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Amandine PERRIN
pipeline_annotation
Commits
c9e13fdf
Commit
c9e13fdf
authored
Feb 03, 2020
by
Amandine PERRIN
Browse files
update blastp installation for prokka
parent
2b3a42dc
Pipeline
#23655
failed with stage
in 6 minutes and 25 seconds
Changes
1
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1
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for_tests/Dockerfile
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c9e13fdf
...
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@@ -8,16 +8,17 @@ RUN apt-get update &&\
# Install packages needed and update pip
RUN
apt-get
install
-y
\
wget
\
python3
-pip
\
python3
python3
\
python3
-pip
RUN
pip3
install
--upgrade
pip
# Update makeblastdb for prokka
# 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
...
...
@@ -83,6 +84,7 @@ 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
/tmp/FastTreeMP /usr/local/bin
## Install FastME FastME 2.1.6.1
WORKDIR
/tmp
RUN
apt-get
install
-y
automake
&&
\
...
...
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