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Amandine PERRIN
pipeline_annotation
Commits
3bf69372
Commit
3bf69372
authored
Jan 22, 2021
by
Amandine PERRIN
Browse files
Add tbl2asm installation
parent
8a98b06f
Pipeline
#46166
passed with stage
in 26 minutes and 58 seconds
Changes
1
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for_tests/Dockerfile
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3bf69372
...
...
@@ -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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