From 3bf69372e21b3a74cb4d7e4c90f271533445cda8 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Fri, 22 Jan 2021 17:23:42 +0100
Subject: [PATCH] Add tbl2asm installation
---
for_tests/Dockerfile | 11 ++++++++++-
1 file changed, 10 insertions(+), 1 deletion(-)
diff --git a/for_tests/Dockerfile b/for_tests/Dockerfile
index c758d433..a578332e 100644
--- a/for_tests/Dockerfile
+++ b/for_tests/Dockerfile
@@ -54,7 +54,7 @@ RUN make &&\
make install
-# Install prokka:
+# Install dependencies for prokka:
WORKDIR /install_dir
RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
libdatetime-perl \
@@ -63,8 +63,17 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
hmmer \
default-jre \
bioperl
+# Install hmmer
RUN echo yes | cpan Bio::SearchIO::hmmer
+# Install bioperl
RUN echo yes | cpan Bio::Perl
+# install tbl2asn
+RUN wget -O tbl2asn.gz ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux.tbl2asn.gz &&\
+ gunzip tbl2asn.gz &&\
+ chmod +x tbl2asn &&\
+ ln -s /install_dir/tbl2asn /usr/local/bin
+
+# Install prokka
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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