Commit dba548e3 authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

test installation of docker image for tests

parent e1f898b7
Pipeline #15883 failed with stage
in 4 minutes and 44 seconds
...@@ -22,73 +22,73 @@ build-test-image: ...@@ -22,73 +22,73 @@ 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
...@@ -5,15 +5,22 @@ RUN apt-get update &&\ ...@@ -5,15 +5,22 @@ RUN apt-get update &&\
apt-get -y upgrade apt-get -y upgrade
# Install package needed and update pip # Install packages needed and update pip
RUN apt-get install -y \ RUN apt-get install -y \
wget \ wget \
python3-pip \ python3-pip \
python3 python3
RUN pip3 install --upgrade pip RUN pip3 install --upgrade pip
# Update makeblastdb
WORKDIR /tmp
RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.9.0+-x64-linux.tar.gz &&\
tar zxvpf ncbi-blast-2.9.0+-x64-linux.tar.gz &&\
cp /tmp/ncbi-blast-2.9.0+/bin/makeblastdb /usr/local/bin/ &&\
rm ncbi-blast-2.9.0+-x64-linux.tar.gz
# Install mash # Install mash
WORKDIR /tmp WORKDIR /tmp
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 &&\
...@@ -41,21 +48,20 @@ RUN apt-get install -y\ ...@@ -41,21 +48,20 @@ RUN apt-get install -y\
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
RUN /tmp/prokka/bin/prokka --setupdb &&\ RUN /tmp/prokka/bin/prokka --setupdb &&\
ln -s /tmp/prokka/bin/prokka /usr/local/bin ln -s /tmp/prokka/bin/prokka /usr/local/bin
# Install mmseqs2 # Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
WORKDIR /tmp WORKDIR /tmp
RUN apt-get install -y cmake &&\ RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
wget https://mmseqs.com/latest/mmseqs-static_sse41.tar.gz &&\ tar xvfz mmseqs-linux-sse41.tar.gz &&\
tar xf mmseqs-static_sse41.tar.gz &&\ rm mmseqs-linux-sse41.tar.gz &&\
rm mmseqs-static_sse41.tar.gz &&\
mv /tmp/mmseqs2/bin/mmseqs /usr/local/bin &&\ mv /tmp/mmseqs2/bin/mmseqs /usr/local/bin &&\
# remove useless files # remove useless files
rm -r /tmp/mmseqs2 rm -r /tmp/mmseqs
# Install mafft 7.313 # Install mafft 7.313
...@@ -70,26 +76,27 @@ RUN make clean &&\ ...@@ -70,26 +76,27 @@ RUN make clean &&\
make install make install
# Install FastTree ## Install FastTree
WORKDIR /tmp #WORKDIR /tmp
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 /tmp/FastTre#eMP /usr/local/bin#
#
#
# Install FastME ## Install FastME
WORKDIR /tmp #WORKDIR /tmp
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 /tmp/FastME
RUN ./configure &&\ #RUN ./configure &&\
make &&\ # make &&\
make install # make install
#
#
# Install quicktree ## Install quicktree
WORKDIR /tmp #WORKDIR /tmp
RUN git clone https://github.com/tseemann/quicktree #RUN git clone https://github.com/tseemann/quicktree
WORKDIR quicktree #WORKDIR quicktree
RUN make &&\ #RUN make &&\
ln -s /tmp/quicktree/quicktree /usr/local/bin # ln -s /tmp/quicktree/quicktree /usr/local/bin
#
\ No newline at end of file
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