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Amandine PERRIN
pipeline_annotation
Commits
0553c2d9
Commit
0553c2d9
authored
Feb 12, 2019
by
Amandine PERRIN
Browse files
add new machines to test installation
parent
fe2fe4e3
Pipeline
#9569
failed with stage
in 4 minutes and 34 seconds
Changes
3
Pipelines
1
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Inline
Side-by-side
for_build/
basics
/Dockerfile
→
for_build/
annote_and_mafft
/Dockerfile
View file @
0553c2d9
...
...
@@ -7,15 +7,20 @@ RUN apt-get update &&\
# Install package needed
RUN
apt-get
install
-y
\
wget
\
python3-pip
# Update pip
RUN
pip3
install
--upgrade
pip
# Install prokka:
WORKDIR
/tmp
RUN
apt-get
install
-y
\
libdatetime-perl
\
libxml-simple-perl
\
libdigest-md5-perl
\
git
\
python3-pip
\
default-jre
\
bioperl
# Update pip
RUN
pip3
install
--upgrade
pip
RUN
rm
/usr/bin/mafft
# remove mafft installed with bioperl
\ No newline at end of file
RUN
git clone https://github.com/tseemann/prokka.git
RUN
/tmp/prokka/bin/prokka
--setupdb
RUN
ln
-s
/tmp/prokka/bin/prokka /usr/local/bin
for_build/mafft/Dockerfile
0 → 100644
View file @
0553c2d9
from
ubuntu:16.04
# Update apt-get packages
RUN
apt-get update
&&
\
apt-get
-y
upgrade
# Install package needed
RUN
apt-get
install
-y
\
wget
\
python3-pip
# Update pip
RUN
pip3
install
--upgrade
pip
RUN
apt-get
install
-y
\
libdatetime-perl
\
libxml-simple-perl
\
libdigest-md5-perl
\
git
\
default-jre
\
bioperl
# Install mafft 7.313
RUN
rm
/usr/bin/mafft
# remove mafft installed with bioperl
WORKDIR
/tmp
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
/tmp/mafft-7.313-with-extensions/core
RUN
make clean
&&
\
make
&&
\
make
install
\ No newline at end of file
for_build/mmseqs_and_fastme/Dockerfile
0 → 100644
View file @
0553c2d9
from
ubuntu:16.04
# Update apt-get packages
RUN
apt-get update
&&
\
apt-get
-y
upgrade
# Install package needed and update pip
RUN
apt-get
install
-y
\
wget
\
python3-pip
RUN
pip3
install
--upgrade
pip
# Install mmseqs2
WORKDIR
/tmp
RUN
apt-get
install
-y
cmake
&&
\
wget https://mmseqs.com/latest/mmseqs-static_sse41.tar.gz
&&
\
tar
xf mmseqs-static_sse41.tar.gz
&&
\
rm
mmseqs-static_sse41.tar.gz
&&
\
mv
/tmp/mmseqs2/bin/mmseqs /usr/local/bin
&&
\
# remove useless files
rm -r /tmp/mmseqs2
# Install FastME
WORKDIR
/tmp
RUN
apt-get
install
-y
automake
&&
\
git clone https://gite.lirmm.fr/atgc/FastME.git
WORKDIR
/tmp/FastME
RUN
./configure
&&
\
make
&&
\
make
install
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