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Amandine PERRIN
pipeline_annotation
Commits
15b6fa4d
Commit
15b6fa4d
authored
Dec 18, 2020
by
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
Changes
2
Pipelines
1
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.gitlab-ci.yml
View file @
15b6fa4d
...
...
@@ -23,73 +23,73 @@ 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 @
15b6fa4d
from
ubuntu:
18
.04
from
ubuntu:
20
.04
# Update apt-get packages
RUN
apt-get update
&&
\
...
...
@@ -12,47 +12,50 @@ RUN apt-get install -y \
python3-pip
# Upgrade pip
RUN
pip3
install
--upgrade
pip
RUN
mkdir
/install_dir
# Update makeblastdb and blastp for prokka
WORKDIR
/
tmp
RUN
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/
LATEST
/ncbi-blast-2.10.1+-x64-linux.tar.gz
&&
\
WORKDIR
/
install_dir
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
&&
\
cp
/
tmp
/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/makeblastdb /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
# Install mash
WORKDIR
/
tmp
WORKDIR
/
install_dir
RUN
wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar
&&
\
tar
-xf
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
# Install barrnap
WORKDIR
/
tmp
WORKDIR
/
install_dir
RUN
wget https://github.com/tseemann/barrnap/archive/0.8.tar.gz
&&
\
tar
-xf
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
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
WORKDIR
/
tmp
WORKDIR
/
install_dir
RUN
wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz
&&
\
tar
-xzf
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
&&
\
make
install
# Install prokka:
WORKDIR
/
tmp
RUN
apt-ge
t
install
-y
\
WORKDIR
/
install_dir
RUN
DEBIAN_FRONTEND
=
"noninteractive"
ap
t
install
-y
\
libdatetime-perl
\
libxml-simple-perl
\
libdigest-md5-perl
\
...
...
@@ -60,68 +63,68 @@ RUN apt-get install -y\
default-jre
\
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
RUN
/
install_dir
/prokka/bin/prokka
--setupdb
&&
\
ln
-s
/
install_dir
/prokka/bin/prokka /usr/local/bin
# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
WORKDIR
/
tmp
WORKDIR
/
install_dir
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
/mmseqs/bin/mmseqs /usr/local/bin
&&
\
mv
/
install_dir
/mmseqs/bin/mmseqs /usr/local/bin
&&
\
# remove useless files
rm -r /
tmp
/mmseqs
rm -r /
install_dir
/mmseqs
# Install mafft 7.313
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
&&
\
tar
xf 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
&&
\
make
&&
\
make
install
# Install FastTree version 2.1.11 Double precision (No SSE3)
WORKDIR
/
tmp
WORKDIR
/
install_dir
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
ln
-s
/
install_dir
/FastTreeMP /usr/local/bin
## Install FastME FastME 2.1.6.1
WORKDIR
/
tmp
WORKDIR
/
install_dir
RUN
apt-get
install
-y
automake
&&
\
git clone https://gite.lirmm.fr/atgc/FastME.git
WORKDIR
/
tmp/FastME
RUN
./configure
&&
\
make
&&
\
make
install
WORKDIR
/
install_dir/FastME/tarball
RUN
tar
xzf fastme-2.1.6.2.tar.gz
&&
\
rm
fastme-2.1.6.2.tar.gz
&&
\
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
WORKDIR
/
tmp
WORKDIR
/
install_dir
RUN
git clone https://github.com/tseemann/quicktree
WORKDIR
quicktree
WORKDIR
/install_dir/
quicktree
RUN
make
&&
\
ln
-s
/
tmp
/quicktree/quicktree /usr/local/bin
ln
-s
/
install_dir
/quicktree/quicktree /usr/local/bin
# 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
tar
-xzf
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
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
tar
-xzf
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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