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New Module Search Tools

The RC/Informatics portal now has a new application for searching modules in the new module system.

https://portal.rc.fas.harvard.edu/apps/modules

This search tool includes all of the modules in the new module system, and provides key information, including application descriptions, how to load the module, and in many cases, build notes that help describe the difference between various builds.

A command line tool has also been deployed, module-query, that provides an output similar to the "module spider" command, but that uses the RC/Informatics portal database. In this case, however, module load statements that have been missing from module spider are available. This command line tool will eventually replace the module spider command.

[akitzmiller@sa01 ~]$ module-query hdf5/1.8.12-fasrc07

---------------------------------------------------------------------------------------
hdf5 : hdf5/1.8.12-fasrc07
---------------------------------------------------------------------------------------
Description:
HDF5 is a data model, library, and file format for storing and
managing data. It supports an unlimited variety of datatypes, and is
designed for flexible and efficient I/O and for high volume and
complex data. HDF5 is portable and is extensible, allowing
applications to evolve in their use of HDF5. The HDF5 Technology
suite includes tools and applications for managing, manipulating,
viewing, and analyzing data in the HDF5 format. HDF5 is used as a
basis for many other file formats, including NetCDF.

Build comments:
Using zlib fasrc05 so that it works with PGI

This module an be loaded as follows:
module load gcc/4.8.2-fasrc01 openmpi/1.8.7-fasrc01 hdf5/1.8.12-fasrc07
module load gcc/4.8.2-fasrc01 openmpi/1.10.0-fasrc01 hdf5/1.8.12-fasrc07
module load gcc/4.8.2-fasrc01 openmpi/1.8.3-fasrc02 hdf5/1.8.12-fasrc07
module load intel/15.0.0-fasrc01 openmpi/1.8.7-fasrc01 hdf5/1.8.12-fasrc07
module load intel/15.0.0-fasrc01 openmpi/1.10.0-fasrc01 hdf5/1.8.12-fasrc07
module load intel/15.0.0-fasrc01 openmpi/1.8.3-fasrc02 hdf5/1.8.12-fasrc07
module load pgi/14.10-fasrc01 openmpi/1.8.7-fasrc01 hdf5/1.8.12-fasrc07
module load pgi/14.10-fasrc01 openmpi/1.10.0-fasrc01 hdf5/1.8.12-fasrc07

This module also loads:
zlib/1.2.8-fasrc05 szip/2.1-fasrc01

This command line tool also supports full text search using the --full-text switch.

[akitzmiller@sa01 ~]$ module-query --full-text Bayesian

------------------------------------------------------------------------------------
rdp_classifier
------------------------------------------------------------------------------------
Description:
The RDP Classifier is a naive Bayesian classifier that can rapidly
and accurately provides taxonomic assignments from domain to
genus, with confidence estimates for each assignment. More
information can be found at http://rdp.cme.msu.edu/. (This package
installed by Bob Freeman, PhD)

Versions:
rdp_classifier/2.10.1-fasrc01

To find detailed information about a module, enter the full name.
For example,

module-query rdp_classifier/2.10.1-fasrc01

------------------------------------------------------------------------------------
BEAST
------------------------------------------------------------------------------------
Description:
BEAST 2 is a cross-platform program for Bayesian MCMC analysis of
molecular sequences. It is entirely orientated towards rooted,
time-measured phylogenies inferred using strict or relaxed
molecular clock models. It can be used as a method of
reconstructing phylogenies but is also a framework for testing
evolutionary hypotheses without conditioning on a single tree
topology. BEAST 2 uses MCMC to average over tree space, so that
each tree is weighted proportional to its posterior probability.
BEAST 2 includes a graphical user-interface for setting up
standard analyses and a suit of programs for analysing the
results.

Versions:
BEAST/2.2.1-fasrc03
BEAST/2.2.1-fasrc02
BEAST/2.2.1-fasrc01
BEAST/2.1.3-fasrc01
BEAST/1.8.2-fasrc02
BEAST/1.8.2-fasrc01

To find detailed information about a module, enter the full name.
For example,

module-query BEAST/1.8.2-fasrc01

------------------------------------------------------------------------------------
diyabc
------------------------------------------------------------------------------------
Description:
DIYABC is a software package for a comprehensive analysis of
population history using approximate Bayesian computation on DNA
polymorphism data. Version 2.0 implements a number of new features
and analytical methods. It allows (i) the analysis of single
nucleotide polymorphism data at large number of loci, apart from
microsatellite and DNA sequence data, (ii) efficient Bayesian
model choice using linear discriminant analysis on summary
statistics and (iii) the serial launching of multiple post-
processing analyses. DIYABC v2.0 also includes a user-friendly
graphical interface with various new options.

Versions:
diyabc/2.0.4-fasrc01

To find detailed information about a module, enter the full name.
For example,

module-query diyabc/2.0.4-fasrc01

------------------------------------------------------------------------------------
iBPP
------------------------------------------------------------------------------------
Description:
Bayesian species delimitation, integrating genes and traits.

Versions:
iBPP/2.1.2-fasrc01

To find detailed information about a module, enter the full name.
For example,

module-query iBPP/2.1.2-fasrc01

------------------------------------------------------------------------------------
relion
------------------------------------------------------------------------------------
Description:
RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-
on) is a stand-alone computer program that employs an empirical
Bayesian approach to refinement of (multiple) 3D reconstructions
or 2D class averages in electron cryo-microscopy (cryo-EM). It is
developed in the group of Sjors Scheres at the MRC Laboratory of
Molecular Biology.

Versions:
relion/1.3-fasrc02
relion/1.3-fasrc01

To find detailed information about a module, enter the full name.
For example,

module-query relion/1.3-fasrc01

------------------------------------------------------------------------------------
beagle
------------------------------------------------------------------------------------
Description:
BEAGLE is a high-performance library that can perform the core
calculations at the heart of most Bayesian and Maximum Likelihood
phylogenetics packages. It can make use of highly-parallel
processors such as those in graphics cards (GPUs) found in many
PCs. The aim is to provide high performance evaluation 'services'
to a wide range of phylogenetic software, both Bayesian samplers
and Maximum Likelihood optimizers. This allows these packages to
make use of implementations that make use of optimized hardware
such as graphics processing units.

Versions:
beagle/2.1.trunk-fasrc03
beagle/2.1.trunk-fasrc02
beagle/2.1.trunk-fasrc01

To find detailed information about a module, enter the full name.
For example,

module-query beagle/2.1.trunk-fasrc01

------------------------------------------------------------------------------------
scythe
------------------------------------------------------------------------------------
Description:
Scythe uses a Naive Bayesian approach to classify contaminant
substrings in sequence reads. It considers quality information,
which can make it robust in picking out 3'-end adapters, which
often include poor quality bases.

Versions:
scythe/20150129-fasrc01

To find detailed information about a module, enter the full name.
For example,

module-query scythe/20150129-fasrc01

------------------------------------------------------------------------------------
phylobayes
------------------------------------------------------------------------------------
Description:
A Bayesian software for phylogenetic reconstruction using mixture
models.

Versions:
phylobayes/4.1b-fasrc01

To find detailed information about a module, enter the full name.
For example,

module-query phylobayes/4.1b-fasrc01

------------------------------------------------------------------------------------
BayesPhylogenies
------------------------------------------------------------------------------------
Description:
BayesPhylogenies is a general package for inferring phylogenetic
trees using Bayesian Markov Chain Monte Carlo (MCMC) or
Metropolis-coupled Markov chain Monte Carlo (MCMCMC) methods. The
program allows a range of models of gene sequence evolution,
models for morphological traits, models for rooted trees, gamma
and beta distributed rate-heterogeneity, and implements a 'mixture
model' (Pagel and Meade, 2004) that allows the user to fit more
than one model of sequence evolution, without partitioning the
data.

Versions:
BayesPhylogenies/2.0.2-fasrc02
BayesPhylogenies/2.0.2-fasrc01

To find detailed information about a module, enter the full name.
For example,

module-query BayesPhylogenies/2.0.2-fasrc01

------------------------------------------------------------------------------------
pb_mpi
------------------------------------------------------------------------------------
Description:
A Bayesian software for phylogenetic reconstruction using mixture
models

Versions:
pb_mpi/1.5a-fasrc02
pb_mpi/1.5a-fasrc01

To find detailed information about a module, enter the full name.
For example,

module-query pb_mpi/1.5a-fasrc01

------------------------------------------------------------------------------------
freebayes
------------------------------------------------------------------------------------
Description:
FreeBayes is a Bayesian genetic variant detector designed to find
small polymorphisms, specifically SNPs (single-nucleotide
polymorphisms), indels (insertions and deletions), MNPs (multi-
nucleotide polymorphisms), and complex events (composite insertion
and substitution events) smaller than the length of a short-read
sequencing alignment. FreeBayes is haplotype-based, in the sense
that it calls variants based on the literal sequences of reads
aligned to a particular target, not their precise alignment. This
model is a straightforward generalization of previous ones (e.g.
PolyBayes, samtools, GATK) which detect or report variants based
on alignments. This method avoids one of the core problems with
alignment-based variant detection--- that identical sequences may
have multiple possible alignments

Versions:
freebayes/2015Feb18-fasrc01

To find detailed information about a module, enter the full name.
For example,

module-query freebayes/2015Feb18-fasrc01

Last updated: April 21, 2016 at 11:18 am

CC BY-NC 4.0 This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. Permissions beyond the scope of this license may be available at Attribution.