Skip to content
Snippets Groups Projects
Commit c9e13fdf authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

update blastp installation for prokka

parent 2b3a42dc
No related branches found
No related tags found
No related merge requests found
Pipeline #23655 failed
...@@ -8,16 +8,17 @@ RUN apt-get update &&\ ...@@ -8,16 +8,17 @@ RUN apt-get update &&\
# Install packages needed and update pip # Install packages needed and update pip
RUN apt-get install -y \ RUN apt-get install -y \
wget \ wget \
python3-pip \ python3 \
python3 python3-pip
RUN pip3 install --upgrade pip RUN pip3 install --upgrade pip
# Update makeblastdb for prokka # Update makeblastdb and blastp for prokka
WORKDIR /tmp WORKDIR /tmp
RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.0+-x64-linux.tar.gz &&\ 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 &&\ 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/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 rm ncbi-blast-2.10.0+-x64-linux.tar.gz
...@@ -83,6 +84,7 @@ RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\ ...@@ -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 &&\ 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 /tmp/FastTreeMP /usr/local/bin
## Install FastME FastME 2.1.6.1 ## Install FastME FastME 2.1.6.1
WORKDIR /tmp WORKDIR /tmp
RUN apt-get install -y automake &&\ RUN apt-get install -y automake &&\
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment