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Switch to Debian in Singularity image #1018

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Switch to Debian in Singularity image #1018

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Switch to Debian in Singularity image
Donaim Sep 20, 2023
264cfe2
Singularity: install requirements.txt, not its basespace version
Donaim Mar 11, 2024
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79 changes: 25 additions & 54 deletions Singularity
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# Generate the Singularity container to run MiCall on Kive.
Bootstrap: docker
From: centos:7
From: python:3.8

%help
MiCall maps all the reads from a sample against a set of reference
Expand Down Expand Up @@ -53,48 +53,28 @@ From: centos:7

%post
echo ===== Installing Prerequisites ===== >/dev/null
yum update -q -y

yum groupinstall -q -y 'development tools'
yum install -q -y epel-release
yum install -q -y unzip wget fontconfig bzip2-devel xz-devel openssl-devel \
libffi-devel sqlite-devel

echo ===== Installing Python ===== >/dev/null
wget -q https://www.python.org/ftp/python/3.8.3/Python-3.8.3.tar.xz
tar xJf Python*
rm Python*.xz
cd Python*
./configure --enable-optimizations
make altinstall
cd ..
rm -rf Python*
ln -s /usr/local/bin/python3.8 /usr/local/bin/python3
apt-get update -q
apt-get install -q -y unzip wget

echo ===== Installing blast ===== >/dev/null
cd /root
# Saved our own copy, because download was slow from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-1.x86_64.rpm
wget -q /~https://github.com/cfe-lab/MiCall/releases/download/v7.12.dev28/ncbi-blast-2.6.0+-1.x86_64.rpm
yum install -q -y ncbi-blast-2.6.0+-1.x86_64.rpm
rm ncbi-blast-2.6.0+-1.x86_64.rpm
python3 /opt/micall/micall/blast_db/make_blast_db.py
apt-get install -q -y ncbi-blast+

echo ===== Installing Rust and merge-mates ===== >/dev/null
yum install -q -y rust cargo
wget -qO rustup.sh https://sh.rustup.rs
chmod +x /rustup.sh
/rustup.sh -y -q
. /root/.cargo/env
rm rustup.sh
cargo install --quiet --root / --git /~https://github.com/jeff-k/merge-mates.git --rev 2fec61363f645e2008a4adff553d098beae21469

## Miniconda (Python 2) (Don't use this)
#wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh
#bash miniconda.sh -b -p /opt/miniconda

echo ===== Installing bowtie2 ===== >/dev/null
wget -q -O bowtie2.zip /~https://github.com/BenLangmead/bowtie2/releases/download/v2.2.8/bowtie2-2.2.8-linux-x86_64.zip
unzip -qq bowtie2.zip -d /opt/
unzip bowtie2.zip -d /opt/
ln -s /opt/bowtie2-2.2.8/ /opt/bowtie2
rm bowtie2.zip

echo ===== Installing IVA dependencies ===== >/dev/null
yum install -q -y tcsh ncurses-devel zlib-devel
apt-get install -q -y zlib1g-dev libncurses5-dev libncursesw5-dev
cd /bin
wget -q http://sun.aei.polsl.pl/kmc/download-2.1.1/linux/kmc
wget -q http://sun.aei.polsl.pl/kmc/download-2.1.1/linux/kmc_dump
Expand Down Expand Up @@ -122,32 +102,23 @@ From: centos:7
tar -xzf smalt-0.7.6-bin.tar.gz --no-same-owner
ln -s /opt/smalt-0.7.6-bin/smalt_x86_64 /bin/smalt

echo ===== Installing Haploflow ===== >/dev/null
apt-get install -q -y libboost-all-dev build-essential sudo git ronn cmake
cd /opt/
git clone /~https://github.com/hzi-bifo/Haploflow
cd Haploflow
git checkout 9a5a0ff6c3a0435e723e41f98fe82ec2ad19cf50
yes | sh build.sh

echo ===== Installing Python packages ===== >/dev/null
# Install dependencies for genetracks/drawsvg
apt-get install -q -y libcairo2-dev
# Also trigger matplotlib to build its font cache.
wget -q https://bootstrap.pypa.io/get-pip.py
python3 get-pip.py
rm get-pip.py
cd /opt
pip install --quiet -r /opt/micall/requirements.txt
ln -s /usr/local/bin/cutadapt /usr/local/bin/cutadapt-1.11
python3 -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot'

# Install dependencies for genetracks/drawsvg
yum install -q -y cairo-devel cairo cairo-tools zlib-devel

yum groupremove -q -y 'development tools'
yum remove -q -y epel-release wget unzip
yum autoremove -q -y
yum clean all

rm -rf /var/cache/yum

## CAUTION! This changes the default python command to python3!
## This breaks many things, including yum!
## To switch back to python2, use this command:
# sudo alternatives --set python /usr/bin/python2
alternatives --install /usr/bin/python python /usr/bin/python2 50
alternatives --install /usr/bin/python python /usr/local/bin/python3 60
pip install --upgrade pip
pip install -r /opt/micall/requirements.txt
python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot'
python /opt/micall/micall/blast_db/make_blast_db.py

%environment
export PATH=/opt/bowtie2:/bin:/usr/local/bin
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