From dba548e3261dcdb79e94f6c644e596cb2d8478fe Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Mon, 7 Oct 2019 10:07:54 +0200
Subject: [PATCH] test installation of docker image for tests
---
.gitlab-ci.yml | 130 +++++++++++++++++++++----------------------
for_tests/Dockerfile | 73 +++++++++++++-----------
2 files changed, 105 insertions(+), 98 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7031d7cb..f4f15f00 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -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
diff --git a/for_tests/Dockerfile b/for_tests/Dockerfile
index 93598740..2f9547b4 100644
--- a/for_tests/Dockerfile
+++ b/for_tests/Dockerfile
@@ -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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