From 17fa4e51ad95c997269b9c2b173768e1aab37bcb Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Wed, 10 May 2017 14:37:26 +0200
Subject: [PATCH] Add a new docker image with only prokka
Installation script should install only the pipeline, as barrnap is not necessary to run prokka
---
.gitlab-ci.yml | 10 ++++++++++
for_build/prokka_only/Dockerfile | 26 ++++++++++++++++++++++++++
2 files changed, 36 insertions(+)
create mode 100644 for_build/prokka_only/Dockerfile
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 163ba757..349aa33f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -38,3 +38,13 @@ build-install-barrnap:
- git checkout master -- pythoncode/requirements.txt
- docker build --pull -t "$CI_REGISTRY_IMAGE:install-ubuntu-barrnapOnly" for_build/barrnap_only
- docker push "$CI_REGISTRY_IMAGE:install-ubuntu-barrnapOnly"
+
+build-install-prokka:
+ only:
+ - docker
+ stage: build
+ script:
+ - apk update ; apk add git
+ - git checkout master -- pythoncode/requirements.txt
+ - docker build --pull -t "$CI_REGISTRY_IMAGE:install-ubuntu-prokkaOnly" for_build/prokka_only
+ - docker push "$CI_REGISTRY_IMAGE:install-ubuntu-prokkaOnly"
diff --git a/for_build/prokka_only/Dockerfile b/for_build/prokka_only/Dockerfile
new file mode 100644
index 00000000..54a54a40
--- /dev/null
+++ b/for_build/prokka_only/Dockerfile
@@ -0,0 +1,26 @@
+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
--
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