Commit 15b6fa4d authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

new version of docker image for tests:

- prokka with updated tbl2asn binary
- use ubuntu 20.04
parent 0ae15a62
Pipeline #43702 failed with stage
in 21 seconds
...@@ -23,73 +23,73 @@ build-test-image: ...@@ -23,73 +23,73 @@ build-test-image:
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: # 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
from ubuntu:18.04 from ubuntu:20.04
# Update apt-get packages # Update apt-get packages
RUN apt-get update &&\ RUN apt-get update &&\
...@@ -12,47 +12,50 @@ RUN apt-get install -y \ ...@@ -12,47 +12,50 @@ RUN apt-get install -y \
python3-pip python3-pip
# Upgrade pip # Upgrade pip
RUN pip3 install --upgrade pip RUN pip3 install --upgrade pip
RUN mkdir /install_dir
# 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 mash # Install mash
WORKDIR /tmp WORKDIR /install_dir
RUN wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\ RUN wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\
tar -xf mash-Linux64-v2.2.tar &&\ tar -xf mash-Linux64-v2.2.tar &&\
rm mash-Linux64-v2.2.tar &&\ rm mash-Linux64-v2.2.tar &&\
mv /tmp/mash-Linux64-v2.2/mash /usr/local/bin &&\ mv /install_dir/mash-Linux64-v2.2/mash /usr/local/bin &&\
rm -r mash-Linux64-v2.2 rm -r mash-Linux64-v2.2
# 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 &&\
mv /tmp/barrnap-0.8/bin/barrnap /usr/local/bin &&\ mv /install_dir/barrnap-0.8/bin/barrnap /usr/local/bin &&\
# Remove heavy useless files # Remove heavy useless files
rm -r /tmp/barrnap-0.8/examples /tmp/barrnap-0.8/build/*.aln rm -r /install_dir/barrnap-0.8/examples /install_dir/barrnap-0.8/build/*.aln
# Install prodigal # Install prodigal
WORKDIR /tmp WORKDIR /install_dir
RUN wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz &&\ RUN wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz &&\
tar -xzf v2.6.3.tar.gz &&\ tar -xzf v2.6.3.tar.gz &&\
rm v2.6.3.tar.gz rm v2.6.3.tar.gz
WORKDIR /tmp/Prodigal-2.6.3 WORKDIR /install_dir/Prodigal-2.6.3
RUN make &&\ RUN make &&\
make install make install
# 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 \
...@@ -60,68 +63,68 @@ RUN apt-get install -y\ ...@@ -60,68 +63,68 @@ RUN apt-get install -y\
default-jre \ default-jre \
bioperl bioperl
RUN git clone https://github.com/tseemann/prokka.git RUN git clone https://github.com/tseemann/prokka.git
RUN /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
# 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 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
# Install FastTree version 2.1.11 Double precision (No SSE3) # Install FastTree version 2.1.11 Double precision (No SSE3)
WORKDIR /tmp WORKDIR /install_dir
RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\ 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 &&\ gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP FastTree.c -lm &&\
ln -s /tmp/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 /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
# 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
# Install iqtree # Install iqtree
WORKDIR /tmp WORKDIR /install_dir
RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz
RUN tar -xzf iqtree-1.6.12-Linux.tar.gz &&\ RUN tar -xzf iqtree-1.6.12-Linux.tar.gz &&\
rm iqtree-1.6.12-Linux.tar.gz &&\ rm iqtree-1.6.12-Linux.tar.gz &&\
ln -s /tmp/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin ln -s /install_dir/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin
# Install iqtree2 # Install iqtree2
WORKDIR /tmp WORKDIR /install_dir
RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v2.0.6/iqtree-2.0.6-Linux.tar.gz RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v2.0.6/iqtree-2.0.6-Linux.tar.gz
RUN tar -xzf iqtree-2.0.6-Linux.tar.gz &&\ RUN tar -xzf iqtree-2.0.6-Linux.tar.gz &&\
rm iqtree-2.0.6-Linux.tar.gz &&\ rm iqtree-2.0.6-Linux.tar.gz &&\
ln -s /tmp/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin ln -s /install_dir/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin
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