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Amandine PERRIN
panacota
Commits
bd5845b1
Commit
bd5845b1
authored
4 years ago
by
Amandine PERRIN
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install softwares in install-dir instead of /tmp
parent
fff84538
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Pipeline
#40844
passed
4 years ago
Stage: test
Stage: coverage
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bd5845b1
...
@@ -22,43 +22,43 @@ RUN pip3 install --upgrade pip
...
@@ -22,43 +22,43 @@ RUN pip3 install --upgrade pip
# Update makeblastdb and blastp for prokka
# Update makeblastdb and blastp for prokka
WORKDIR
/
tmp
WORKDIR
/
install-dir
RUN
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.1+-x64-linux.tar.gz
&&
\
RUN
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.1+-x64-linux.tar.gz
&&
\
tar
zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz
&&
\
tar
zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz
&&
\
cp
/
tmp
/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/
&&
\
cp
/
install-dir
/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/
&&
\
cp
/
tmp
/ncbi-blast-2.10.1+/bin/blastp /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
rm
ncbi-blast-2.10.1+-x64-linux.tar.gz
# Install mash
# Install mash
WORKDIR
/
tmp
WORKDIR
/
install-dir
RUN
wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar
&&
\
RUN
wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar
&&
\
tar
-xf
mash-Linux64-v2.2.tar
&&
\
tar
-xf
mash-Linux64-v2.2.tar
&&
\
rm
mash-Linux64-v2.2.tar
&&
\
rm
mash-Linux64-v2.2.tar
&&
\
mv
/
tmp
/mash-Linux64-v2.2/mash /usr/local/bin
&&
\
mv
/
install-dir
/mash-Linux64-v2.2/mash /usr/local/bin
&&
\
rm
-r
mash-Linux64-v2.2
rm
-r
mash-Linux64-v2.2
# Install barrnap
# Install barrnap
WORKDIR
/
tmp
WORKDIR
/
install-dir
RUN
wget https://github.com/tseemann/barrnap/archive/0.8.tar.gz
&&
\
RUN
wget https://github.com/tseemann/barrnap/archive/0.8.tar.gz
&&
\
tar
-xf
0.8.tar.gz
&&
\
tar
-xf
0.8.tar.gz
&&
\
rm
0.8.tar.gz
&&
\
rm
0.8.tar.gz
&&
\
mv
/
tmp
/barrnap-0.8/bin/barrnap /usr/local/bin
&&
\
mv
/
install-dir
/barrnap-0.8/bin/barrnap /usr/local/bin
&&
\
# Remove heavy useless files
# Remove heavy useless files
rm -r /
tmp
/barrnap-0.8/examples /
tmp
/barrnap-0.8/build/*.aln
rm -r /
install-dir
/barrnap-0.8/examples /
install-dir
/barrnap-0.8/build/*.aln
# Install prodigal
# Install prodigal
WORKDIR
/
tmp
WORKDIR
/
install-dir
RUN
wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz
&&
\
RUN
wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz
&&
\
tar
-xzf
v2.6.3.tar.gz
&&
\
tar
-xzf
v2.6.3.tar.gz
&&
\
rm
v2.6.3.tar.gz
rm
v2.6.3.tar.gz
WORKDIR
/
tmp
/Prodigal-2.6.3
WORKDIR
/
install-dir
/Prodigal-2.6.3
RUN
make
&&
\
RUN
make
&&
\
make
install
make
install
# Install prokka:
# Install prokka:
WORKDIR
/
tmp
WORKDIR
/
install-dir
RUN
apt-get
install
-y
\
RUN
apt-get
install
-y
\
libdatetime-perl
\
libdatetime-perl
\
libxml-simple-perl
\
libxml-simple-perl
\
...
@@ -67,77 +67,77 @@ RUN apt-get install -y\
...
@@ -67,77 +67,77 @@ RUN apt-get install -y\
default-jre
\
default-jre
\
bioperl
bioperl
RUN
git clone https://github.com/tseemann/prokka.git
RUN
git clone https://github.com/tseemann/prokka.git
RUN
/
tmp
/prokka/bin/prokka
--setupdb
&&
\
RUN
/
install-dir
/prokka/bin/prokka
--setupdb
&&
\
ln
-s
/
tmp
/prokka/bin/prokka /usr/local/bin
ln
-s
/
install-dir
/prokka/bin/prokka /usr/local/bin
# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
WORKDIR
/
tmp
WORKDIR
/
install-dir
RUN
wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz
&&
\
RUN
wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz
&&
\
tar
xvfz mmseqs-linux-sse41.tar.gz
&&
\
tar
xvfz mmseqs-linux-sse41.tar.gz
&&
\
rm
mmseqs-linux-sse41.tar.gz
&&
\
rm
mmseqs-linux-sse41.tar.gz
&&
\
mv
/
tmp
/mmseqs/bin/mmseqs /usr/local/bin
&&
\
mv
/
install-dir
/mmseqs/bin/mmseqs /usr/local/bin
&&
\
# remove useless files
# remove useless files
rm -r /
tmp
/mmseqs
rm -r /
install-dir
/mmseqs
# Install mafft 7.313
# Install mafft 7.313
RUN
rm
/usr/bin/mafft
# remove mafft installed with bioperl
RUN
rm
/usr/bin/mafft
# remove mafft installed with bioperl
WORKDIR
/
tmp
WORKDIR
/
install-dir
RUN
wget https://mafft.cbrc.jp/alignment/software/mafft-7.313-with-extensions-src.tgz
&&
\
RUN
wget https://mafft.cbrc.jp/alignment/software/mafft-7.313-with-extensions-src.tgz
&&
\
tar
xf mafft-7.313-with-extensions-src.tgz
&&
\
tar
xf mafft-7.313-with-extensions-src.tgz
&&
\
rm
mafft-7.313-with-extensions-src.tgz
rm
mafft-7.313-with-extensions-src.tgz
WORKDIR
/
tmp
/mafft-7.313-with-extensions/core
WORKDIR
/
install-dir
/mafft-7.313-with-extensions/core
RUN
make clean
&&
\
RUN
make clean
&&
\
make
&&
\
make
&&
\
make
install
make
install
# Install FastTree version 2.1.11 Double precision (No SSE3)
# Install FastTree version 2.1.11 Double precision (No SSE3)
WORKDIR
/
tmp
WORKDIR
/
install-dir
RUN
wget http://www.microbesonline.org/fasttree/FastTree.c
&&
\
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
&&
\
gcc
-DOPENMP
-fopenmp
-DUSE_DOUBLE
-Wall
-O3
-finline-functions
-funroll-loops
-o
FastTreeMP FastTree.c
-lm
&&
\
ln
-s
/
tmp
/FastTreeMP /usr/local/bin
ln
-s
/
install-dir
/FastTreeMP /usr/local/bin
## Install FastME FastME 2.1.6.1
## Install FastME FastME 2.1.6.1
WORKDIR
/
tmp
WORKDIR
/
install-dir
RUN
apt-get
install
-y
automake
&&
\
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
/
tmp
/FastME
WORKDIR
/
install-dir
/FastME
RUN
./configure
&&
\
RUN
./configure
&&
\
make
&&
\
make
&&
\
make
install
make
install
# Install quicktree
# Install quicktree
WORKDIR
/
tmp
WORKDIR
/
install-dir
RUN
git clone https://github.com/tseemann/quicktree
RUN
git clone https://github.com/tseemann/quicktree
WORKDIR
quicktree
WORKDIR
quicktree
RUN
make
&&
\
RUN
make
&&
\
ln
-s
/
tmp
/quicktree/quicktree /usr/local/bin
ln
-s
/
install-dir
/quicktree/quicktree /usr/local/bin
# Install iqtree
# Install iqtree
WORKDIR
/
tmp
WORKDIR
/
install-dir
RUN
wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz
RUN
wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz
RUN
tar
-xzf
iqtree-1.6.12-Linux.tar.gz
&&
\
RUN
tar
-xzf
iqtree-1.6.12-Linux.tar.gz
&&
\
rm
iqtree-1.6.12-Linux.tar.gz
&&
\
rm
iqtree-1.6.12-Linux.tar.gz
&&
\
ln
-s
/
tmp
/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin
ln
-s
/
install-dir
/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin
# Install iqtree2
# Install iqtree2
WORKDIR
/
tmp
WORKDIR
/
install-dir
RUN
wget https://github.com/Cibiv/IQ-TREE/releases/download/v2.0.6/iqtree-2.0.6-Linux.tar.gz
RUN
wget https://github.com/Cibiv/IQ-TREE/releases/download/v2.0.6/iqtree-2.0.6-Linux.tar.gz
RUN
tar
-xzf
iqtree-2.0.6-Linux.tar.gz
&&
\
RUN
tar
-xzf
iqtree-2.0.6-Linux.tar.gz
&&
\
rm
iqtree-2.0.6-Linux.tar.gz
&&
\
rm
iqtree-2.0.6-Linux.tar.gz
&&
\
ln
-s
/
tmp
/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin
ln
-s
/
install-dir
/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin
# Install PanACoTA
# Install PanACoTA
WORKDIR
/
tmp
WORKDIR
/
install-dir
RUN
git clone https://gitlab.pasteur.fr/aperrin/pipeline_annotation.git
RUN
git clone https://gitlab.pasteur.fr/aperrin/pipeline_annotation.git
WORKDIR
/
tmp
/pipeline_annotation
WORKDIR
/
install-dir
/pipeline_annotation
RUN
git checkout dev
&&
\
RUN
git checkout dev
&&
\
./make
./make
...
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