version 0.5.2 (#493)

* Add Dockerfile for newest Patchwork version 0.5.0

* Add files via upload

New version 0.5.2

* Delete Dockerfile

* new version 0.5.2

* julia 1.8.2

* correct patchwork compilation step

Author: ClaraKoehne

patchwork/0.5.2/Dockerfile

@@ -0,0 +1,65 @@
+# BASE IMAGE, Stage 1 #########################################################################################################
+
+FROM ubuntu:20.04 AS build
+
+RUN apt-get update --fix-missing && apt-get install -y sudo apt-utils --fix-missing
+RUN sudo apt-get update --fix-missing && sudo apt-get install -y wget gcc --fix-missing
+
+RUN groupadd --gid 1000 patchwork \
+    && useradd --uid 1000 --gid patchwork --shell /bin/bash --create-home patchwork \
+    && chmod -R a+rwx /home/patchwork
+WORKDIR /home/patchwork
+USER patchwork
+ENV VERSION 0.5.2
+
+RUN wget https://julialang-s3.julialang.org/bin/linux/x64/1.8/julia-1.8.3-linux-x86_64.tar.gz \
+    && tar xzvf julia-1.8.3-linux-x86_64.tar.gz 
+RUN wget http://github.com/bbuchfink/diamond/releases/download/v2.0.13/diamond-linux64.tar.gz \
+    && tar xvzf diamond-linux64.tar.gz
+ENV PATH /home/patchwork/julia-1.8.3/bin:$PATH
+RUN wget https://github.com/fethalen/Patchwork/archive/v$VERSION.tar.gz \
+    && tar xvzf v$VERSION.tar.gz && cd Patchwork-$VERSION \ 
+    && julia --project=. -e "import Pkg; Pkg.instantiate()" \
+    && julia --project=. src/compile.jl . src/precompiled.jl ../patchwork-$VERSION
+
+
+# To reduce the final image size, use a multi-stage build:
+# The final image doesn't contain a Julia installation, just Ubuntu as base image, the Patchwork binary and DIAMOND. 
+
+# BASE IMAGE, Stage 2 #########################################################################################################
+
+FROM ubuntu:20.04
+
+# METADATA ####################################################################################################################
+
+LABEL base_image="ubuntu:20.04"
+LABEL version="1"
+LABEL software="Patchwork"
+LABEL software.version="0.5.2"
+LABEL about.author="Felix Thalén <[email protected]>"
+LABEL about.summary="Alignment-based Exon Retrieval and Concatenation with Phylogenomic Applications"
+LABEL about.home="https://github.com/fethalen/Patchwork"
+LABEL about.documentation="https://github.com/fethalen/Patchwork#readme"
+LABEL about.license="SPDX:GPL-3.0"
+LABEL about.license_file="https://github.com/fethalen/Patchwork/blob/main/LICENSE"
+LABEL about.tags="phylogenomics"
+
+# MAINTAINER ##################################################################################################################
+
+# MAINTAINER Felix Thalén <[email protected]>
+
+# BUILD #######################################################################################################################
+
+RUN groupadd --gid 1000 patchwork \
+    && useradd --uid 1000 --gid patchwork --shell /bin/bash --create-home patchwork \
+    && chmod -R a+rwx /home/patchwork
+WORKDIR /home/patchwork
+USER patchwork
+ENV VERSION 0.5.2
+
+COPY --from=build /home/patchwork/patchwork-$VERSION patchwork-$VERSION
+COPY --from=build /home/patchwork/diamond diamond
+RUN ln -s patchwork-$VERSION/bin/patchwork patchwork
+ENV PATH /home/patchwork:$PATH
+
+CMD patchwork --help