From 101afc36af7dd4efcfc8afae0cfd957fad088675 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Mon, 7 Oct 2019 13:55:43 +0200
Subject: [PATCH] build all test images
---
.gitlab-ci.yml | 22 +++++++++++-----------
for_build/mmseqs_and_fastme/Dockerfile | 2 +-
for_tests/Dockerfile | 19 ++++++++-----------
3 files changed, 20 insertions(+), 23 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1abc8bd5..7031d7cb 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -10,17 +10,17 @@ variables:
before_script:
- docker login -u gitlab-ci-token -p "$CI_BUILD_TOKEN" registry-gitlab.pasteur.fr
-# build-test-image:
-# only:
-# - docker
-# stage: build
-# script:
-# - apk update # ; apk add git ; apk add apt-utils
-# # - git checkout master -- requirements.txt
-# - docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests
-# - docker push "$CI_REGISTRY_IMAGE/testing-ubuntu"
-# tags:
-# - k8s
+build-test-image:
+ only:
+ - docker
+ stage: build
+ script:
+ - apk update # ; apk add git ; apk add apt-utils
+ # - git checkout master -- requirements.txt
+ - docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests
+ - docker push "$CI_REGISTRY_IMAGE/testing-ubuntu"
+ tags:
+ - k8s
build-install-barrnap:
only:
diff --git a/for_build/mmseqs_and_fastme/Dockerfile b/for_build/mmseqs_and_fastme/Dockerfile
index c02a9ee3..4a8873b4 100644
--- a/for_build/mmseqs_and_fastme/Dockerfile
+++ b/for_build/mmseqs_and_fastme/Dockerfile
@@ -16,7 +16,7 @@ RUN apt-get install -y \
RUN pip3 install --upgrade pip
-# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
+# Install MMseqs2 (Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e ?)
WORKDIR /tmp
RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
tar xvfz mmseqs-linux-sse41.tar.gz &&\
diff --git a/for_tests/Dockerfile b/for_tests/Dockerfile
index 4a339786..5989324d 100644
--- a/for_tests/Dockerfile
+++ b/for_tests/Dockerfile
@@ -79,10 +79,8 @@ RUN make clean &&\
# Install FastTree version 2.1.11 Double precision (No SSE3)
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 FastME 2.1.6.1
+ gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP astTree.c -lm &&\
+ ln -s /tmp/FastTre#eMP /usr/local/bin## Install FastME FastME 2.1.6.1
WORKDIR /tmp
RUN apt-get install -y automake &&\
git clone https://gite.lirmm.fr/atgc/FastME.git
@@ -92,10 +90,9 @@ RUN ./configure &&\
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
+# Install quicktree
+WORKDIR /tmp
+RUN git clone https://github.com/tseemann/quicktree
+WORKDIR quicktree
+RUN make &&\
+ ln -s /tmp/quicktree/quicktree /usr/local/bin
--
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