Skip to content
Snippets Groups Projects
Commit a8e3b551 authored by Amandine PERRIN's avatar Amandine PERRIN
Browse files

Change dockerfile for CI

parent 277686ac
No related branches found
No related tags found
No related merge requests found
Pipeline #106981 passed
Stage: test
Stage: coverage
Hide whitespace changes
Inline Side-by-side
Showing
with 97 additions and 83 deletions
containers/Dockerfile
+ 97
− 83
View file @ a8e3b551
from ubuntu:20.04
from ubuntu:22.04
# setting these ARGs as global variables, so they persist across all build layers (but not in final production image)
ARG PROKKA_VER="1.14.6"
ARG BEDTOOLS_VER="2.29.0"
ARG BARRNAP_VER="0.9"
ARG BLAST_VER="2.10.1"
ARG MASH_VER="v2.2"
ARG PRODIGAL_VER="2.6.3"
ARG MAFFT_VER="7.313"
ARG FASTME_VER="2.1.6.1"
# re-instantiating for the app build layer
ARG PROKKA_VER
ARG BEDTOOLS_VER
ARG BARRNAP_VER
ARG BLAST_VER
ARG MASH_VER
ARG PRODIGAL_VER
ARG MAFFT_VER
ARG FASTME_VER
# Update apt-get packages
RUN apt-get update &&\
apt-get -y upgrade
# Install packages needed and update pip
RUN apt-get install -y \
wget \
......@@ -15,69 +34,71 @@ RUN apt-get install -y \
RUN pip3 install --upgrade pip
RUN mkdir /install_dir
# Update makeblastdb and blastp for prokka
WORKDIR /install_dir
RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
cp /install_dir/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\
cp /install_dir/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\
rm ncbi-blast-2.10.1+-x64-linux.tar.gz
RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VER}/ncbi-blast-${BLAST_VER}+-x64-linux.tar.gz &&\
tar zxvpf ncbi-blast-${BLAST_VER}+-x64-linux.tar.gz &&\
cp /install_dir/ncbi-blast-${BLAST_VER}+/bin/makeblastdb /usr/local/bin/ &&\
cp /install_dir/ncbi-blast-${BLAST_VER}+/bin/blastp /usr/local/bin/ &&\
rm ncbi-blast-${BLAST_VER}+-x64-linux.tar.gz
# Install mash
WORKDIR /install_dir
RUN wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\
tar -xf mash-Linux64-v2.2.tar &&\
rm mash-Linux64-v2.2.tar &&\
mv /install_dir/mash-Linux64-v2.2/mash /usr/local/bin &&\
rm -r mash-Linux64-v2.2
# Install barrnap
WORKDIR /install_dir
RUN wget https://github.com/tseemann/barrnap/archive/0.8.tar.gz &&\
tar -xf 0.8.tar.gz &&\
rm 0.8.tar.gz &&\
mv /install_dir/barrnap-0.8/bin/barrnap /usr/local/bin &&\
# Remove heavy useless files
rm -r /install_dir/barrnap-0.8/examples /install_dir/barrnap-0.8/build/*.aln
RUN wget https://github.com/marbl/Mash/releases/download/${MASH_VER}/mash-Linux64-${MASH_VER}.tar &&\
tar -xf mash-Linux64-${MASH_VER}.tar &&\
rm mash-Linux64-${MASH_VER}.tar &&\
mv /install_dir/mash-Linux64-${MASH_VER}/mash /usr/local/bin &&\
rm -r mash-Linux64-${MASH_VER}
# Install prodigal
WORKDIR /install_dir
RUN wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz &&\
tar -xzf v2.6.3.tar.gz &&\
rm v2.6.3.tar.gz
WORKDIR /install_dir/Prodigal-2.6.3
RUN make &&\
make install
# Install dependencies for prokka:
WORKDIR /install_dir
RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
libdatetime-perl \
libxml-simple-perl \
libdigest-md5-perl \
hmmer \
default-jre \
bioperl
# Install hmmer
RUN echo yes | cpan Bio::SearchIO::hmmer
# Install bioperl
RUN echo yes | cpan Bio::Perl
# install tbl2asn manually since the one included with prokka is expired.
# Probably will have to do again in Dec 2021 unless Torsten removes it from prokka
RUN wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz -O linux64.tbl2asn.gz && \
gunzip linux64.tbl2asn.gz && \
mv linux64.tbl2asn /usr/bin/tbl2asn && \
chmod 755 /usr/bin/tbl2asn
# 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
# install tbl2asn (used by prokka)
RUN wget -O tbl2asn.gz https://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/table2asn/linux64.table2asn.gz &&\
gunzip tbl2asn.gz &&\
chmod +x tbl2asn &&\
ln -s /install_dir/tbl2asn /usr/local/bin
RUN apt-get install -y prokka
WORKDIR /install_dir
# RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
# libdatetime-perl \
# libxml-simple-perl \
# libdigest-md5-perl \
# hmmer \
# default-jre \
# bioperl
# # Install hmmer
# RUN echo yes | cpan Bio::SearchIO::hmmer
# # Install bioperl
# RUN echo yes | cpan Bio::Perl
# # Install prokka
RUN wget https://github.com/tseemann/prokka/archive/refs/tags/v${PROKKA_VER}.tar.gz
RUN tar -xzf v${PROKKA_VER}.tar.gz &&\
rm -rf v${PROKKA_VER}.tar.gz
RUN /install_dir/prokka-${PROKKA_VER}/bin/prokka --setupdb &&\
ln -s /install_dir/prokka-${PROKKA_VER}/bin/prokka /usr/local/bin
# # install tbl2asn (used by prokka)
# RUN wget -O tbl2asn.gz https://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/table2asn/linux64.table2asn.gz &&\
# gunzip tbl2asn.gz &&\
# chmod +x tbl2asn &&\
# ln -s /install_dir/tbl2asn /usr/local/bin
# more Examples/commands/2-Annotate.sh
# PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prokka -l Examples/input_files/list_genomes.lst -n GENO --l90 3 --nbcont 10
# Install prodigal
RUN apt-get install prodigal
# WORKDIR /install_dir
# RUN wget https://github.com/hyattpd/Prodigal/archive/v${PRODIGAL_VER}.tar.gz &&\
# tar -xzf v${PRODIGAL_VER}.tar.gz &&\
# rm v${PRODIGAL_VER}.tar.gz
# WORKDIR /install_dir/Prodigal-${PRODIGAL_VER}
# RUN make
# RUN make install
# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
WORKDIR /install_dir
......@@ -88,34 +109,31 @@ RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
# remove useless files
rm -r /install_dir/mmseqs
# Install mafft 7.313
RUN rm /usr/bin/mafft # remove mafft installed with bioperl
WORKDIR /install_dir
RUN wget https://mafft.cbrc.jp/alignment/software/mafft-7.313-with-extensions-src.tgz &&\
tar xf mafft-7.313-with-extensions-src.tgz &&\
rm mafft-7.313-with-extensions-src.tgz
WORKDIR /install_dir/mafft-7.313-with-extensions/core
RUN make clean &&\
make &&\
make install
# Install FastTree version 2.1.11 Double precision (No SSE3)
# # Install mafft 7.313
# RUN rm /usr/bin/mafft # remove mafft installed with bioperl
# WORKDIR /install_dir
# RUN wget https://mafft.cbrc.jp/alignment/software/mafft-${MAFFT_VER}-with-extensions-src.tgz &&\
# tar xf mafft-7.313-with-extensions-src.tgz &&\
# rm mafft-7.313-with-extensions-src.tgz
# WORKDIR /install_dir/mafft-7.313-with-extensions/core
# RUN make clean &&\
# make &&\
# make install
# # Install FastTree version 2.1.11 Double precision (No SSE3)
WORKDIR /install_dir
RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\
gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP FastTree.c -lm &&\
ln -s /install_dir/FastTreeMP /usr/local/bin
# Install FastME FastME 2.1.6.1
WORKDIR /install_dir
RUN apt-get install -y automake &&\
git clone https://gite.lirmm.fr/atgc/FastME.git
git clone https://gite.lirmm.fr/atgc/FastME.git
WORKDIR /install_dir/FastME/tarball
RUN tar xzf fastme-2.1.6.4.tar.gz &&\
rm fastme-2.1.6.4.tar.gz &&\
ln -s /install_dir/FastME/tarball/fastme-2.1.6.2/binaries/fastme-2.1.6.4-linux64-omp /usr/local/bin/fastme
ln -s /install_dir/FastME/tarball/fastme-2.1.6.4/binaries/fastme-2.1.6.2-linux64-omp /usr/local/bin/fastme
# Install quicktree
WORKDIR /install_dir
......@@ -124,7 +142,6 @@ WORKDIR /install_dir/quicktree
RUN make &&\
ln -s /install_dir/quicktree/quicktree /usr/local/bin
# Install iqtree
WORKDIR /install_dir
RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz
......@@ -132,7 +149,6 @@ RUN tar -xzf iqtree-1.6.12-Linux.tar.gz &&\
rm iqtree-1.6.12-Linux.tar.gz &&\
ln -s /install_dir/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin
# Install iqtree2
WORKDIR /install_dir
RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v2.0.6/iqtree-2.0.6-Linux.tar.gz
......@@ -140,14 +156,12 @@ RUN tar -xzf iqtree-2.0.6-Linux.tar.gz &&\
rm iqtree-2.0.6-Linux.tar.gz &&\
ln -s /install_dir/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin
# # # Install PanACoTA
# # WORKDIR /install-dir
# # RUN wget https://github.com/gem-pasteur/PanACoTA/archive/refs/tags/1.4.0.tar.gz
# # RUN tar -xzf v1.4.0.tar.gz
# # WORKDIR /install-dir/PanACoTA-1.4.0
# # RUN ./make
# Install PanACoTA
WORKDIR /install-dir
RUN wget https://github.com/gem-pasteur/PanACoTA/archive/refs/tags/1.4.0.tar.gz
RUN tar -xzf v1.4.0.tar.gz
WORKDIR /install-dir/PanACoTA-1.4.0
RUN ./make
ENTRYPOINT ["/usr/local/bin/PanACoTA"]
CMD ['-h']
# # ENTRYPOINT ["/usr/local/bin/PanACoTA"]
# # CMD ['-h']
\ No newline at end of file
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment