Commit 4368fd32 authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

update prokka install for annote_and_1tree docker image

parent 3bf69372
Pipeline #46181 passed with stage
in 13 minutes and 1 second
......@@ -22,7 +22,7 @@ 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 prokka:
# Install dependencies for prokka:
WORKDIR /install_dir
RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
libdatetime-perl \
......@@ -31,12 +31,22 @@ 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
RUN rm /usr/bin/mafft # remove mafft installed with bioperl
# Install quicktree
......
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