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Commit 075a0535 authored by Amandine PERRIN's avatar Amandine PERRIN
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update all docker images used for tests

parent a9558439
Pipeline #43709 failed with stage
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.gitlab-ci.yml
View file @ 075a0535
...@@ -20,76 +20,76 @@ build-test-image: ...@@ -20,76 +20,76 @@ build-test-image:
# - 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:
# - k8s
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"
tags: tags:
- k8s - k8s
# build-install-barrnap: 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 "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" for_build/barrnap_only - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" for_build/annote_and_1tree
# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree"
# tags: tags:
# - k8s - k8s
# 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"
# tags:
# - 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: build-mmseqs_and_fastme:
# 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 "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" for_build/mmseqs_and_fastme - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" for_build/mmseqs_and_fastme
# - docker push "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" - docker push "$CI_REGISTRY_IMAGE/install-mmseqs-fastme"
# tags: tags:
# - k8s - k8s
# build-install-prodigal: build-install-prodigal:
# only: only:
# - docker - docker
# stage: build stage: build
# script: script:
# - apk update - apk update
# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-prodigal" for_build/prodigal - docker build --pull -t "$CI_REGISTRY_IMAGE/install-prodigal" for_build/prodigal
# - docker push "$CI_REGISTRY_IMAGE/install-prodigal" - docker push "$CI_REGISTRY_IMAGE/install-prodigal"
# tags: tags:
# - k8s - k8s
for_build/annote_and_1tree/Dockerfile
View file @ 075a0535
from ubuntu:18.04 from ubuntu:20.04
# Update apt-get packages # Update apt-get packages
RUN apt-get update &&\ RUN apt-get update &&\
...@@ -13,30 +13,31 @@ RUN apt-get install -y \ ...@@ -13,30 +13,31 @@ RUN apt-get install -y \
RUN pip3 install --upgrade pip RUN pip3 install --upgrade pip
# Update makeblastdb and blastp for prokka # Update makeblastdb and blastp for prokka
WORKDIR /tmp WORKDIR /install_dir
RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.1+-x64-linux.tar.gz &&\ RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\ tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
cp /tmp/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\ cp /install_dir/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\
cp /tmp/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\ cp /install_dir/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\
rm ncbi-blast-2.10.1+-x64-linux.tar.gz rm ncbi-blast-2.10.1+-x64-linux.tar.gz
# Install prokka: # Install prokka:
WORKDIR /tmp WORKDIR /install_dir
RUN apt-get install -y\ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
libdatetime-perl \ libdatetime-perl \
libxml-simple-perl \ libxml-simple-perl \
libdigest-md5-perl \ libdigest-md5-perl \
git \ git \
default-jre \ default-jre \
bioperl &&\ bioperl
git clone https://github.com/tseemann/prokka.git &&\ RUN git clone https://github.com/tseemann/prokka.git
/tmp/prokka/bin/prokka --setupdb &&\ RUN /install_dir/prokka/bin/prokka --setupdb &&\
ln -s /tmp/prokka/bin/prokka /usr/local/bin ln -s /install_dir/prokka/bin/prokka /usr/local/bin
RUN rm /usr/bin/mafft # remove mafft installed with bioperl
# Install quicktree # Install quicktree
WORKDIR /tmp WORKDIR /install_dir
RUN git clone https://github.com/tseemann/quicktree RUN git clone https://github.com/tseemann/quicktree
WORKDIR quicktree WORKDIR /install_dir/quicktree
RUN make &&\ RUN make &&\
ln -s /tmp/quicktree/quicktree /usr/local/bin ln -s /install_dir/quicktree/quicktree /usr/local/bin
for_build/barrnap_only/Dockerfile
View file @ 075a0535
from ubuntu:18.04 from ubuntu:20.04
# Update apt-get packages # Update apt-get packages
RUN apt-get update &&\ RUN apt-get update &&\
...@@ -18,12 +18,14 @@ RUN apt-get install -y \ ...@@ -18,12 +18,14 @@ RUN apt-get install -y \
RUN pip3 install --upgrade pip RUN pip3 install --upgrade pip
# Install barrnap # Install barrnap
WORKDIR /tmp WORKDIR /install_dir
RUN wget https://github.com/tseemann/barrnap/archive/0.8.tar.gz &&\ RUN wget https://github.com/tseemann/barrnap/archive/0.8.tar.gz &&\
tar -xf 0.8.tar.gz &&\ tar -xf 0.8.tar.gz &&\
rm 0.8.tar.gz rm 0.8.tar.gz &&\
RUN ln -s /tmp/barrnap-0.8/bin/barrnap /usr/local/bin mv /install_dir/barrnap-0.8/bin/barrnap /usr/local/bin &&\
# Remove heavy useless files
rm -r /install_dir/barrnap-0.8/examples /install_dir/barrnap-0.8/build/*.aln
RUN rm /usr/bin/mafft # remove mafft installed with bioperl RUN rm /usr/bin/mafft # remove mafft installed with bioperl
\ No newline at end of file
for_build/mafft/Dockerfile
View file @ 075a0535
from ubuntu:18.04 from ubuntu:20.04
# Update apt-get packages # Update apt-get packages
RUN apt-get update &&\ RUN apt-get update &&\
...@@ -25,11 +25,11 @@ RUN apt-get install -y \ ...@@ -25,11 +25,11 @@ RUN apt-get install -y \
# Install mafft 7.313 # Install mafft 7.313
RUN rm /usr/bin/mafft # remove mafft installed with bioperl RUN rm /usr/bin/mafft # remove mafft installed with bioperl
WORKDIR /tmp WORKDIR /install_dir
RUN wget https://mafft.cbrc.jp/alignment/software/mafft-7.313-with-extensions-src.tgz &&\ RUN wget https://mafft.cbrc.jp/alignment/software/mafft-7.313-with-extensions-src.tgz &&\
tar xf mafft-7.313-with-extensions-src.tgz &&\ tar xf mafft-7.313-with-extensions-src.tgz &&\
rm mafft-7.313-with-extensions-src.tgz rm mafft-7.313-with-extensions-src.tgz
WORKDIR /tmp/mafft-7.313-with-extensions/core WORKDIR /install_dir/mafft-7.313-with-extensions/core
RUN make clean &&\ RUN make clean &&\
make &&\ make &&\
make install make install
for_build/mmseqs_and_fastme/Dockerfile
View file @ 075a0535
from ubuntu:18.04 from ubuntu:20.04
# Update apt-get packages # Update apt-get packages
...@@ -16,21 +16,21 @@ RUN apt-get install -y \ ...@@ -16,21 +16,21 @@ RUN apt-get install -y \
RUN pip3 install --upgrade pip RUN pip3 install --upgrade pip
# Install MMseqs2 (Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e ?) # Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
WORKDIR /tmp WORKDIR /install_dir
RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\ RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
tar xvfz mmseqs-linux-sse41.tar.gz &&\ tar xvfz mmseqs-linux-sse41.tar.gz &&\
rm mmseqs-linux-sse41.tar.gz &&\ rm mmseqs-linux-sse41.tar.gz &&\
mv /tmp/mmseqs/bin/mmseqs /usr/local/bin &&\ mv /install_dir/mmseqs/bin/mmseqs /usr/local/bin &&\
# remove useless files # remove useless files
rm -r /tmp/mmseqs rm -r /install_dir/mmseqs
# Install FastME # Install FastME FastME 2.1.6.1
WORKDIR /tmp WORKDIR /install_dir
RUN apt-get install -y automake &&\ RUN apt-get install -y automake &&\
git clone https://gite.lirmm.fr/atgc/FastME.git git clone https://gite.lirmm.fr/atgc/FastME.git
WORKDIR /tmp/FastME WORKDIR /install_dir/FastME/tarball
RUN ./configure &&\ RUN tar xzf fastme-2.1.6.2.tar.gz &&\
make &&\ rm fastme-2.1.6.2.tar.gz &&\
make install ln -s /install_dir/FastME/tarball/fastme-2.1.6.2/binaries/fastme-2.1.6.2-linux64-omp /usr/local/bin/fastme
for_build/prodigal/Dockerfile
View file @ 075a0535
from ubuntu:18.04 from ubuntu:20.04
# Update apt-get packages # Update apt-get packages
RUN apt-get update &&\ RUN apt-get update &&\
...@@ -14,8 +14,12 @@ RUN apt-get install -y \ ...@@ -14,8 +14,12 @@ RUN apt-get install -y \
# Upgrade pip # Upgrade pip
RUN pip3 install --upgrade pip RUN pip3 install --upgrade pip
# Install prodigal # Install prodigal
RUN apt-get install zlib1g-dev &&\ WORKDIR /install_dir
git clone https://github.com/hyattpd/Prodigal.git RUN wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz &&\
WORKDIR Prodigal tar -xzf v2.6.3.tar.gz &&\
RUN make install rm v2.6.3.tar.gz
WORKDIR /install_dir/Prodigal-2.6.3
RUN make &&\
make install
\ No newline at end of file
for_build/ubuntu/Dockerfile
View file @ 075a0535
from ubuntu:18.04 from ubuntu:20.04
# Update apt-get packages # Update apt-get packages
RUN apt-get update &&\ RUN apt-get update &&\
......
for_tests/Dockerfile
View file @ 075a0535
...@@ -96,7 +96,7 @@ RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\ ...@@ -96,7 +96,7 @@ RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\
ln -s /install_dir/FastTreeMP /usr/local/bin ln -s /install_dir/FastTreeMP /usr/local/bin
## Install FastME FastME 2.1.6.1 # Install FastME FastME 2.1.6.1
WORKDIR /install_dir WORKDIR /install_dir
RUN apt-get install -y automake &&\ RUN apt-get install -y automake &&\
git clone https://gite.lirmm.fr/atgc/FastME.git git clone https://gite.lirmm.fr/atgc/FastME.git
......
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