Commit cf9dd300 authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

build image with prokka and quicktree

parent ffb8f45f
Pipeline #11088 passed with stage
in 6 minutes and 26 seconds
......@@ -9,35 +9,35 @@ 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 "$CI_REGISTRY_IMAGE/testing-ubuntu"
# build-install-barrnap:
# build-test-image:
# only:
# - docker
# stage: build
# script:
# - apk update ; apk add git
# - git checkout master -- requirements.txt
# - docker build --pull -t "$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 "$CI_REGISTRY_IMAGE/testing-ubuntu"
# build-install-annote-and-quicktree:
# build-install-barrnap:
# only:
# - docker
# stage: build
# script:
# - apk update ; apk add git
# - git checkout master -- requirements.txt
# - docker build --pull -t "$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 "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly"
build-install-annote-and-fastme:
only:
- docker
stage: build
script:
- apk update ; apk add git
- git checkout master -- requirements.txt
- docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-fastme" for_build/annote_and_1tree
- docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-fastme"
# build-ubuntu:
# only:
......
......@@ -27,8 +27,9 @@ RUN apt-get install -y\
RUN rm /usr/bin/mafft # remove mafft installed with bioperl
# Install FastTree
# Install quicktree
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/FastTreeMP /usr/local/bin
RUN git clone https://github.com/tseemann/quicktree
WORKDIR quicktree
RUN make &&\
ln -s /tmp/quicktree/quicktree /usr/local/bin
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