    && apt-get clean -y \
-    && rm -rf /var/lib/apt/lists/*
-
-# Switch back to dialog for any ad-hoc use of apt-get
-ENV DEBIAN_FRONTEND=dialog
-
-# install ViennaRNA package from bioconda
-RUN conda config --add channels conda-forge && \
-    conda config --add channels bioconda && \
-    conda update --all && \
-    conda install viennarna && \
-    conda clean -afy
-ENV PKG_CONFIG_PATH /opt/conda/lib/pkgconfig:$PKG_CONFIG_PATH
-
+RUN apk add --no-cache musl-dev gcc g++ cmake make ninja git pkgconfig zlib-static
+
+# HiGHS
+RUN git clone https://github.com/ERGO-Code/HiGHS \
+    && cd HiGHS \
+    && cmake -DFAST_BUILD=ON -DCMAKE_BUILD_TYPE=Release -G Ninja -B build \
+    && cmake --build build \
+    && cmake --install build --strip \
+    && cd ..
+
+# ViennaRNA
+COPY --from=satoken/viennarna:latest /usr/local/ /usr/local/
 # build from the source
 # RUN wget -q https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.17.tar.gz \
 #     && tar zxvf ViennaRNA-2.4.17.tar.gz \
 #     && cd ViennaRNA-2.4.17 \
-#     && ./configure --without-perl --without-python --without-python3 --without-forester --without-rnalocmin \
+#     && ./configure --without-perl --without-python --without-python2 --without-forester --without-rnalocmin \
 #     && make && make install \
 #     && cd .. && rm -rf ViennaRNA-2.4.17 ViennaRNA-2.4.17.tar.gz 
 
-COPY . .
+# IPknot
+COPY . . 
+RUN cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_HIGHS=ON -DSTATIC_BUILD=ON -G Ninja -B build \
+    && cmake --build build \
+    && cmake --install build --strip 
 
-RUN rm -rf build && mkdir build \
-    && cd build \
-    && cmake -DCMAKE_BUILD_TYPE=Release .. \
-    #&& cmake -DCMAKE_BUILD_TYPE=Release -DSTATIC_BUILD=ON .. \
-    && make && make install
+FROM alpine:latest
+COPY --from=builder /usr/local/bin/ipknot /usr/local/bin/ipknot

README.md

@@ -4,12 +4,16 @@ IPknot for predicting RNA pseudoknot structures using integer programming
 Requirements
 ------------
 
+* C++17 compatible compiler (tested on Apple clang version 14.0.0 and GCC version 10.2.1) 
+* cmake (>= 3.8)
+* pkg-config
 * [Vienna RNA package](https://www.tbi.univie.ac.at/RNA/) (>= 2.2.0)
-* [GNU Linear Programming Kit](http://www.gnu.org/software/glpk/) (>=4.41),
-  [Gurobi Optimizer](http://www.gurobi.com/) (>=8.0),
-  or [ILOG CPLEX](https://www.ibm.com/products/ilog-cplex-optimization-studio) (>=12.0)
-  or [SCIP](https://scipopt.org/) (>= 8.0.3)
-  or [HiGHS](https://highs.dev/) (>= 1.5.0)
+* one of these MIP solvers
+	* [GNU Linear Programming Kit](http://www.gnu.org/software/glpk/) (>=4.41)
+	* [Gurobi Optimizer](http://www.gurobi.com/) (>=8.0)
+	* [ILOG CPLEX](https://www.ibm.com/products/ilog-cplex-optimization-studio) (>=12.0)
+	* [SCIP](https://scipopt.org/) (>= 8.0.3)
+	* [HiGHS](https://highs.dev/) (>= 1.5.0)
 
 Install
 -------
@@ -100,6 +104,16 @@ IPknot can fold a given sequence or alignment with some constraints. The constra
 
 This example shows folding with constraints that 16th base and 100th base are paired, 41st and 42nd bases are unpaired.
 
+### Run with Docker
+
+	docker build . -t ipknot
+	docker run -it --rm -v $(pwd):$(pwd) -w $(pwd) ipknot ipknot examples/RF00005.fa
+
+### Run with the web server
+
+The IPknot web server is available at http://ws.sato-lab.org/rtips/ipknot++/.
+
+
 References
 ----------
 

src/ip.cpp

@@ -494,6 +494,7 @@ class IPimpl
     : model_()
   {
     highs_.setOptionValue("output_flag", false);
+    highs_.setOptionValue("threads", n_th);
     switch (dir)
     {
       default: