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Amandine PERRIN
pipeline_annotation
Commits
dba548e3
Commit
dba548e3
authored
Oct 07, 2019
by
Amandine PERRIN
Browse files
test installation of docker image for tests
parent
e1f898b7
Pipeline
#15883
failed with stage
in 4 minutes and 44 seconds
Changes
2
Pipelines
1
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.gitlab-ci.yml
View file @
dba548e3
...
...
@@ -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
for_tests/Dockerfile
View file @
dba548e3
...
...
@@ -5,15 +5,22 @@ RUN apt-get update &&\
apt-get
-y
upgrade
# Install package needed and update pip
# Install package
s
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
mm
seqs2
# Install
MM
seqs2
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/mmseqs
2
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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