From 4dcd2774d2ef2ea0fe095508d35961cf3987e4ba Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Fri, 29 Jan 2021 10:41:33 +0100
Subject: [PATCH] install tbl2asn after prokka
---
for_build/annote_and_1tree/Dockerfile | 11 ++++++-----
for_tests/Dockerfile | 10 +++++-----
2 files changed, 11 insertions(+), 10 deletions(-)
diff --git a/for_build/annote_and_1tree/Dockerfile b/for_build/annote_and_1tree/Dockerfile
index 216d1139..a8bfb7ce 100644
--- a/for_build/annote_and_1tree/Dockerfile
+++ b/for_build/annote_and_1tree/Dockerfile
@@ -22,11 +22,6 @@ 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 tbl2asn (used by prokka)
-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 dependencies for prokka:
WORKDIR /install_dir
RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
@@ -46,6 +41,12 @@ 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
+# install tbl2asn (used by prokka)
+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
+
RUN rm /usr/bin/mafft # remove mafft installed with bioperl
diff --git a/for_tests/Dockerfile b/for_tests/Dockerfile
index 7bf6a539..27f9f2bf 100644
--- a/for_tests/Dockerfile
+++ b/for_tests/Dockerfile
@@ -54,11 +54,6 @@ RUN make &&\
make install
-# install tbl2asn (used by prokka)
-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 dependencies for prokka:
WORKDIR /install_dir
RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
@@ -77,6 +72,11 @@ 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
+# install tbl2asn (used by prokka)
+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 MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
--
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