diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 1abc8bd5bc159110f2ee22647ceafaec6cec8752..7031d7cb7b100cba56cf93a57f887e989551d8c5 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -10,17 +10,17 @@ variables: before_script: - docker login -u gitlab-ci-token -p "$CI_BUILD_TOKEN" registry-gitlab.pasteur.fr -# build-test-image: -# only: -# - docker -# stage: build -# script: -# - apk update # ; apk add git ; apk add apt-utils -# # - git checkout master -- requirements.txt -# - docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests -# - docker push "$CI_REGISTRY_IMAGE/testing-ubuntu" -# tags: -# - k8s +build-test-image: + only: + - docker + stage: build + script: + - apk update # ; apk add git ; apk add apt-utils + # - git checkout master -- requirements.txt + - docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests + - docker push "$CI_REGISTRY_IMAGE/testing-ubuntu" + tags: + - k8s build-install-barrnap: only: diff --git a/for_build/mmseqs_and_fastme/Dockerfile b/for_build/mmseqs_and_fastme/Dockerfile index c02a9ee34e00ab0a12b7931297d1ab23374acf7a..4a8873b4c8d70f84a687f36b5f41580fa4a8deaf 100644 --- a/for_build/mmseqs_and_fastme/Dockerfile +++ b/for_build/mmseqs_and_fastme/Dockerfile @@ -16,7 +16,7 @@ RUN apt-get install -y \ RUN pip3 install --upgrade pip -# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e +# Install MMseqs2 (Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e ?) WORKDIR /tmp RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\ tar xvfz mmseqs-linux-sse41.tar.gz &&\ diff --git a/for_tests/Dockerfile b/for_tests/Dockerfile index 4a3397863dfc2040f43b8d683bec4e3655add01b..5989324d37705a0bf5f6cc8bfec237978432c019 100644 --- a/for_tests/Dockerfile +++ b/for_tests/Dockerfile @@ -79,10 +79,8 @@ RUN make clean &&\ # Install FastTree version 2.1.11 Double precision (No SSE3) WORKDIR /tmp RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\ - gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP FastTree.c -lm &&\# ln -s /tmp/FastTre#eMP /usr/local/bin# - - -# Install FastME FastME 2.1.6.1 + gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP astTree.c -lm &&\ + ln -s /tmp/FastTre#eMP /usr/local/bin## Install FastME FastME 2.1.6.1 WORKDIR /tmp RUN apt-get install -y automake &&\ git clone https://gite.lirmm.fr/atgc/FastME.git @@ -92,10 +90,9 @@ RUN ./configure &&\ make install -## Install quicktree -#WORKDIR /tmp -#RUN git clone https://github.com/tseemann/quicktree -#WORKDIR quicktree -#RUN make &&\ -# ln -s /tmp/quicktree/quicktree /usr/local/bin -# \ No newline at end of file +# Install quicktree +WORKDIR /tmp +RUN git clone https://github.com/tseemann/quicktree +WORKDIR quicktree +RUN make &&\ + ln -s /tmp/quicktree/quicktree /usr/local/bin