From 4368fd32c4c611719416189fd9e06d25f6ac7e5e Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Fri, 22 Jan 2021 18:39:44 +0100
Subject: [PATCH] update prokka install for annote_and_1tree docker image
---
for_build/annote_and_1tree/Dockerfile | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/for_build/annote_and_1tree/Dockerfile b/for_build/annote_and_1tree/Dockerfile
index 94181905..b57e7ead 100644
--- a/for_build/annote_and_1tree/Dockerfile
+++ b/for_build/annote_and_1tree/Dockerfile
@@ -22,7 +22,7 @@ RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2
rm ncbi-blast-2.10.1+-x64-linux.tar.gz
-# Install prokka:
+# Install dependencies for prokka:
WORKDIR /install_dir
RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
libdatetime-perl \
@@ -31,12 +31,22 @@ 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
+
RUN rm /usr/bin/mafft # remove mafft installed with bioperl
# Install quicktree
--
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