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Amandine PERRIN
pipeline_annotation
Commits
cf9dd300
Commit
cf9dd300
authored
Apr 09, 2019
by
Amandine PERRIN
Browse files
build image with prokka and quicktree
parent
ffb8f45f
Pipeline
#11088
passed with stage
in 6 minutes and 26 seconds
Changes
2
Pipelines
1
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.gitlab-ci.yml
View file @
cf9dd300
...
...
@@ -9,35 +9,35 @@ variables:
before_script
:
-
docker login -u gitlab-ci-token -p "$CI_BUILD_TOKEN" registry-gitlab.pasteur.fr
build-test-image
:
only
:
-
docker
stage
:
build
script
:
-
apk update ; apk add git
-
git checkout master -- requirements.txt
-
docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests
-
docker push "$CI_REGISTRY_IMAGE/testing-ubuntu"
# build-install-barrnap:
# build-test-image:
# only:
# - docker
# stage: build
# script:
# - apk update ; apk add git
# - git checkout master -- requirements.txt
# - docker build --pull -t "$CI_REGISTRY_IMAGE/
install-ubuntu-barrnaponly" for_build/barrnap_only
# - docker push "$CI_REGISTRY_IMAGE/
install-ubuntu-barrnaponly
"
# - docker build --pull -t "$CI_REGISTRY_IMAGE/
testing-ubuntu" for_tests
# - docker push "$CI_REGISTRY_IMAGE/
testing-ubuntu
"
# build-install-
annote-and-quicktree
:
# build-install-
barrnap
:
# only:
# - docker
# stage: build
# script:
# - apk update ; apk add git
# - git checkout master -- requirements.txt
# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" for_build/annote_and_1tree
# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree"
# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" for_build/barrnap_only
# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly"
build-install-annote-and-fastme
:
only
:
-
docker
stage
:
build
script
:
-
apk update ; apk add git
-
git checkout master -- requirements.txt
-
docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-fastme" for_build/annote_and_1tree
-
docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-fastme"
# build-ubuntu:
# only:
...
...
for_build/annote_and_1tree/Dockerfile
View file @
cf9dd300
...
...
@@ -27,8 +27,9 @@ RUN apt-get install -y\
RUN
rm
/usr/bin/mafft
# remove mafft installed with bioperl
# Install
FastT
ree
# Install
quickt
ree
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
RUN
git clone https://github.com/tseemann/quicktree
WORKDIR
quicktree
RUN
make
&&
\
ln
-s
/tmp/quicktree/quicktree /usr/local/bin
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