diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index b4dd82cb0f0edbea30af277e4d3c9c4f538a457c..405fa32b4caf81132208f035a0439a0c884d7126 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -9,36 +9,36 @@ variables: before_script: - docker login -u gitlab-ci-token -p "$CI_BUILD_TOKEN" registry-gitlab.pasteur.fr -build-test-image: - only: - - docker - stage: build - script: - - apk update ; apk add git - - git checkout master -- requirements.txt - - docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests - - docker push "$CI_REGISTRY_IMAGE/testing-ubuntu" - - mmseqs - -# build-install-barrnap: +# build-test-image: # only: # - docker # stage: build # script: # - apk update ; apk add git # - git checkout master -- requirements.txt -# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" for_build/barrnap_only -# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" +# - docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests +# - docker push "$CI_REGISTRY_IMAGE/testing-ubuntu" +# - mmseqs -# build-install-annote-and-quicktree: +# build-install-barrnap: # only: # - docker # stage: build # script: # - apk update ; apk add git # - git checkout master -- requirements.txt -# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" for_build/annote_and_1tree -# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" +# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" for_build/barrnap_only +# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" + +build-install-annote-and-fasttree: + only: + - docker + stage: build + script: + - apk update ; apk add git + - git checkout master -- requirements.txt + - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-fasttree" for_build/annote_and_1tree + - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-fasttree" # build-ubuntu: # only: diff --git a/for_build/annote_and_1tree/Dockerfile b/for_build/annote_and_1tree/Dockerfile index b1ca7f499fee0bbd678ffc40e11decb0418287e7..34e8941d2e99cee4514a948db8ef56079dc265c7 100644 --- a/for_build/annote_and_1tree/Dockerfile +++ b/for_build/annote_and_1tree/Dockerfile @@ -27,9 +27,8 @@ RUN apt-get install -y\ RUN rm /usr/bin/mafft # remove mafft installed with bioperl -# Install quicktree +# Install FastTree WORKDIR /tmp -RUN git clone https://github.com/tseemann/quicktree -WORKDIR quicktree -RUN make &&\ - ln -s /tmp/quicktree/quicktree /usr/local/bin +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/FastTreeMP /usr/local/bin