From 3d1ad6a19d83fb0cc9709fd13268e02280c6cb25 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Fri, 18 Dec 2020 12:37:22 +0100
Subject: [PATCH] update prokka installation in docker image
- need to set 'yes' by default to install libxml-simple-perl library (RUN DEBIAN_FRONTEND="noninteractive" apt install)
- need to install bioperl from cpan (RUN echo yes | cpan Bio::Perl)
---
for_build/annote_and_1tree/Dockerfile | 1 +
for_build/mafft/Dockerfile | 2 +-
for_tests/Dockerfile | 1 +
3 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/for_build/annote_and_1tree/Dockerfile b/for_build/annote_and_1tree/Dockerfile
index 33143dd0..390bbb03 100644
--- a/for_build/annote_and_1tree/Dockerfile
+++ b/for_build/annote_and_1tree/Dockerfile
@@ -30,6 +30,7 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
git \
default-jre \
bioperl
+RUN echo yes | cpan Bio::Perl
RUN git clone https://github.com/tseemann/prokka.git
RUN /install_dir/prokka/bin/prokka --setupdb &&\
ln -s /install_dir/prokka/bin/prokka /usr/local/bin
diff --git a/for_build/mafft/Dockerfile b/for_build/mafft/Dockerfile
index 2c277cff..759b757a 100644
--- a/for_build/mafft/Dockerfile
+++ b/for_build/mafft/Dockerfile
@@ -16,7 +16,7 @@ RUN apt-get install -y \
RUN pip3 install --upgrade pip
# Install packages to install mafft
-RUN apt-get install -y \
+RUN DEBIAN_FRONTEND="noninteractive" apt-get install -y \
libdatetime-perl \
libxml-simple-perl \
libdigest-md5-perl \
diff --git a/for_tests/Dockerfile b/for_tests/Dockerfile
index e122f673..391c148f 100644
--- a/for_tests/Dockerfile
+++ b/for_tests/Dockerfile
@@ -62,6 +62,7 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
git \
default-jre \
bioperl
+RUN echo yes | cpan Bio::Perl
RUN git clone https://github.com/tseemann/prokka.git
RUN /install_dir/prokka/bin/prokka --setupdb &&\
ln -s /install_dir/prokka/bin/prokka /usr/local/bin
--
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