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Commit 8a574b83 authored by Amandine  PERRIN's avatar Amandine PERRIN
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Add dockerfile to buid image with only prodigal

parent 842a93d2
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...@@ -10,74 +10,85 @@ variables: ...@@ -10,74 +10,85 @@ variables:
before_script: before_script:
- docker login -u gitlab-ci-token -p "$CI_BUILD_TOKEN" registry-gitlab.pasteur.fr - docker login -u gitlab-ci-token -p "$CI_BUILD_TOKEN" registry-gitlab.pasteur.fr
build-test-image: # build-test-image:
only: # only:
- docker # - docker
stage: build # stage: build
script: # script:
- apk update # ; apk add git ; apk add apt-utils # - apk update # ; apk add git ; apk add apt-utils
# - git checkout master -- requirements.txt # # - git checkout master -- requirements.txt
- docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests # - docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests
- docker push "$CI_REGISTRY_IMAGE/testing-ubuntu" # - docker push "$CI_REGISTRY_IMAGE/testing-ubuntu"
tags: # tags:
- k8s # - k8s
build-install-barrnap: # build-install-barrnap:
only: # only:
- docker # - docker
stage: build # stage: build
script: # script:
- apk update #; apk add git # - apk update #; apk add git
# - git checkout master -- requirements.txt # # - git checkout master -- requirements.txt
- docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" for_build/barrnap_only # - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" for_build/barrnap_only
- docker push "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" # - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly"
tags: # tags:
- k8s # - k8s
build-install-annote-and-quicktree: # build-install-annote-and-quicktree:
only: # only:
- docker # - docker
stage: build # stage: build
script: # script:
- apk update #; apk add git # - apk update #; apk add git
# - git checkout master -- requirements.txt # # - git checkout master -- requirements.txt
- docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" for_build/annote_and_1tree # - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" for_build/annote_and_1tree
- docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" # - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree"
tags: # tags:
- k8s # - k8s
build-ubuntu: # build-ubuntu:
only: # only:
- docker # - docker
stage: build # stage: build
script: # script:
- apk update # ; apk add git # - apk update # ; apk add git
# - git checkout master -- requirements.txt # # - git checkout master -- requirements.txt
- docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/ubuntu # - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/ubuntu
- docker push "$CI_REGISTRY_IMAGE/install-ubuntu" # - docker push "$CI_REGISTRY_IMAGE/install-ubuntu"
tags: # tags:
- k8s # - k8s
build-mafft: # build-mafft:
only: # only:
- docker # - docker
stage: build # stage: build
script: # script:
- apk update # ; apk add git # - apk update # ; apk add git
# - git checkout master -- requirements.txt # # - git checkout master -- requirements.txt
- docker build --pull -t "$CI_REGISTRY_IMAGE/install-mafft" for_build/mafft # - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mafft" for_build/mafft
- docker push "$CI_REGISTRY_IMAGE/install-mafft" # - docker push "$CI_REGISTRY_IMAGE/install-mafft"
tags: # tags:
- k8s # - 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: build-install-prodigal:
only: only:
- docker - docker
stage: build stage: build
script: script:
- apk update # ; apk add git - apk update
# - git checkout master -- requirements.txt - docker build --pull -t "$CI_REGISTRY_IMAGE/install-prodigal" for_build/prodigal
- docker build --pull -t "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" for_build/mmseqs_and_fastme - docker push "$CI_REGISTRY_IMAGE/install-prodigal"
- docker push "$CI_REGISTRY_IMAGE/install-mmseqs-fastme"
tags: tags:
- k8s - k8s
from ubuntu:latest
# Update apt-get packages
RUN apt-get update &&\
apt-get -y upgrade
# Install package needed
RUN apt-get install -y \
python3\
git \
python3-pip
# Upgrade pip
RUN pip3 install --upgrade pip
# Install prodigal
RUN git clone https://github.com/hyattpd/Prodigal.git
WORKDIR Prodigal
RUN make install
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