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Amandine PERRIN
panacota
Commits
84bf5588
There was a problem fetching the pipeline summary.
Commit
84bf5588
authored
7 years ago
by
Amandine PERRIN
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Add sphinx installation on test machine
parent
3090c581
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for_tests/Dockerfile
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-14
23 additions, 14 deletions
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84bf5588
from
ubuntu:16.04
from
ubuntu:16.04
# Update apt-get packages
# Update apt-get packages
RUN
apt-get update
&&
\
RUN
apt-get update
&&
\
apt-get
-y
upgrade
apt-get
-y
upgrade
# Install package needed
# Install package needed and update pip
RUN
apt-get
install
-y
\
RUN
apt-get
install
-y
\
wget
\
wget
\
python3-pip
\
python3-pip
\
cmake
# to install mmseqs
cmake
# to install mmseqs
# Update pip
RUN
pip3
install
--upgrade
pip
RUN
pip3
install
--upgrade
pip
# Install barrnap
# Install barrnap
WORKDIR
/tmp
WORKDIR
/tmp
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
&&
\
RUN
mv
/tmp/barrnap-0.8/bin/barrnap /usr/local/bin
mv
/tmp/barrnap-0.8/bin/barrnap /usr/local/bin
&&
\
# Remove heavy useless files
# Remove heavy useless files
RUN
rm
-r
/tmp/barrnap-0.8/examples /tmp/barrnap-0.8/build/
*
.aln
rm -r /tmp/barrnap-0.8/examples /tmp/barrnap-0.8/build/*.aln
# Install prokka:
# Install prokka:
WORKDIR
/tmp
WORKDIR
/tmp
...
@@ -30,17 +33,23 @@ RUN apt-get install -y\
...
@@ -30,17 +33,23 @@ RUN apt-get install -y\
libdigest-md5-perl
\
libdigest-md5-perl
\
git
\
git
\
default-jre
\
default-jre
\
bioperl
bioperl
&&
\
RUN
git clone https://github.com/tseemann/prokka.git
git clone https://github.com/tseemann/prokka.git
RUN
/tmp/prokka/bin/prokka
--setupdb
RUN
/tmp/prokka/bin/prokka
--setupdb
&&
\
RUN
ln
-s
/tmp/prokka/bin/prokka /usr/local/bin
ln
-s
/tmp/prokka/bin/prokka /usr/local/bin
# Install mmseqs2
# Install mmseqs2
WORKDIR
/tmp
WORKDIR
/tmp
RUN
wget https://mmseqs.com/latest/mmseqs-static_sse41.tar.gz
&&
\
RUN
wget https://mmseqs.com/latest/mmseqs-static_sse41.tar.gz
&&
\
tar
xf mmseqs-static_sse41.tar.gz
&&
\
tar
xf mmseqs-static_sse41.tar.gz
&&
\
rm
mmseqs-static_sse41.tar.gz
rm
mmseqs-static_sse41.tar.gz
&&
\
RUN
mv
/tmp/mmseqs2/bin/mmseqs /usr/local/bin
mv
/tmp/mmseqs2/bin/mmseqs /usr/local/bin
&&
\
# remove useless files
# remove useless files
RUN
rm
-r
/tmp/mmseqs2
rm -r /tmp/mmseqs2
# Install sphinx
RUN
pip3
install
sphinx
&&
\
pip3
install
sphinx_rtd_theme
\ No newline at end of file
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