From e12488497f33a3b07e8c397caf3ef6e14e702dba Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Wed, 13 Dec 2017 16:38:33 +0100
Subject: [PATCH] Add image with quicktree installed
---
.gitlab-ci.yml | 11 +++++++++
for_build/annote_and_1tree/Dockerfile | 33 +++++++++++++++++++++++++++
2 files changed, 44 insertions(+)
create mode 100644 for_build/annote_and_1tree/Dockerfile
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 37cb1a7b..aedbf71a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -48,3 +48,14 @@ build-install-prokka:
- git checkout master -- requirements.txt
- docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-prokkaonly" for_build/prokka_only
- docker push "$CI_REGISTRY_IMAGE/install-ubuntu-prokkaonly"
+
+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"
+
\ No newline at end of file
diff --git a/for_build/annote_and_1tree/Dockerfile b/for_build/annote_and_1tree/Dockerfile
new file mode 100644
index 00000000..30228729
--- /dev/null
+++ b/for_build/annote_and_1tree/Dockerfile
@@ -0,0 +1,33 @@
+from ubuntu:16.04
+
+# Update apt-get packages
+RUN apt-get update &&\
+ apt-get -y upgrade
+
+# Install package needed
+RUN apt-get install -y \
+ wget \
+ python3-pip
+
+# Update pip
+RUN pip3 install --upgrade pip
+
+# Install prokka:
+WORKDIR /tmp
+RUN apt-get install -y\
+ libdatetime-perl \
+ libxml-simple-perl \
+ libdigest-md5-perl \
+ git \
+ default-jre \
+ bioperl
+RUN git clone https://github.com/tseemann/prokka.git
+RUN /tmp/prokka/bin/prokka --setupdb
+RUN ln -s /tmp/prokka/bin/prokka /usr/local/bin
+
+# 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
--
GitLab