Commit 1888c9f3 authored by mmassaviol's avatar mmassaviol
Browse files

Add missing medaka dependencies

parent 4cd867b0
......@@ -91,7 +91,7 @@ singularity run --app appName this_container.sif
wget -O miniasm.tar.gz
tar -xvzf miniasm.tar.gz
cd miniasm-0.3
make -j 10
cd .. rm miniasm.tar.gz
echo 'export PATH="/opt/biotools/miniasm-0.3:$PATH"' >>$SINGULARITY_ENVIRONMENT
......@@ -100,8 +100,26 @@ singularity run --app appName this_container.sif
tar -xvzf racon.tar.gz
cd racon-v1.4.10
cmake -DCMAKE_BUILD_TYPE=Release
make -j 10
echo 'export PATH="/opt/biotools/racon-v1.4.10/bin:$PATH"' >>$SINGULARITY_ENVIRONMENT
wget -O htslib.tar.bz2
tar -xvjf htslib.tar.bz2
cd htslib-1.9
make -j 10
make install
cd /opt/biotools
tar -xvjf samtools-1.9.tar.bz2
cd samtools-1.9
./configure && make -j 10
cd ..
mv samtools-1.9/samtools bin/samtools
rm -r samtools-1.9 samtools-1.9.tar.bz2
apt-get -y install tabix
pip3 install medaka==0.10.1
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