From 15b6fa4da0a5b01d88ac63f37677a2d177683444 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Fri, 18 Dec 2020 11:55:18 +0100
Subject: [PATCH] new version of docker image for tests:
- prokka with updated tbl2asn binary
- use ubuntu 20.04
---
.gitlab-ci.yml | 130 +++++++++++++++++++++----------------------
for_tests/Dockerfile | 73 ++++++++++++------------
2 files changed, 103 insertions(+), 100 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 42d41b80..1ce2e8af 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -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
diff --git a/for_tests/Dockerfile b/for_tests/Dockerfile
index 463042ba..63324a43 100644
--- a/for_tests/Dockerfile
+++ b/for_tests/Dockerfile
@@ -1,4 +1,4 @@
-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-get install -y\
+WORKDIR /install_dir
+RUN DEBIAN_FRONTEND="noninteractive" apt 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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