diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index dc1f4f8c311c8bed9000cd9a277a96a6f97ff967..b1310cbbd959be708e694a3c9f25d0a2782aa910 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -19,34 +19,25 @@ build-test-image: - docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests - docker push "$CI_REGISTRY_IMAGE/testing-ubuntu" -# 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" - -# build-install-prokka: -# only: -# - docker -# stage: build -# script: -# - apk update ; apk add git -# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-prokkaonly" for_build/prokka_only -# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-prokkaonly" +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" -# 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" +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" build-ubuntu: only: @@ -58,16 +49,6 @@ build-ubuntu: - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/ubuntu - docker push "$CI_REGISTRY_IMAGE/install-ubuntu" -# build-annote_and_mafft: -# only: -# - docker -# stage: build -# script: -# - apk update ; apk add git -# - git checkout master -- requirements.txt -# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/annote_and_mafft -# - docker push "$CI_REGISTRY_IMAGE/install-annote-and-mafft" - build-mafft: only: - docker @@ -78,12 +59,12 @@ build-mafft: - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mafft" for_build/mafft - docker push "$CI_REGISTRY_IMAGE/install-mafft" -# build-mmseqs_and_fastme: -# only: -# - docker -# stage: build -# script: -# - apk update ; apk add git -# - git checkout master -- requirements.txt -# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/mmseqs_and_fastme -# - docker push "$CI_REGISTRY_IMAGE/install-mmseqs-and-fastme" +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" diff --git a/for_build/annote_and_mafft/Dockerfile b/for_build/annote_and_mafft/Dockerfile deleted file mode 100644 index 54a54a40616f16c2783458f8f83bf4194d37deab..0000000000000000000000000000000000000000 --- a/for_build/annote_and_mafft/Dockerfile +++ /dev/null @@ -1,26 +0,0 @@ -from ubuntu:16.04 - -# Update apt-get packages -RUN apt-get update &&\ - apt-get -y upgrade - -# Install package needed -RUN apt-get install -y \ - wget \ - python3-pip - -# Update pip -RUN pip3 install --upgrade pip - -# Install prokka: -WORKDIR /tmp -RUN apt-get install -y\ - libdatetime-perl \ - libxml-simple-perl \ - libdigest-md5-perl \ - git \ - default-jre \ - bioperl -RUN git clone https://github.com/tseemann/prokka.git -RUN /tmp/prokka/bin/prokka --setupdb -RUN ln -s /tmp/prokka/bin/prokka /usr/local/bin diff --git a/for_build/prokka_only/Dockerfile b/for_build/prokka_only/Dockerfile deleted file mode 100644 index 47c01cd439dbda1b3a1791ad1f5203dee3b02168..0000000000000000000000000000000000000000 --- a/for_build/prokka_only/Dockerfile +++ /dev/null @@ -1,28 +0,0 @@ -from ubuntu:16.04 - -# Update apt-get packages -RUN apt-get update &&\ - apt-get -y upgrade - -# Install package needed -RUN apt-get install -y \ - wget \ - python3-pip - -# Update pip -RUN pip3 install --upgrade pip - -# Install prokka: -WORKDIR /tmp -RUN apt-get install -y\ - libdatetime-perl \ - libxml-simple-perl \ - libdigest-md5-perl \ - git \ - default-jre \ - bioperl -RUN git clone https://github.com/tseemann/prokka.git -RUN /tmp/prokka/bin/prokka --setupdb -RUN ln -s /tmp/prokka/bin/prokka /usr/local/bin - -RUN rm /usr/bin/mafft # remove mafft installed with bioperl