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Amandine PERRIN
pipeline_annotation
Commits
26536521
Commit
26536521
authored
Jan 22, 2021
by
Amandine PERRIN
Browse files
install tbl2asn before bioperl and hmmer
parent
4368fd32
Pipeline
#46185
passed with stage
in 12 minutes and 26 seconds
Changes
2
Pipelines
1
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for_build/annote_and_1tree/Dockerfile
View file @
26536521
...
...
@@ -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
...
...
for_tests/Dockerfile
View file @
26536521
...
...
@@ -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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