In July 2019, this group was formed with the aim of getting the VirMAP pipeline to work on NCI Raijin.
Where do I find what I'm looking for?
More background information - all this goes into /docs
Progress and critical issues tracking - check out /worklogs
Docker container - a Dockerfile is at the root of this repository
Reference databases - see /referencedbs
VirMAP parameter descriptions - see parameters
VirMap result aggregation script - see aggreg_stats
Important: Complete the installation steps below first. Then proceed to https://github.com/rsoftone/virmap/tree/master/10-helper-scripts to setup databases (from NCBI Taxonomy and Genbank)
Step 1: Clone this repository as virmap_install using “git clone https://github.com/rsoftone/virmap.git virmap_install”. This will give you the installation related scripts and will avoid the confusion of everything being called virmap. On Katana you should clone the repository into your scratch directory.
git clone https://github.com/rsoftone/virmap.git virmap_install
Step 2: Change into the directory virmap_install and run the installation script
Installation on Katana
cd virmap_install
bash install_virmap_katana.sh
Installation on Gadi
cd virmap_install
bash install_virmap_gadi.sh
The following is a description of what happens in the install script, using the Gadi installation as an example.
#!/bin/bash
# Raijin specific: $TMPDIR is /short/<some-project>/<some-uid>/tmp
#
# All build and installation will be prefixed in $TMPDIR
#
# Download and install Miniconda
#
INSTALL_DIR=$TMPDIR/virmap
MINICONDA_DIR=$TMPDIR/miniconda3
cd $TMPDIR
wget https://repo.anaconda.com/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh -O $TMPDIR/miniconda.sh
#
# The next line is Raijin specific (we prefix the environments to store them in my $MINICONDA_DIR directory)
#
/bin/bash $TMPDIR/miniconda.sh -u -b -p $MINICONDA_DIR
# sudo yum install -y openssl-devel
# If using Ubuntu Server 18:
sudo apt-get install build-essential openssl libssl-dev zlib1g-dev
mkdir $INSTALL_DIR
cd $INSTALL_DIR
source $MINICONDA_DIR/etc/profile.d/conda.sh
cat - <<EOF >environment.yml
name: virmap
channels:
- bioconda
- agbiome
- conda-forge
- defaults
dependencies:
- diamond
- blast
- bbmap=38.67 # versions after this introduce spaces into the fasta header
- megahit
- khmer
- vsearch
- lbzip2
- pigz
- zstd
- sra-tools
- coreutils
- kraken2
- parallel
- pv # not strictly required
EOF
#
# Create Conda Environment
#
# The next line is Raijin specific. We need ~10GB space to hold the source packages…
# and Raijin $HOME is very limited in space…
#
#
# The lines below are no longer needed for Gadi (re-enable them if you are on Raijin)
#
# export CONDA_PKGS_DIRS=/short/yi98/sy0928/pkgs
#
conda env create -f environment.yml
#
# Finished Anaconda packages...proceed to Perl and associated packages
#
wget http://www.cpan.org/src/5.0/perl-5.28.0.tar.gz -O $TMPDIR/perl-5.28.0.tar.gz
cd $TMPDIR && tar zxvf perl-5.28.0.tar.gz
cd perl-5.28.0
#
# The lines below are no longer needed for Gadi (re-enable them if you are on Raijin)
#
# module load gcc/4.9.0
# export CC=/apps/gcc/4.9.0/wrapper/gcc
#
# On Raijin: this will build a multithreaded Perl with gcc 4.9 (needed for C++11), without Perl docs
# On Gadi: We can use system gcc, and omit -Dcc=..
#
#
# The lines below are no longer needed for Gadi (re-enable them if you are on Raijin)
#
# ./Configure -des -Dusethreads -Dprefix=$INSTALL_DIR -Dcc=/apps/gcc/4.9.0/wrapper/gcc -Dman1dir=none -Dman3dir=none
./Configure -des -Dusethreads -Dprefix=$INSTALL_DIR -Dman1dir=none -Dman3dir=none
make
make install
#
# Finished Perl 5.28.0...proceed to install VirMap itself
#
cd $INSTALL_DIR && git clone https://github.com/cmmr/virmap.git
#
# binutils is old on Raijin...load a module with updated /bin/as
#
#
# The lines below are no longer needed for Gadi (re-enable them if you are on Raijin)
#
# module load binutils/2.32
#
# Setup a simple activation script, usage:
# source $INSTALL_DIR/activate.sh
#
cat - <<EOF >$INSTALL_DIR/activate.sh
INSTALL_DIR=$INSTALL_DIR
MINICONDA_DIR=$MINICONDA_DIR
#
# Setup conda in the shell and activate the environment
#
source "\$MINICONDA_DIR/etc/profile.d/conda.sh"
conda activate virmap
#
# Get suitable PATH for VirMap and Perl 5.28.0
#
export PERL5LIB=\$INSTALL_DIR/lib/perl5
export PATH=\$INSTALL_DIR/virmap:\$INSTALL_DIR/bin:\$PATH
EOF
#
#
#
conda activate virmap
export PERL5LIB=$INSTALL_DIR/lib/perl5
export PATH=$INSTALL_DIR/virmap:$INSTALL_DIR/bin:$PATH
cpan App::cpanminus
#
# For RocksDB (make sure environment variable CC is set correctly!)
#
cpanm --local-lib=$INSTALL_DIR --force RocksDB
#
# For other dependencies
#
cpanm --local-lib=$INSTALL_DIR OpenSourceOrg::API
cpanm --local-lib=$INSTALL_DIR --force POSIX::1003::Sysconf
cpanm --local-lib=$INSTALL_DIR --force POSIX::RT::Semaphore
cpanm --local-lib=$INSTALL_DIR Compress::Zstd
# Sereal::Decoder can have trouble compiling the Zstd lib on Gadi, but will
# happily compile against existing zstd, even though it can't use it properly.
# Sereal's internal support for Zstd (i.e. *not* what is used by VirMap)
# will be broken, and tests for that fail
module load zstd
cpanm --local-lib=$INSTALL_DIR --force Sereal
module unload zstd
cpanm --local-lib=$INSTALL_DIR Text::Levenshtein::Damerau::XS
cpanm --local-lib=$INSTALL_DIR Text::Levenshtein::XS
cpanm --local-lib=$INSTALL_DIR Statistics::Basic
cpanm --local-lib=$INSTALL_DIR Cpanel::JSON::XS
module unload binutils
cd $INSTALL_DIR/lib/perl5 && wget https://raw.githubusercontent.com/ucdavis-bioinformatics/assemblathon2-analysis/master/FAlite.pm
cd ~
#
# Test the Perl installation
#
perl -e 'use Compress::Zstd; use English; use Thread::Semaphore; use Thread::Queue qw( ); use threads::shared; use strict; use RocksDB; use Statistics::Basic qw(:all); use Sereal; use Text::Levenshtein::XS; use Text::Levenshtein::Damerau::XS; use OpenSourceOrg::API; use POSIX::1003::Sysconf; use POSIX::RT::Semaphore; use FAlite'
# First logout, then login again to Raijin
#
# You'll want to substitute $INSTALL_DIR here manually,
# as it was set in the previous session
source $INSTALL_DIR/activate.sh
# module load gcc/4.9.0
Virmap.pl
# This should return:
# usage: Virmap.pl [options] <databases> --readF ReadSet1_R1.fastq.bz2 ReadSet2_R1.fastq.gz --readR ReadSet1_R2.fastq.bz2 ReadSet2_R2.fastq.bz2 --readUnpaired ReadsUnpaired.fastq.bz2
# Test dependent application...
which megahit
# This should return:
# $MINICONDA_DIR/envs/virmap/bin/megahit
A wrapper script virmap_wrapper.sh is provided in this repository, which can:
- Store common parameters (e.g. database paths) in a config file
virmap_config.sh - Perform database parameter sanity checks
- Automatically setup the environment (sources
activate.sh)
# Copy the wrapper script into the directory where we installed VirMAP
cp -s virmap_wrapper.sh "$INSTALL_DIR/"
# Run the wrapper once to generate a template config file
"$INSTALL_DIR/virmap_wrapper.sh"
# Fill the config file with database paths
edit "$INSTALL_DIR/virmap_config.sh"qsub -P u71 -q normal -l walltime=6:00:00,mem=48G,ncpus=12,wd,jobfs=100GB,storage=scratch/u71+gdata/u71 -joe <<EOF
source $INSTALL_DIR/activate.sh
Virmap.pl \
--readUnpaired "/path/to/my/sample.fastq" \
--outputDir "/path/to/my/sample/output_dir" \
--tmp "/path/to/my/sample/output_tmp" `# Optional` \
--sampleName "sample_name" \
--threads "48" \
--gbBlastx "/g/data1a/u71/VirMap/191205-gbblastx.dmnd" \
--gbBlastn "/g/data1a/u71/VirMap/191205-gbBlastn/191205-gbBlastn" \
--virBbmap "/g/data1a/u71/VirMap/191205-virBbmap" \
--virDmnd "/g/data1a/u71/VirMap/191205-virdiamond.dmnd" \
--taxaJson "/g/data1a/u71/VirMap/taxaJson.dat"
EOFcd /path/to/store/output
qsub -P u71 -q normal -l walltime=6:00:00,mem=48G,ncpus=12,wd,jobfs=100GB,storage=scratch/u71+gdata/u71 -joe -- \
$INSTALL_DIR/virmap_wrapper.sh \
--readUnpaired "/path/to/my/sample/.fastq" \
--sampleName "sample_name"