diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index ed336988e0e054682d0eea49c00adea16e85fe56..3e8932c136120938c6480b7492fb2b5f8ae177c7 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -20,76 +20,76 @@ build-test-image: # - git checkout master -- requirements.txt - docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests - docker push "$CI_REGISTRY_IMAGE/testing-ubuntu" + # tags: + # - k8s + +build-install-barrnap: + only: + - docker + stage: build + script: + - apk update #; apk add git + # - git checkout master -- requirements.txt + - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" for_build/barrnap_only + - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" tags: - k8s -# build-install-barrnap: -# only: -# - docker -# stage: build -# script: -# - apk update #; apk add git -# # - git checkout master -- requirements.txt -# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" for_build/barrnap_only -# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" -# tags: -# - k8s - -# build-install-annote-and-quicktree: -# only: -# - docker -# stage: build -# script: -# - apk update #; apk add git -# # - git checkout master -- requirements.txt -# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" for_build/annote_and_1tree -# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" -# tags: -# - k8s +build-install-annote-and-quicktree: + only: + - docker + stage: build + script: + - apk update #; apk add git + # - git checkout master -- requirements.txt + - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" for_build/annote_and_1tree + - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" + tags: + - k8s -# build-ubuntu: -# only: -# - docker -# stage: build -# script: -# - apk update # ; apk add git -# # - git checkout master -- requirements.txt -# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/ubuntu -# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu" -# tags: -# - k8s +build-ubuntu: + only: + - docker + stage: build + script: + - apk update # ; apk add git + # - git checkout master -- requirements.txt + - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/ubuntu + - docker push "$CI_REGISTRY_IMAGE/install-ubuntu" + tags: + - k8s -# build-mafft: -# only: -# - docker -# stage: build -# script: -# - apk update # ; apk add git -# # - git checkout master -- requirements.txt -# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mafft" for_build/mafft -# - docker push "$CI_REGISTRY_IMAGE/install-mafft" -# tags: -# - k8s +build-mafft: + only: + - docker + stage: build + script: + - apk update # ; apk add git + # - git checkout master -- requirements.txt + - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mafft" for_build/mafft + - docker push "$CI_REGISTRY_IMAGE/install-mafft" + tags: + - k8s -# build-mmseqs_and_fastme: -# only: -# - docker -# stage: build -# script: -# - apk update # ; apk add git -# # - git checkout master -- requirements.txt -# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" for_build/mmseqs_and_fastme -# - docker push "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" -# tags: -# - k8s +build-mmseqs_and_fastme: + only: + - docker + stage: build + script: + - apk update # ; apk add git + # - git checkout master -- requirements.txt + - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" for_build/mmseqs_and_fastme + - docker push "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" + tags: + - k8s -# build-install-prodigal: -# only: -# - docker -# stage: build -# script: -# - apk update -# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-prodigal" for_build/prodigal -# - docker push "$CI_REGISTRY_IMAGE/install-prodigal" -# tags: -# - k8s +build-install-prodigal: + only: + - docker + stage: build + script: + - apk update + - docker build --pull -t "$CI_REGISTRY_IMAGE/install-prodigal" for_build/prodigal + - docker push "$CI_REGISTRY_IMAGE/install-prodigal" + tags: + - k8s diff --git a/for_build/annote_and_1tree/Dockerfile b/for_build/annote_and_1tree/Dockerfile index ae036220932167779d39ab1353a80f291fa8823b..33143dd076bf6ca1aeb53cf4fef01e90f35e107e 100644 --- a/for_build/annote_and_1tree/Dockerfile +++ b/for_build/annote_and_1tree/Dockerfile @@ -1,4 +1,4 @@ -from ubuntu:18.04 +from ubuntu:20.04 # Update apt-get packages RUN apt-get update &&\ @@ -13,30 +13,31 @@ RUN apt-get install -y \ RUN pip3 install --upgrade pip # Update makeblastdb and blastp for prokka -WORKDIR /tmp -RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.1+-x64-linux.tar.gz &&\ +WORKDIR /install_dir +RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2.10.1+-x64-linux.tar.gz &&\ tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\ - cp /tmp/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\ - cp /tmp/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\ + cp /install_dir/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\ + cp /install_dir/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\ rm ncbi-blast-2.10.1+-x64-linux.tar.gz + # Install prokka: -WORKDIR /tmp -RUN apt-get install -y\ +WORKDIR /install_dir +RUN DEBIAN_FRONTEND="noninteractive" apt install -y\ libdatetime-perl \ libxml-simple-perl \ libdigest-md5-perl \ git \ default-jre \ - bioperl &&\ - git clone https://github.com/tseemann/prokka.git &&\ - /tmp/prokka/bin/prokka --setupdb &&\ - ln -s /tmp/prokka/bin/prokka /usr/local/bin -RUN rm /usr/bin/mafft # remove mafft installed with bioperl + bioperl +RUN git clone https://github.com/tseemann/prokka.git +RUN /install_dir/prokka/bin/prokka --setupdb &&\ + ln -s /install_dir/prokka/bin/prokka /usr/local/bin + # Install quicktree -WORKDIR /tmp +WORKDIR /install_dir RUN git clone https://github.com/tseemann/quicktree -WORKDIR quicktree +WORKDIR /install_dir/quicktree RUN make &&\ - ln -s /tmp/quicktree/quicktree /usr/local/bin + ln -s /install_dir/quicktree/quicktree /usr/local/bin diff --git a/for_build/barrnap_only/Dockerfile b/for_build/barrnap_only/Dockerfile index bedd3541364f034eea6ccb95c0ce0352a83e0958..cf8796561540b457f4f0776865d9e9d50f0feff4 100644 --- a/for_build/barrnap_only/Dockerfile +++ b/for_build/barrnap_only/Dockerfile @@ -1,4 +1,4 @@ -from ubuntu:18.04 +from ubuntu:20.04 # Update apt-get packages RUN apt-get update &&\ @@ -18,12 +18,14 @@ RUN apt-get install -y \ RUN pip3 install --upgrade pip - # Install barrnap -WORKDIR /tmp +WORKDIR /install_dir RUN wget https://github.com/tseemann/barrnap/archive/0.8.tar.gz &&\ tar -xf 0.8.tar.gz &&\ - rm 0.8.tar.gz -RUN ln -s /tmp/barrnap-0.8/bin/barrnap /usr/local/bin + rm 0.8.tar.gz &&\ + mv /install_dir/barrnap-0.8/bin/barrnap /usr/local/bin &&\ + # Remove heavy useless files + rm -r /install_dir/barrnap-0.8/examples /install_dir/barrnap-0.8/build/*.aln + RUN rm /usr/bin/mafft # remove mafft installed with bioperl \ No newline at end of file diff --git a/for_build/mafft/Dockerfile b/for_build/mafft/Dockerfile index b704424253098b713afb435de46ad7383e2590b7..2c277cffd96534a059b45a984d40c8dd02c1aa1d 100644 --- a/for_build/mafft/Dockerfile +++ b/for_build/mafft/Dockerfile @@ -1,4 +1,4 @@ -from ubuntu:18.04 +from ubuntu:20.04 # Update apt-get packages RUN apt-get update &&\ @@ -25,11 +25,11 @@ RUN apt-get install -y \ # Install mafft 7.313 RUN rm /usr/bin/mafft # remove mafft installed with bioperl -WORKDIR /tmp +WORKDIR /install_dir RUN wget https://mafft.cbrc.jp/alignment/software/mafft-7.313-with-extensions-src.tgz &&\ tar xf mafft-7.313-with-extensions-src.tgz &&\ rm mafft-7.313-with-extensions-src.tgz -WORKDIR /tmp/mafft-7.313-with-extensions/core +WORKDIR /install_dir/mafft-7.313-with-extensions/core RUN make clean &&\ make &&\ make install diff --git a/for_build/mmseqs_and_fastme/Dockerfile b/for_build/mmseqs_and_fastme/Dockerfile index 4a8873b4c8d70f84a687f36b5f41580fa4a8deaf..97362ba9ee190a1832087d650aa8ecba669c7a03 100644 --- a/for_build/mmseqs_and_fastme/Dockerfile +++ b/for_build/mmseqs_and_fastme/Dockerfile @@ -1,4 +1,4 @@ -from ubuntu:18.04 +from ubuntu:20.04 # Update apt-get packages @@ -16,21 +16,21 @@ RUN apt-get install -y \ RUN pip3 install --upgrade pip -# Install MMseqs2 (Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e ?) -WORKDIR /tmp +# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e +WORKDIR /install_dir RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\ tar xvfz mmseqs-linux-sse41.tar.gz &&\ rm mmseqs-linux-sse41.tar.gz &&\ - mv /tmp/mmseqs/bin/mmseqs /usr/local/bin &&\ + mv /install_dir/mmseqs/bin/mmseqs /usr/local/bin &&\ # remove useless files - rm -r /tmp/mmseqs + rm -r /install_dir/mmseqs -# Install FastME -WORKDIR /tmp +# Install FastME FastME 2.1.6.1 +WORKDIR /install_dir RUN apt-get install -y automake &&\ git clone https://gite.lirmm.fr/atgc/FastME.git -WORKDIR /tmp/FastME -RUN ./configure &&\ - make &&\ - make install +WORKDIR /install_dir/FastME/tarball +RUN tar xzf fastme-2.1.6.2.tar.gz &&\ + rm fastme-2.1.6.2.tar.gz &&\ + ln -s /install_dir/FastME/tarball/fastme-2.1.6.2/binaries/fastme-2.1.6.2-linux64-omp /usr/local/bin/fastme diff --git a/for_build/prodigal/Dockerfile b/for_build/prodigal/Dockerfile index 7a96db04b3e806653f13fefc2caa8895ff09408a..1635900c2dd2d66b1b67de2dc011e370c9dc9bb8 100644 --- a/for_build/prodigal/Dockerfile +++ b/for_build/prodigal/Dockerfile @@ -1,4 +1,4 @@ -from ubuntu:18.04 +from ubuntu:20.04 # Update apt-get packages RUN apt-get update &&\ @@ -14,8 +14,12 @@ RUN apt-get install -y \ # Upgrade pip RUN pip3 install --upgrade pip + # Install prodigal -RUN apt-get install zlib1g-dev &&\ - git clone https://github.com/hyattpd/Prodigal.git -WORKDIR Prodigal -RUN make install +WORKDIR /install_dir +RUN wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz &&\ + tar -xzf v2.6.3.tar.gz &&\ + rm v2.6.3.tar.gz +WORKDIR /install_dir/Prodigal-2.6.3 +RUN make &&\ + make install \ No newline at end of file diff --git a/for_build/ubuntu/Dockerfile b/for_build/ubuntu/Dockerfile index 47efcbda77e16e4c6fdc2a71ee5ebea0a30da2e6..609ade9713b46622cf4793f05f747427c2cd59fb 100644 --- a/for_build/ubuntu/Dockerfile +++ b/for_build/ubuntu/Dockerfile @@ -1,4 +1,4 @@ -from ubuntu:18.04 +from ubuntu:20.04 # Update apt-get packages RUN apt-get update &&\ diff --git a/for_tests/Dockerfile b/for_tests/Dockerfile index 63324a439e6231badc2621b097291ad9bc075d03..e122f6735230347ad143af89635c8e844694e34e 100644 --- a/for_tests/Dockerfile +++ b/for_tests/Dockerfile @@ -96,7 +96,7 @@ RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\ ln -s /install_dir/FastTreeMP /usr/local/bin -## Install FastME FastME 2.1.6.1 +# Install FastME FastME 2.1.6.1 WORKDIR /install_dir RUN apt-get install -y automake &&\ git clone https://gite.lirmm.fr/atgc/FastME.git