IGM IT

JAGS 3.4.0,  Just Another Gibbs Sampler.  It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation  not wholly unlike BUGS.

http://mcmc-jags.sourceforge.net/

---------------------------------------------------------------------------------

FASTX-Toolkit 0.0.13 has been added to the cluster (24/02/2014)

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
http://hannonlab.cshl.edu/fastx_toolkit/
-------------------------------------------------------------------

$ module load apps/fastx

apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

| — libs/gcc/system … SKIPPED (already loaded)

OK

$ ls $FASTXDIR

bin  share

ls $FASTXBIN

fasta_clipping_histogram.pl     fastx_barcode_splitter.pl

fasta_formatter                 fastx_clipper

fasta_nucleotide_changer        fastx_collapser

fastq_masker                    fastx_nucleotide_distribution_graph.sh

fastq_quality_boxplot_graph.sh  fastx_nucleotide_distribution_line_graph.sh

fastq_quality_converter         fastx_quality_stats

fastq_quality_filter            fastx_renamer

fastq_quality_trimmer           fastx_reverse_complement

fastq_to_fasta                  fastx_trimmer

fastx_artifacts_filter          fastx_uncollapser

——————————————————————-

$ module whatis apps/fastx

apps/fastx :
Title: fastx

Summary: A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing

License: AGPLv3+

Group: Bioinformatics

URL: http://hannonlab.cshl.edu/fastx_toolkit/

Name: fastx

Version: 0.0.13

Module: apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

Module path: /opt/gridware/etc/modules/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

Package path: /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

Repository: git+http://download.alces-software.com/git/packager-base@0d67d87

Package: apps/fastx/0.0.13@3f151052

Last update: 2012-09-09

Builder: root@headnode1.lampredi.cluster.local

Build date: 2014-02-24T10:41:52

Build modules: libs/gtextutils/0.6/gcc-4.4.6

Compiler: compilers/gcc/system

System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64

Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)

Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

——————————————————————-

$ module help apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

———– Module Specific Help for ‘apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6’ —————————

======== fastx ========

A collection of command line tools for Short-Reads

FASTA/FASTQ files preprocessing

======================

This module sets up your environment for the use of the ‘fastx’

application. This module sets up version ‘0.0.13’ of the

application.

>> SYNOPSIS <<

The FASTX-Toolkit is a collection of command line tools for

Short-Reads FASTA/FASTQ files preprocessing.

Next-Generation sequencing machines usually produce FASTA or FASTQ

files, containing multiple short-reads sequences (possibly with

quality information).

The main processing of such FASTA/FASTQ files is mapping (aka

aligning) the sequences to reference genomes or other databases

using specialized programs. Example of such mapping programs are:

Blat, SHRiMP, LastZ, MAQ and many many others.

However, it is sometimes more productive to preprocess the

FASTA/FASTQ files before mapping the sequences to the genome –

manipulating the sequences to produce better mapping results. The

FASTX-Toolkit tools perform some of these preprocessing tasks.

>> LICENSING <<

This package is made available subject to the following license(s):

AGPLv3+

Please refer to the website for further details regarding licensing.

>> FURTHER INFORMATION <<

More information about this software can be found at the website:

http://hannonlab.cshl.edu/fastx_toolkit/

For further details regarding this module, including the environment

modifications it will apply, execute:

module show apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

>> GET STARTED <<

Please refer to the website for further details on usage of this

package.

——————————————————————-

$ module show apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

/opt/gridware/etc/modules/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6:

module-whatis

Title: fastx

Summary: A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing

License: AGPLv3+

Group: Bioinformatics

URL: http://hannonlab.cshl.edu/fastx_toolkit/

Name: fastx

Version: 0.0.13

Module: apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

Module path: /opt/gridware/etc/modules/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

Package path: /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

Repository: git+http://download.alces-software.com/git/packager-base@0d67d87

Package: apps/fastx/0.0.13@3f151052

Last update: 2012-09-09

Builder: root@headnode1.lampredi.cluster.local

Build date: 2014-02-24T10:41:52

Build modules: libs/gtextutils/0.6/gcc-4.4.6

Compiler: compilers/gcc/system

System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64

Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)

Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

module-prereq libs/gcc/system

module-conflict apps/fastx

setenv FASTXDIR /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6

setenv FASTXBIN /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6/bin

setenv FASTXLIB /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6/lib

prepend-path GDFONTPATH /usr/share/fonts/dejavu

setenv GNUPLOT_DEFAULT_GDFONT DejaVuSans

prepend-path PATH /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6/bin

prepend-path LD_LIBRARY_PATH /opt/gridware/pkg/apps/fastx/0.0.13/gcc-4.4.6+gtextutils-0.6/lib

——————————————————————-

Lampredi HPC
igm-lampredi-users@ncl.ac.uk

IGM IT
igmithelp@ncl.ac.uk
x8625

LoFreq 0.6.1 was added to the cluster (05/12/2013)

A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.

http://sourceforge.net/p/lofreq/wiki/Home/

——————————————————————-

$ module load apps/lofreq
apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
| — libs/gcc/system
| * –> OK
| — apps/python/2.7.3/gcc-4.4.6
| | — libs/gcc/system … SKIPPED (already loaded)
| * –> OK
|
OK

$ ls $LOFREQDIR
bin python

$ ls $LOFREQBIN
base_qual_calib_wrapper.sh lofreq_bonf.py lofreq_pileup_summary.py lofreq_snpcaller.py lofreq_varpos_to_vcf.py
bwa_unique.sh lofreq_diff.py lofreq_regionbed.py lofreq_uniq_pipeline.py lofreq_version.py
lofreq_alnoffset.py lofreq_filter.py lofreq_samtools lofreq_uniq.py

——————————————————————-

$ module whatis apps/lofreq
apps/lofreq :

Title: LoFreq
Summary: fast and sensitive variant-caller for inferring SNVs from high-throughput sequencing data
License: BSD License
Group: Bioinformatics
URL: http://sourceforge.net/p/lofreq/wiki/Home/

Name: lofreq
Version: 0.6.1
Module: apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
Module path: /opt/gridware/etc/modules/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
Package path: /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

Repository: git+http://download.alces-software.com/git/packager-base@85035c8
Package: apps/lofreq/0.6.1@18d95c51
Last update: 2013-12-05

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-12-05T16:00:29
Build modules: apps/python/2.7.3/gcc-4.4.6
Compiler: compilers/gcc/system
System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)
apps/python/2.7.3/gcc-4.4.6 (using: apps/python/2.7.3/gcc-4.4.6)

For further information, execute:

module help apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

——————————————————————-

$ module help apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

———– Module Specific Help for ‘apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3’ —————————

======== LoFreq ========
fast and sensitive variant-caller for inferring SNVs from
high-throughput sequencing data
=======================

This module sets up your environment for the use of the ‘lofreq’
application. This module sets up version ‘0.6.1’ of the
application.

>> SYNOPSIS << LoFreq is a fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data. It is designed to robustly call low-frequency variants by exploiting base-call quality values. LoFreq has been used to call rare variants in viral and bacterial sequencing datasets and can be used to study mitochondrial heteroplasmy and rare somatic mutations in heterogeneous tumors. LoFreq makes full use of base-call qualities (and versions >=0.5
also use read mapping qualities) which are usually ignored by other
methods or only used for filtering. It is very sensitive; most
notably, it is able to predict variants below the average base-call
quality (i.e. sequencing error rate). Each SNV call is assigned a
p-value which allows for rigorous false positive control. Even
though it uses no approximations or heuristics, it is very efficient
due to several runtime optimizations. LoFreq is generic and fast
enough to be applied to high-coverage data and large genomes. It
takes a minute to analyze Dengue genome sequencing data with nearly
4000X coverage, roughly one hour to call SNVs on a 600X coverage
E.coli genome and 1.5 hours to run on a 100X coverage human exome
dataset.

>> LICENSING << This package is made available subject to the following license(s): BSD License Please refer to the website for further details regarding licensing. >> FURTHER INFORMATION << More information about this software can be found at the website: http://sourceforge.net/p/lofreq/wiki/Home/ For further details regarding this module, including the environment modifications it will apply, execute: module show apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3 >> GET STARTED <<

Please refer to the website for further details on usage of this
package.

——————————————————————-

$ module show apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
——————————————————————-
/opt/gridware/etc/modules/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3:

module-whatis

Title: LoFreq
Summary: fast and sensitive variant-caller for inferring SNVs from high-throughput sequencing data
License: BSD License
Group: Bioinformatics
URL: http://sourceforge.net/p/lofreq/wiki/Home/

Name: lofreq
Version: 0.6.1
Module: apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
Module path: /opt/gridware/etc/modules/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
Package path: /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

Repository: git+http://download.alces-software.com/git/packager-base@85035c8
Package: apps/lofreq/0.6.1@18d95c51
Last update: 2013-12-05

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-12-05T16:00:29
Build modules: apps/python/2.7.3/gcc-4.4.6
Compiler: compilers/gcc/system
System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)
apps/python/2.7.3/gcc-4.4.6 (using: apps/python/2.7.3/gcc-4.4.6)

For further information, execute:

module help apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

module-prereq libs/gcc/system
module-prereq apps/python/2.7.3/gcc-4.4.6
module-conflict apps/lofreq
setenv LOFREQDIR /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
setenv LOFREQBIN /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3/bin
setenv LOFREQPYTHON /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3/python
prepend-path PATH /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3/bin
prepend-path PYTHONPATH /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3/python/lib/python2.7/site-packages

——————————————————————-

Lampredi HPC
igm-lampredi-users@ncl.ac.uk

IGM IT
igmithelp@ncl.ac.uk
x8625