Abyss

Abyss is installed on Maple and can be loaded using its module:
module load abyss

anvi’o

anvi’o is installed on Maple:
module load python
source activate anvio-6.2

Autometa

Autometa is installed on Maple. Load the autometa module, then run:
source activate autometa
to activate the required Anaconda Python environment.

AWS CLI

The Amazon Web Services Command Line Interface tool is available on Maple by loading the awscli module.

BAli-Phy

BAli-Phy is available on Maple. It was compiled from the project git repository on 2020/03/13, which means it is version 3.5.0 or later. To use it, load the bali-phy module, which will prompt you to activate the bali-phy environment:
module load bali-phy
source activate bali-phy

BBMap

BBMap is available on all systems. On Maple, load the bbmap module.

On Sequoia/Catalpa, add /usr/local/apps/bbmap to your PATH and load the java module.

BEAST

BEAST 2.6.2 is available on Maple. Just load the beast module. Version 2.5.2 is also available.

packagemanager will need to be run on the head node due to the need for Internet access. However, it usually starts up too many threads and is shut down by the process limits we have in place to protect the head nodes. Email MCSR staff if you need assistance installing BEAST packages.

user@maple:~> packagemanager -add MODEL_SELECTION
Error occurred during initialization of VM
java.lang.OutOfMemoryError: unable to create new native thread

BEAST 2.3.0 is available on Sequoia/Catalpa, but there is no module.

BiG-SCAPE

BiG-SCAPE is available on Maple. Load the bigscape module.

You’ll then be prompted to activate the bigscape Python environment:
source activate bigscape

BlobTools

BlobTools is available on all systems:
module load python
source activate blobtools

Burrows-Wheeler Aligner

Burrows-Wheeler Aligner is available on Maple by loading the bwa module. The executable name is bwa.

BUSCO

BUSCO 4.0.6 is available on Maple:
module load python
source activate busco

The main executable’s name is busco.

BUSCO 3.x is available on Maple via the busco module. The main command for it is run_BUSCO.py.

Circlator

Circlator 1.5.5 is available on Maple. Load the python module, then activate the circlator environment:
module load python
source activate circlator

ClonalFrameML

ClonalFrameML is available on all systems. Load the clonalframeml module.

Concoct

Concoct is available on Maple:
module load python
source activate concoct

D’accord

D’accord is now available on Maple:
module load daccord

EMSAR

EMSAR is available on Maple by loading the emsar module.

EukCC

EukCC is available on Maple:
module load eukcc
source activate eukcc

The EukCC database is available at ${CONDA_HOME}/eukccdb.

EukDetect

EukDetect is available on Maple. To use:
module load python
source activate eukdetect

The executable name is eukdetect. Each user will need to copy /usr/local/apps/EukDetect/default_configfile.yml and modify it to suit your needs.

ezTree

ezTree is available on Maple:
module load ezTree
source activate bioinf

FastTree

FastTree is available on Maple:
module load fasttree

FastQC

FastQC is available on all systems by loading the fastqc module.

Gaussian

Gaussian is computational chemistry software that is most of our most popular software packages.

Version 09 is installed on Sequoia and version 16 (Revision C.01) is installed on Maple. The version currently installed will not run on Maple’s GPUs.

Unfortunately, the license to run a single Gaussian job across multiple nodes is quite expensive, so Gaussian jobs on our systems can only run on multiple cores on a single node.

g09sub

On Sequoia and Catalpa there is a script called g09sub that will write a PBS script and submit it for you. Just run it without arguments for more information.

Example jobs

The Sequoia example job can be found at /usr/local/apps/example_jobs/g09_sequoia_example. It will work on Catalpa as well. The example job for Maple can be found at /usr/local/apps/example_jobs/g16_maple_example.

Maple’s example job detects whether it is on an old node or new node and uses the appropriate version of Gaussian (AVX or AVX2). Maple’s PBS tries to assign jobs to the newer nodes first, so jobs will generally end up on the newer nodes (AVX2) unless it requests lots of resources or the system is busy.

Gaussian utilities

Unfortunately, there is no module for Gaussian due to the way it is setup. To run Gaussian interactively, or use its utility programs, first run:

On Maple:

export g16root=/usr/local/apps/gaussian/g16-c01-avx . $g16root/g16/bsd/g16.profile

These lines are already included in the example PBS scripts.

Gblocks

Gblocks is available on Maple. Load the gblocks module:
module load gblocks

GeneMark-ES/ET/EP

GeneMark-ES/ET/EP is available on Maple:
module load genemark

Genome Analysis Toolkit (GATK)

The Genome Analysis Toolkit is available on Maple by loading the gatk module.

GROMACS

An MPI-enabled version of GROMACS 2020 is installed on Maple. A partially working example job is available. We could use some help finishing it up.

GROMACS is available on other systems, but they are fairly out of date at this point.

IGVTools

IGVTools is available on all systems:
module load igvtools

Intel Compilers

MCSR maintains a license for Intel’s C (icc), C++ (icpc) and Fortran (ifort) compilers. These compilers tend to be faster than GNU compilers (gcc, etc.), but some code will not compile with Intel compilers.

On Maple, load the compilers like so:
module load intel/compiler

The Intel Math Kernel Library (MKL) provides many functions optimized for Intel processors, such as BLAS, LAPACK, and FFTW. You can load the MKL like this:
module load intel/mkl

Julia

The Julia programming language is available on Maple by loading the julia module.

MetaPhlAn

MetaPhlAn 3 is available on Maple:
module load python
source activate metaphlan3

Helper programs hclust2 and GraPhlAn are available in a separate Python environment:
module load python
source activate hclust2

Minimap2

Minimap2 is available on Maple:
module load minimap2

Molpro

Molpro is available on all systems. All systems have an example job available.

Version 2019.02 (Patch Level 3) is available on Maple using the molpro module.

NWChem

NWChem is available on all systems. The most recent installation is 7.0.0 on Maple. To use it, load the nwchem module.

There is a default .nwchemrc file at /usr/local/apps/nwchem/7.0.0/data/default.nwchemrc. To copy it to your home directory, run:
cp /usr/local/apps/nwchem/7.0.0/data/default.nwchemrc ~/.nwchemrc

Orthofinder

Orthofinder is available on Maple:
module load python
source activate orthofinder

PacBio Tools

PacBio tools blasr and ccs are available on Maple. To use:
module load python
source activate pacbio

To have other PacBio tools installed, contact the MCSR staff.

PBSuite

PBSuite is available on Maple:
module load pbsuite
source activate pbsuite

Picard

Picard (or PicardTools) is available with the picard module on Maple. The module sets up an environmental variable and an alias. It can be run like so:

java -jar $PICARD

or using the alias:

picard

Remember that any process that uses more than a minute of CPU and/or a reasonable about of RAM should be run inside a PBS job.

Pilon

Pilon is available inside the python module on Maple:
module load python

PPanGGOLiN

PPanGGOLiN is available on Maple:
module load python
source activate ppanggolin

PBSuite

PBSuite is available on Maple:
module load pbsuite
source activate pbsuite

phyloFlash

phyloFlash is available on Maple:
export PHYLOFLASH_DBHOME=/ddn/home2/appl/138
module load python/3
source activate phyloflash

Picrust

Picrust is available on Maple:
module load python
source activate picrust

Python

By default, all our systems have the default Python that came with the operating system. This will work for simple scripts.

Users that need iPython or additional modules should load the Anaconda Python module:

module load python

Anaconda provides NumPy, SciPy, matplotlib, PANDAS, and many other packages.

Increasingly, Anaconda is also the easiest way to install many software packages and libraries.

To install Anaconda packages, create an environment for a specific purpose and install all the needed packages inside the environment:

1. conda create --name name_of_environment
2. source activate name_of_environment
3. conda install package_names

QIIME2

QIIME2 2020.2 is available on Maple, Sequoia, and Catalpa. To use it, run the following:
module load python
source activate qiime2-2020.2

R

R is a programming language for statistics and data analysis. It has become very popular lately, particularly in social sciences, life sciences, education, pharmaceuticals, finance, etc.

Most MCSR systems have a system R installed that may be suitable for some purposes. However, serious users will want to load one of the R modules available. The most recent version of R can always be loaded by running:
module load R

We have example jobs for R for both Sequoia and Maple. If you want to run R interactively, please use an interactive PBS session.

Installing R modules

Users that need non-standard R modules should install them in their home directory.

To install a library in your home directory, first ensure that you have the appropriate R module loaded. Then, run the following command from inside R:
install.packages("package_name")
where package_name is the name of the package you’d like to install. R will note that you do not have permission to write to the global R library and ask if you’d like to create an R directory in your home directory. It will then install the package and any dependencies.

If you find that an R package you installed is suddenly not there, make sure you’re on the correct system and that you’re using the correct version of R. If a new version of R has been installed, you’ll need to load the older version of R or reinstall your package.

REAPR

REAPR is available on Maple:
module load reapr

SingleM

SingleM is available on Maple:
module load python

SolidBin

A few different versions of SolidBin are installed on Maple. The latest was installed in March 2020 from the project’s git repository. It is located in /usr/local/apps/SolidBin-202003. The setup the environment properly, run:
module load python
source activate solidbin-202003

SPAdes

SPAdes is installed on several systems. The most recent installation is 3.14.1 on Maple. Load the spades module.

SqueezeMeta

SqueezeMeta is available on Maple:
module load python
source activate squeezemeta

SRA Toolkit

The SRA Toolkit is installed on Maple. To use it, load the sratoolkit module:
module load sratoolkit

You will also need to configure the toolkit before using it. Do this by running:
vdb-config -i

Remember that Maple does not allow connections to the Internet from compute nodes. This can be done from the head node provided that no processing is done or large amounts of memory used.

SSU-ALIGN

SSU-ALIGN 0.1.1 is available on Maple:
module load ssu-align

STAR

STAR is available on all systems. Load the star module:
module load star

The command name is uppercase: STAR

Subread

Subread is available on Maple:
module load subread

Trimmomatic

Trimmomatic 0.39 is available on all systems. Loading the trimmomatic module sets up a trimmomatic alias and a TRIMMOMATIC environmental variable that points to the Trimmomatic JAR file.

UGENE

UGENE is available on Maple:
module load ugene

Unicycler

Unicycler is available on all systems:
module load python
source activate unicycler