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Amandine PERRIN
panacota
Commits
4dcd2774
Commit
4dcd2774
authored
4 years ago
by
Amandine PERRIN
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install tbl2asn after prokka
parent
169b3e03
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Pipeline
#46816
passed
4 years ago
Stage: build
Changes
2
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1
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for_build/annote_and_1tree/Dockerfile
+6
-5
6 additions, 5 deletions
for_build/annote_and_1tree/Dockerfile
for_tests/Dockerfile
+5
-5
5 additions, 5 deletions
for_tests/Dockerfile
with
11 additions
and
10 deletions
for_build/annote_and_1tree/Dockerfile
+
6
−
5
View file @
4dcd2774
...
...
@@ -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
...
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for_tests/Dockerfile
+
5
−
5
View file @
4dcd2774
...
...
@@ -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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