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:
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:
- 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:
# - 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-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:
only:
- docker
stage: build
script:
- apk update # ; apk add git
# - git checkout master -- requirements.txt
- docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/ubuntu
- docker push "$CI_REGISTRY_IMAGE/install-ubuntu"
tags:
- k8s
# build-ubuntu:
# only:
# - docker
# stage: build
# script:
# - apk update # ; apk add git
# # - git checkout master -- requirements.txt
# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/ubuntu
# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu"
# tags:
# - k8s
build-mafft:
only:
- docker
stage: build
script:
- apk update # ; apk add git
# - git checkout master -- requirements.txt
- docker build --pull -t "$CI_REGISTRY_IMAGE/install-mafft" for_build/mafft
- docker push "$CI_REGISTRY_IMAGE/install-mafft"
tags:
- k8s
# build-mafft:
# only:
# - docker
# stage: build
# script:
# - apk update # ; apk add git
# # - git checkout master -- requirements.txt
# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mafft" for_build/mafft
# - docker push "$CI_REGISTRY_IMAGE/install-mafft"
# tags:
# - 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:
# 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-install-prodigal:
only:
- docker
stage: build
script:
- apk update
- docker build --pull -t "$CI_REGISTRY_IMAGE/install-prodigal" for_build/prodigal
- docker push "$CI_REGISTRY_IMAGE/install-prodigal"
tags:
- k8s
# build-install-prodigal:
# only:
# - docker
# stage: build
# script:
# - apk update
# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-prodigal" for_build/prodigal
# - docker push "$CI_REGISTRY_IMAGE/install-prodigal"
# tags:
# - k8s
......@@ -5,15 +5,22 @@ RUN apt-get update &&\
apt-get -y upgrade
# Install package needed and update pip
# Install packages needed and update pip
RUN apt-get install -y \
wget \
python3-pip \
python3
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
WORKDIR /tmp
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\
libdigest-md5-perl \
git \
default-jre \
bioperl &&\
git clone https://github.com/tseemann/prokka.git
bioperl
RUN git clone https://github.com/tseemann/prokka.git
RUN /tmp/prokka/bin/prokka --setupdb &&\
ln -s /tmp/prokka/bin/prokka /usr/local/bin
# Install mmseqs2
# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
WORKDIR /tmp
RUN apt-get install -y cmake &&\
wget https://mmseqs.com/latest/mmseqs-static_sse41.tar.gz &&\
tar xf mmseqs-static_sse41.tar.gz &&\
rm mmseqs-static_sse41.tar.gz &&\
RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
tar xvfz mmseqs-linux-sse41.tar.gz &&\
rm mmseqs-linux-sse41.tar.gz &&\
mv /tmp/mmseqs2/bin/mmseqs /usr/local/bin &&\
# remove useless files
rm -r /tmp/mmseqs2
rm -r /tmp/mmseqs
# Install mafft 7.313
......@@ -70,26 +76,27 @@ RUN make clean &&\
make install
# Install FastTree
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
# Install FastME
WORKDIR /tmp
RUN apt-get install -y automake &&\
git clone https://gite.lirmm.fr/atgc/FastME.git
WORKDIR /tmp/FastME
RUN ./configure &&\
make &&\
make install
# Install quicktree
WORKDIR /tmp
RUN git clone https://github.com/tseemann/quicktree
WORKDIR quicktree
RUN make &&\
ln -s /tmp/quicktree/quicktree /usr/local/bin
## Install FastTree
#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/FastTre#eMP /usr/local/bin#
#
#
## Install FastME
#WORKDIR /tmp
#RUN apt-get install -y automake &&\
# git clone https://gite.lirmm.fr/atgc/FastME.git
#WORKDIR /tmp/FastME
#RUN ./configure &&\
# make &&\
# make install
#
#
## Install quicktree
#WORKDIR /tmp
#RUN git clone https://github.com/tseemann/quicktree
#WORKDIR quicktree
#RUN make &&\
# ln -s /tmp/quicktree/quicktree /usr/local/bin
#
\ No newline at end of file
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