From 26536521664e5dbbc54d95f2b8b7cbde8114086c Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Fri, 22 Jan 2021 18:46:08 +0100
Subject: [PATCH] install tbl2asn before bioperl and hmmer
---
for_build/annote_and_1tree/Dockerfile | 10 +++++-----
for_tests/Dockerfile | 10 +++++-----
2 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/for_build/annote_and_1tree/Dockerfile b/for_build/annote_and_1tree/Dockerfile
index b57e7ead..216d1139 100644
--- a/for_build/annote_and_1tree/Dockerfile
+++ b/for_build/annote_and_1tree/Dockerfile
@@ -22,6 +22,11 @@ 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\
@@ -35,11 +40,6 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
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
diff --git a/for_tests/Dockerfile b/for_tests/Dockerfile
index a578332e..2609fed5 100644
--- a/for_tests/Dockerfile
+++ b/for_tests/Dockerfile
@@ -54,6 +54,11 @@ 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\
@@ -67,11 +72,6 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
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
--
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