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Amandine PERRIN
pipeline_annotation
Commits
e808b1b7
Commit
e808b1b7
authored
Jul 22, 2020
by
Amandine PERRIN
Browse files
download new blast+ latest version
parent
0d158e47
Pipeline
#34357
failed with stage
in 9 minutes and 3 seconds
Changes
1
Pipelines
1
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Side-by-side
for_build/annote_and_1tree/Dockerfile
View file @
e808b1b7
...
...
@@ -4,7 +4,6 @@ from ubuntu:18.04
RUN
apt-get update
&&
\
apt-get
-y
upgrade
# Install packages needed and update pip
RUN
apt-get
install
-y
\
wget
\
...
...
@@ -13,15 +12,13 @@ RUN apt-get install -y \
# Upgrade pip
RUN
pip3
install
--upgrade
pip
# Update makeblastdb and blastp for prokka
WORKDIR
/tmp
RUN
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.0+-x64-linux.tar.gz
&&
\
tar
zxvpf ncbi-blast-2.10.0+-x64-linux.tar.gz
&&
\
cp
/tmp/ncbi-blast-2.10.0+/bin/makeblastdb /usr/local/bin/
&&
\
cp
/tmp/ncbi-blast-2.10.0+/bin/blastp /usr/local/bin/
&&
\
rm
ncbi-blast-2.10.0+-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
&&
\
cp
/tmp/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/
&&
\
cp
/tmp/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/
&&
\
rm
ncbi-blast-2.10.1+-x64-linux.tar.gz
# Install prokka:
WORKDIR
/tmp
...
...
@@ -35,7 +32,6 @@ RUN apt-get install -y\
git clone https://github.com/tseemann/prokka.git
&&
\
/tmp/prokka/bin/prokka
--setupdb
&&
\
ln
-s
/tmp/prokka/bin/prokka /usr/local/bin
RUN
rm
/usr/bin/mafft
# remove mafft installed with bioperl
# Install quicktree
...
...
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