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QChem

Software Description: 

Q-Chem is a comprehensive ab initio quantum chemistry package. Its capabilities range from the highest performance DFT/HF calculations to high level post-HF correlation methods.

The QChem module is available on the Itasca and Cascade clusters.

 

Software Support Level: 
Secondary Support
Itasca Documentation: 

To run the application interactively in the Linux environment run the commands:

module load qchem
qchem water.in

Other versions of qchem are available. The "serial" type installations support single threaded and multi-threaded (OpenMP) execution. The "parallel" type installations support MPI execution (via a QChem-internal version of MPICH). The naming scheme for each type follows: 

qchem/4.1_parallel
qchem/4.1_serial
qchem/parallel
qchem/serial (default)

To run QChem in multi-threaded (OpenMP) mode, specify the number of threads with "-nt": 

qchem -nt 4 DFT_glutamine.in output.out
Software Access Level: 
Open Access
PBS Example: 

The following example demonstrates how to run Q-Chem with 16 MPI processes:

#!/bin/bash -l

#PBS -l walltime=01:00:00,mem=21gb,nodes=2:ppn=8
#PBS -m abe

module load qchem/4.1_parallel

cat $PBS_NODEFILE               

# Uncomment these lines to get 1 proc per node (the ppn=8 must
# remain above)
#cat $PBS_NODEFILE | sort -u > $PBS_O_WORKDIR/machinefile
#export PBS_NODEFILE=$PBS_O_WORKDIR/machinefile

NN=`cat $PBS_NODEFILE | wc -l`
echo "Launching job for NN=$NN processes"

cd $PBS_O_WORKDIR

# Sample input files are available with each module
cp /soft/qchem/3.2_parallel/samples/DFT_glutamine.in .

qchem -pbs -np $NN $PBS_O_WORKDIR/DFT_glutamine.in \

$PBS_O_WORKDIR/output.out 
Software Interactive/GUI: 
No

Haploview

Software Description: 

Haploview is a graphical program for haplotype analysis. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. It supports the following functionalities: LD haplotype block analysis- haplotype population frequency estimation- single SNP and haplotype association tests- permutation testing for association significance- implementation of Paul de Bakker's Tagger tag SNP selection algorithm- automatic download of phased genotype data from HapMap visualization and plotting of PLINK whole genome association results including advanced filtering options.

Software Support Level: 
Secondary Support
Software Access Level: 
Open Access
Software Categories: 
Software Interactive/GUI: 
No
General Linux Documentation: 

Haploview requires a large amount of memory so it is recommended that you request more memory through the isub command line:

isub -m 6gb
module load haploview
haploview

To run haploview with more memory (in megabytes) use the -memory option:

haploview -memory 2000

Haploview may report out-of-memory errors when working with large datasets on cl or blr nodes. Try logging out and reconnecting using isub until you are connected to a lab node, where Haploview runs without a problem.

For additional information

 

AMDIS NIST

Software Description: 

The Automated Mass Spectral Deconvolution and Identification System (AMDIS) is a computer program that extracts spectra for individual components in a GC/MS data file and identifies target compounds by matching these spectra against a reference library. It was developed at NIST with support from the United States Department of Defense and is freely available

Software Support Level: 
Secondary Support
Citrix Documentation: 

To run this software under Windows, connect using instruction provided in our Windows systems page. Once logged in, navigate to

Start > All Programs > AMDIS.

Software Access Level: 
Open Access
Software Categories: 
Software Interactive/GUI: 
No

NX Downloads

The NX clients available for download on this page are known to be compatible with the NX server running at MSI. Choose the installation file appropriate to your computer from the selections below: Windows NoMachine Enterprise Client for Windows Mac NoMachine Enterprise Client for Mac Linux 64-bit...

HyPhy

Software Description: 

HyPhy stands for hypothesis testing using phylogenies. It is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It also features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface) and it can be compiled as a shared library and called from other programming environments such as Python or R.

Software Support Level: 
Primary Support
Itasca Documentation: 

To launch this software interactively in a Linux environment run the commands:

module load hyphy
HYPHYMPI

It requires a batch file to run the job.  For more detailed instruction on the program, please refer to:

http://hyphy.org/w/index.php/Main_Page

Software Access Level: 
Open Access
Software Categories: 
Lab Documentation: 

To launch this software interactively in a Linux environment run the commands:

module load hyphy
HYPHYMPI

It requires a batch file to run the job.  For more detailed instruction on the program, please refer to:

http://hyphy.org/w/index.php/Main_Page

Software Interactive/GUI: 
No

antiSMASH

Software Description: 

antiSMASH - antibiotics & Secondary Metabolite Analysis SHell

From the web site:

The secondary metabolism of bacteria and fungi constitutes a rich source of bioactive compounds of potential pharmaceutical value, comprising biosynthetic pathways of many chemicals that have been and are being utilized as e.g. antibiotics, cholesterol-lowering drugs or antitumor drugs.
Interestingly, the genes encoding the biosynthetic pathway responsible for the production of such a secondary metabolite are very often spatially clustered together at a certain position on the chromosome; such a compendium of genes is referred to as a 'secondary metabolite biosynthesis gene cluster'.
This genetic architecture has opened up the possibility for straightforward detection of secondary metabolite biosynthesis pathways by locating their gene clusters. In recent years, the costs of sequencing bacterial and fungi has dropped dramatically, and many genome sequences have become available. Based on profile hidden Markov models of genes that are specific for certain types of gene clusters, antiSMASH is able to accurately identify the gene clusters encoding secondary metabolites of all known broad chemical classes.
antiSMASH not only detects the gene clusters, but also offers detailed sequence analysis.
Software Support Level: 
Secondary Support
Software Interactive/GUI: 
No
General Linux Documentation: 

The antiSMASH application cannot be run as a loaded module. It must be installed and run from local user space.

An antiSMASH install script is available on the MSI Lab cluster, Itasca and Mesabi.

Steps for a local installation:

1) Login to MSI Lab cluster, Itasca orMesabi.

2) Create an install directory within your local directory (for instance /home/YOUR_GROUP/YOUR_USER_NAME/antiSMASH)

3) CD to the directory created in step 2 and run the following command:

>/home/support/public/antiSMASH/msi_antismash_install.sh 

This command will load modules, download and untar code, download and prepare needed databases all within the directory created in step 2. The install will take a few minutes.

4) To run, put the 'run_antismash_wrapper' script into your path.

Do not call run_antismash.py directly. Use the wrapper since it invokes the virtaul environment.

4) The command

./run_antismash_wrapper.sh -help

will provide a list of available antiSMASH commands.

Help documentation is available from the antiSMASH web site.

MaxQuant

Software Description: 

MaxQuant is a quantitative proteomics software package designed for analyzing large-scale mass-spectrometric data sets.

Software Support Level: 
Secondary Support
Citrix Documentation: 

To run this software under Windows, connect using instructions provided in our Windows systems page.  Once logged in, navigate to

Start > All Programs > MaxQuant<VERSION> > MaxQuant
Software Access Level: 
Open Access
Software Categories: 
Software Interactive/GUI: 
No
General Linux Documentation: 

Currently MQ in Linux works only from the command line; the GUI is not currently working.  Mono is required in order to run it.  The process for running on Linux is as follows:

 

1. Download a version of MaxQuant that is compatible with Linux (>= v1.6.1.0) and copy it to your MSI home directory.
2.  In Windows, set up your MaxQuant jobs and parameters completely. Specify your input (raw) files, your search database, PTMs, thread count, etc.  Do everything except hit run.
3.  In Windows, go to File -> Save Parameters.  Specify a file name and location for the xml file.  If you're running it on Citrix make sure to save it to your own directory (rather than a volume local to Citrix) so you can easily pull it up on Mesabi or Itasca.
4.  In Linux, edit the parameters file to denote the file locations for your search database and raw files.  You may want to then save it under a different name.
5.  In Linux, use the command "module load mono" to load mono
6.  In Linux, use the command "mono MaxQuantCmd.exe my_mq_params.xml" where "my_mq_params.xml" is the file edited in 3.  You'll likely need to specify the full path for "MaxQauntCmd.exe" as well; it is in your MaxQuant directory under "MaxQuant/bin"
 
A couple notes:
1.  The version you use to create the xml configuration file in Windows must *exactly* match the version you are running in Linux.  Configuration files that correspond to mismatched MQ versions will cause MQ to crash in most cases.
2.  In most cases the jobs will need to be submitted to a job queue
 
The official documentation can be found here.
 

ALLPATHS-LG

Software Description: 

ALLPATHS-LG is a whole-genome shotgun assembler that can generate high-quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers. The significant difference between ALLPATHS and traditional assemblers such as Arachne is that ALLPATHS assemblies are not necessarily linear, but instead are presented in the form of a graph. This graph representation retains ambiguities, such as those arising from polymorphism, uncorrected read errors, and unresolved repeats, thereby providing information that has been absent from previous genome assemblies.

Software Support Level: 
Secondary Support
Software Access Level: 
Open Access
PBS Example: 

An example PBS script for submitting ALLPATHS-LG jobs to the queue is shown below.

#PBS -l nodes=1:ppn=8,mem=1gb,walltime=4:00:00
#PBS -m abe
module load allpaths-lg

# Prepare input data
mkdir -p test.genome/data
PrepareAllPathsInput.pl \
DATA_DIR=$PWD/test.genome/data

# Assemble data
RunAllPathsLG \
PRE=$PWD \
DATA_SUBDIR=data \
RUN=run \
REFERENCE_NAME=test.genome
Software Categories: 
Software Interactive/GUI: 
No
General Linux Documentation: 

To run this software interactively in a Linux environment run the commands:

module load allpathslg
PrepareAllPathsInputs.pl DATA_DIR=/path/to/data
RunAllPathsLG PRE=<pre> DATA_SUBDIR=<data> RUN=<ref> REFERENCE_NAME=<ref>

Note:

  • The PrepareAllPathsInputs.pl script requires one parameter, the path to the directory containing the input data.<pre> is the root directory ALLPATHS-LG will use. <data> is the subdirectory containing the input data. <run> is the directory used for assembly pre-processing. <ref> is the organism or reference genome name.

  • ALLPATHS-LG is composed of a number of modules, each of which performs a step in the assembly process.  While each module can be run individually, ALLPATHS-LG provides a module that controls the entire assembly pipeline, called RunAllPathsLG.  In addition, before ALLPATHS-LG can be used, data must be converted using the Perl script PrepareAllPathsInputs.pl.

  • AllPathsLG assembler has specific requirement for the paired-end read libraries.  It requires the paired read to be actually interwinded. 

A more detailed discussion of each of these directories, as well as a list of other command-line arguments, is avaible in the user manual.  Other ALLPATHS-LG utilities may be found in the directory

/soft/allpathslg/VER/bin

where VER is the version of ALLPATHS-LG you are using.

An example PBS script for submitting ALLPATHS-LG jobs to the queue is shown below.

#PBS -l nodes=1:ppn=8,mem=1gb,walltime=4:00:00
#PBS -m abe
module load allpaths-lg

# Prepare input data
mkdir -p test.genome/data
PrepareAllPathsInput.pl \
DATA_DIR=$PWD/test.genome/data

# Assemble data
RunAllPathsLG \
PRE=$PWD \
DATA_SUBDIR=data \
RUN=run \
REFERENCE_NAME=test.genome

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