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HPC – Lampredi – software update – FASTX-Toolkit 0.0.13

 Uncategorized  No Responses »
Feb 242014
 

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

HPC – Lampredi – software update – FASTQC 0.10.1

 Uncategorized  No Responses »
Feb 242014
 

FASTQC 0.10.1, a quality control tool for high throughput sequence data, has been added to the cluster (24/02/2014)

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

The main functions of FastQC are

  • Import of data from BAM, SAM or FastQ files (any variant)
  • Providing a quick overview to tell you in which areas there may be problems
  • Summary graphs and tables to quickly assess your data
  • Export of results to an HTML based permanent report
  • Offline operation to allow automated generation of reports without running the interactive application

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

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

$ module load apps/fastqc

apps/fastqc/0.10.1/noarch

|

OK

$ ls $FASTQCDIR

app  bin  doc

$ fastqc –version

FastQC v0.10.1

———————————————————————————

$ module whatis apps/fastqc

apps/fastqc          :

 

Title: FastQC

Summary: A quality control tool for high throughput sequence data

License: GPLv3+

Group: Bioinformatics

URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

 

Name: fastqc

Version: 0.10.1

Module: apps/fastqc/0.10.1/noarch

Module path: /opt/gridware/etc/modules/apps/fastqc/0.10.1/noarch

Package path: /opt/gridware/pkg/apps/fastqc/0.10.1/noarch

 

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

Package: apps/fastqc/0.10.1@0380e731

Last update: 2012-10-31

 

Builder: root@headnode1.lampredi.cluster.local

Build date: 2014-02-24T10:41:03

Compiler: N/A

 

For further information, execute:

module help apps/fastqc/0.10.1/noarch

 

———————————————————————————

$ module help apps/fastqc/0.10.1/noarch

 

———– Module Specific Help for ‘apps/fastqc/0.10.1/noarch’ —————————

 

 

======== FastQC ========

A quality control tool for high throughput sequence data

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

 

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

application. This module sets up version ‘0.10.1’ of the

application.

 

 

>> SYNOPSIS <<

 

FastQC aims to provide a simple way to do some quality control

checks on raw sequence data coming from high throughput sequencing

pipelines. It provides a modular set of analyses which you can use

to give a quick impression of whether your data has any problems of

which you should be aware before doing any further analysis.

 

The main functions of FastQC are:

 

* Import of data from BAM, SAM or FastQ files (any variant)

* Providing a quick overview to tell you in which areas there may

be problems

* Summary graphs and tables to quickly assess your data

* Export of results to an HTML based permanent report

* Offline operation to allow automated generation of reports

without running the interactive application

 

 

>> LICENSING <<

 

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

 

GPLv3+

 

Please refer to the website for further details regarding licensing.

 

 

>> FURTHER INFORMATION <<

 

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

 

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

 

For further details regarding this module, including the environment

modifications it will apply, execute:

 

module show apps/fastqc/0.10.1/noarch

 

 

>> GET STARTED <<

 

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

package.

———————————————————————————

$ module show apps/fastqc/0.10.1/noarch

 

/opt/gridware/etc/modules/apps/fastqc/0.10.1/noarch:

 

module-whatis

 

Title: FastQC

Summary: A quality control tool for high throughput sequence data

License: GPLv3+

Group: Bioinformatics

URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

 

Name: fastqc

Version: 0.10.1

Module: apps/fastqc/0.10.1/noarch

Module path: /opt/gridware/etc/modules/apps/fastqc/0.10.1/noarch

Package path: /opt/gridware/pkg/apps/fastqc/0.10.1/noarch

 

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

Package: apps/fastqc/0.10.1@0380e731

Last update: 2012-10-31

 

Builder: root@headnode1.lampredi.cluster.local

Build date: 2014-02-24T10:41:03

Compiler: N/A

 

 

For further information, execute:

 

module help apps/fastqc/0.10.1/noarch

 

module-conflict apps/fastqc

setenv FASTQCDIR /opt/gridware/pkg/apps/fastqc/0.10.1/noarch

setenv FASTQCBIN /opt/gridware/pkg/apps/fastqc/0.10.1/noarch/bin

setenv FASTQCAPP /opt/gridware/pkg/apps/fastqc/0.10.1/noarch/app

setenv FASTQCDOC /opt/gridware/pkg/apps/fastqc/0.10.1/noarch/doc

prepend-path PATH /opt/gridware/pkg/apps/fastqc/0.10.1/noarch/bin

———————————————————————————

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

IGM IT
igmithelp@ncl.ac.uk
x8625

HPC – Lampredi – software update – LoFreq 0.6.1

 Uncategorized  No Responses »
Feb 242014
 

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

RAS and My Drives feature

 Uncategorized  No Responses »
Dec 122013
 

The My Drives feature found on ras.ncl.ac.uk allows you to access your H: drive and research folder(s), more commonly known within the IGM as the Z: drive.

Please note:

* On your personal/home computer, you will need to install some software first before you can use RAS. It is available from the welcome page at http://ras.ncl.ac.uk/

* RAS/My Drives will automatically display your H: drive. However, it does not yet know about your Z: drive or any other drives that you may use e.g. Flow Cytometry S: and R: drives. You need to add these drives yourself. Hence these instructions!

Please visit http://ras.ncl.ac.uk and install the RAS client software. There are links to this from the welcome page. Windows and Mac clients are available.

When ready, log into RAS using your ISS login and password, via http://ras.ncl.ac.uk

Click on the My Drives icon and wait. Be patient!

Eventually a window will appear, displaying your drives. Your H: drive is represented by something called “Documents” (found in the Network Location section). The drives found in “Other” usually represent the drives that belong to the computer you are using. You may have a number of “Other” drives, depending on what is attached to your computer.

To Add your Z: drive:

Click on “Map Network Drive” button
Change the Drive: letter to Z
In the Folder: box carefully type: \\campus.ncl.ac.uk\igm
Tick the “Reconnect at logon” option
Click the Finish button

There is an issue whereby the window does not update immediately – it can appear as if nothing has happened! Simply right-click on some white space and choose “refresh” from the menu.

You will now see your new drive, which should be labelled as “igm (\\campus.ncl.ac.uk)”. This Z: drive contains both the IGM shared area and all the various research folders for the Institute.

Important! RAS does not provide a drag and drop environment, so while it may appear similar to Microsoft Windows, it is NOT Microsoft Windows! However, you can copy and paste files/folders between your University drives and the drives that you have on your local computer.

In most cases, double-clicking on a file will bring up the appropriate the program in RAS. For example, if you clicked on a PDF file within RAS, it would launch the RAS hosted version of Adobe Acrobat Reader. When it comes across a file that it does not understand then it will prompt you about it. In some cases, you really are not going to get RAS to open that “unknown” file. You can use the copy/paste technique above to copy the file and use it on another computer.

The drives that appear under “Other” are the drives that RAS identifies as belonging to your local computer. You can browse through any of these drives. You then right-click on a file/folder that you want to copy,
choose “copy” from the menu. You then browse the drive that you want to save the file/folder to, right-click and choose “paste”. That is how you copy items to/from your University/local drives.

 Posted by at 10:35 am  Tagged with:

HPC – Lampredi – software update – FreeBayes 0.9.9.2.20131031

 Uncategorized  No Responses »
Oct 312013
 

FreeBayes 0.9.9.2.20131031 has been added to the cluster (31/10/2013)

This is a Bayesian genetic variant detector designed to find small polymorphisms.

——————————————————————-

$ module load apps/freebayes
apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
| -- libs/gcc/system ... SKIPPED (already loaded)
|
OK

ls $FREEBAYESDIR
bin doc share

$ ls $FREEBAYESDIR/*
/opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0/bin:
bamleftalign freebayes

/opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0/doc:
LICENSE README

/opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0/share:
examples python scripts

$ freebayes
usage: freebayes -f [REFERENCE] [OPTIONS] [BAM FILES] >[OUTPUT]

[snip]

parameters:

-h --help Complete description of options.

author: Erik Garrison , Marth Lab, Boston College, 2010-2012
version: v0.9.9.2

——————————————————————-

$ module whatis apps/freebayes
apps/freebayes :

Title: FreeBayes
Summary: Bayesian genetic variant detector designed to find small polymorphisms
License: MIT
Group: Bioinformatics
URL: https://github.com/ekg/freebayes

Name: freebayes
Version: 0.9.9.2.20131031
Module: apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
Module path: /opt/gridware/etc/modules/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
Package path: /opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0

Repository: git+http://download.alces-software.com/git/packager-base@8cca844
Package: apps/freebayes/0.9.9.2.20131031@7e80c4a4
Last update: 2013-10-31

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-31T12:41:20
Build modules: apps/bamtools/2.3.0/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, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0

——————————————————————-

$ module help apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0

----------- Module Specific Help for 'apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0' ---------------------------

======== FreeBayes ========
Bayesian genetic variant detector designed to find small
polymorphisms
==========================

This module sets up your environment for the use of the 'freebayes'
application. This module sets up version '0.9.9.2.20131031' of the
application.

>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<

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

——————————————————————-

$ module show apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0:

module-whatis

Title: FreeBayes
Summary: Bayesian genetic variant detector designed to find small polymorphisms
License: MIT
Group: Bioinformatics
URL: https://github.com/ekg/freebayes

Name: freebayes
Version: 0.9.9.2.20131031
Module: apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
Module path: /opt/gridware/etc/modules/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
Package path: /opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0

Repository: git+http://download.alces-software.com/git/packager-base@8cca844
Package: apps/freebayes/0.9.9.2.20131031@7e80c4a4
Last update: 2013-10-31

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-31T12:41:20
Build modules: apps/bamtools/2.3.0/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, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0

module-prereq libs/gcc/system
module-conflict apps/freebayes
setenv FREEBAYESDIR /opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0
setenv FREEBAYESBIN /opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0/bin
setenv FREEBAYESDOC /opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0/doc
prepend-path PATH /opt/gridware/pkg/apps/freebayes/0.9.9.2.20131031/gcc-4.4.6+bamtools-2.3.0/bin

——————————————————————-

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

IGM IT
igmithelp@ncl.ac.uk
x8625

 Posted by at 2:31 pm

HPC – Lampredi – software update – MuTect 1.1.4

 Uncategorized  No Responses »
Oct 312013
 

MuTect 1.1.4 has been added to the cluster (31/10/2013)

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

——————————————————————-
$ module load apps/mutect
apps/mutect/1.1.4/bin
|
OK

$ ls $MUTECTDIR
bin doc java

$ ls $MUTECTDIR/*
/opt/gridware/pkg/apps/mutect/1.1.4/bin/bin:
mutect muTect

/opt/gridware/pkg/apps/mutect/1.1.4/bin/doc:
LICENSE.TXT version.txt

/opt/gridware/pkg/apps/mutect/1.1.4/bin/java:
muTect.jar

$ mutect
---------------------------------------------------------------------------------
The Genome Analysis Toolkit (GATK) v2.2-25-g2a68eab, Compiled 2012/11/08 10:30:02
Copyright (c) 2010 The Broad Institute
For support and documentation go to http://www.broadinstitute.org/gatk
---------------------------------------------------------------------------------
---------------------------------------------------------------------------------
usage: java -jar muTect.jar -T [-args ] [-I ] [-rbs ] [-et
] [-K ] [-tag ] [-rf ] [-L ] [-XL ] [-isr
] [-im ] [-ip ] [-R ] [-ndrs]
[--disableRandomization] [-maxRuntime ] [-maxRuntimeUnits ] [-dt ]
[-dfrac ] [-dcov ] [-baq ] [-baqGOP ] [-PF
] [-OQ] [-BQSR ] [-DIQ] [-EOQ] [-preserveQ ] [-DBQ
] [-S ] [-rpr] [-kpr] [-U ] [-nt ] [-nct
] [-mte] [-bfh ] [-rgbl ] [-ped
] [-pedString ] [-pedValidationType ] [-l ] [-log
] [-h]

-T,--analysis_type Type of analysis to run

[snip]

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.2-25-g2a68eab):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Argument with name '--analysis_type' (-T) is missing.
##### ERROR ------------------------------------------------------------------------------------------

——————————————————————-

$ module whatis apps/mutect
apps/mutect :

Title: MuTect
Summary: Reliable and accurate identification of somatic point mutations
License: NONFREE - Free for academic non-commercial research purposes only; see http://j.mp/10q7Mmv
Group: Bioinformatics
URL: http://www.broadinstitute.org/cancer/cga/mutect

Name: mutect
Version: 1.1.4
Module: apps/mutect/1.1.4/bin
Module path: /opt/gridware/etc/modules/apps/mutect/1.1.4/bin
Package path: /opt/gridware/pkg/apps/mutect/1.1.4/bin

Repository: git+http://download.alces-software.com/git/packager-base@8cca844
Package: ext/mutect/@3956ddde
Last update: 2013-04-03

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-31T12:42:07
Build parameters: zipfile=/opt/gridware/ext/muTect-1.1.4-bin.zip
Compiler: N/A

For further information, execute:

module help apps/mutect/1.1.4/bin

——————————————————————-

$ module help apps/mutect/1.1.4/bin

----------- Module Specific Help for 'apps/mutect/1.1.4/bin' ---------------------------

======== MuTect ========
Reliable and accurate identification of somatic point
mutations
=======================

This module sets up your environment for the use of the 'mutect'
application. This module sets up version '1.1.4' of the
application.

>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<

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

——————————————————————-

$ module show apps/mutect/1.1.4/bin
-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/mutect/1.1.4/bin

module-whatis

Title: MuTect
Summary: Reliable and accurate identification of somatic point mutations
License: NONFREE - Free for academic non-commercial research purposes only; see http://j.mp/10q7Mmv
Group: Bioinformatics
URL: http://www.broadinstitute.org/cancer/cga/mutect

Name: mutect
Version: 1.1.4
Module: apps/mutect/1.1.4/bin
Module path: /opt/gridware/etc/modules/apps/mutect/1.1.4/bin
Package path: /opt/gridware/pkg/apps/mutect/1.1.4/bin

Repository: git+http://download.alces-software.com/git/packager-base@8cca844
Package: ext/mutect/@3956ddde
Last update: 2013-04-03

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-31T12:42:07
Build parameters: zipfile=/opt/gridware/ext/muTect-1.1.4-bin.zip
Compiler: N/A

For further information, execute:

module help apps/mutect/1.1.4/bin

module-conflict apps/mutect
setenv MUTECTDIR /opt/gridware/pkg/apps/mutect/1.1.4/bin
setenv MUTECTBIN /opt/gridware/pkg/apps/mutect/1.1.4/bin/bin
setenv MUTECTDOC /opt/gridware/pkg/apps/mutect/1.1.4/bin/doc
setenv MUTECTJAVA /opt/gridware/pkg/apps/mutect/1.1.4/bin/java
setenv MUTECT_JAVA_MEM_MX 2g
setenv MUTECT_JAVA_TMPDIR /tmp
setenv MUTECT_JAVA_OPTS -Xmx$MUTECT_JAVA_MEM_MX -Djava.io.tmpdir=$MUTECT_JAVA_TMPDIR
prepend-path PATH /opt/gridware/pkg/apps/mutect/1.1.4/bin/bin

——————————————————————-

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

IGM IT
igmithelp@ncl.ac.uk
x8625

HPC – Lampredi – software update – Strelka 1.0.12

 Uncategorized  No Responses »
Oct 312013
 

Strelka 1.0.12 has been added to the cluster (31/10/2013)

This is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.

——————————————————————-

$ module load apps/strelka
apps/strelka/1.0.12/gcc-4.4.6
| -- libs/gcc/system
| * --> OK
|
OK

$ ls $STRELKADIR/
bin etc lib libexec opt

$ ls $STRELKADIR/*
/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin:
configureStrelkaWorkflow.pl demo

/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/etc:
strelka_config_bwa_default.ini strelka_config_eland_default.ini strelka_config_isaac_default.ini

/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/lib:
Utils.pm

/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/libexec:
callSomaticVariants.pl consolidateResults.pl countFastaBases filterSomaticVariants.pl strelka2

/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/opt:
Makefile samtools-0.1.18_no_tview vcftools vcftools-r837.tar.gz
samtools samtools-0.1.18_no_tview.tar.bz2 vcftools-r837

$ $STRELKABIN/demo/run_demo.bash

**** Starting demo configuration.
**** Configuration cmd: '/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin/demo/../configureStrelkaWorkflow.pl --tumor=/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin/demo/data/NA12891_dupmark_chr20_region.bam --normal=/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin/demo/data/NA12892_dupmark_chr20_region.bam --ref=/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin/demo/data/chr20_860k_only.fa --config=/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin/demo/strelka_demo_config.ini --output-dir=./strelkaDemoAnalysis'

INFO: Scanning reference genome
INFO: Scanning reference genome complete

Successfully configured analysis and created makefile '/users/alces-cluster/strelkaDemoAnalysis/Makefile'.

To run the analysis locally using make, run:

make -C /users/alces-cluster/strelkaDemoAnalysis

...or:

cd /users/alces-cluster/strelkaDemoAnalysis
make

**** Completed demo configuration.

**** Starting demo workflow execution.
**** Workflow cmd: 'make -C ./strelkaDemoAnalysis'

make: Entering directory `/users/alces-cluster/strelkaDemoAnalysis'
/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/libexec/callSomaticVariants.pl --config=/users/alces-cluster/strelkaDemoAnalysis/config/run.config.ini --chrom=chr20 --bin=0001 && touch /users/alces-cluster/strelkaDemoAnalysis/chromosomes/chr20/bins/0001/task.complete
/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/libexec/callSomaticVariants.pl --config=/users/alces-cluster/strelkaDemoAnalysis/config/run.config.ini --chrom=chr20 --bin=0002 && touch /users/alces-cluster/strelkaDemoAnalysis/chromosomes/chr20/bins/0002/task.complete
/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/libexec/callSomaticVariants.pl --config=/users/alces-cluster/strelkaDemoAnalysis/config/run.config.ini --chrom=chr20 --bin=0000 && touch /users/alces-cluster/strelkaDemoAnalysis/chromosomes/chr20/bins/0000/task.complete
/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/libexec/filterSomaticVariants.pl --config=/users/alces-cluster/strelkaDemoAnalysis/config/run.config.ini --chrom=chr20 && touch /users/alces-cluster/strelkaDemoAnalysis/chromosomes/chr20/task.complete
/opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/libexec/consolidateResults.pl --config=/users/alces-cluster/strelkaDemoAnalysis/config/run.config.ini && touch /users/alces-cluster/strelkaDemoAnalysis/task.complete

Analysis complete. Final somatic calls can be found in /users/alces-cluster/strelkaDemoAnalysis/results

make: Leaving directory `/users/alces-cluster/strelkaDemoAnalysis'

**** Completed demo workflow execution.

**** Starting comparison to expected results.
**** Expected results dir: /opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin/demo/expected_results
**** Demo results dir: ./strelkaDemoAnalysis/results

**** No differences between expected and computed results.

**** Demo/verification successfully completed

——————————————————————-

$ module whatis apps/strelka
apps/strelka :

Title: Strelka
Summary: Somatic variant calling workflow for matched tumor-normal samples
License: NONFREE - Illumina Open Source Source License
Group: Bioinformatics
URL: https://sites.google.com/site/strelkasomaticvariantcaller/

Name: strelka
Version: 1.0.12
Module: apps/strelka/1.0.12/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/strelka/1.0.12/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@8cca844
Package: ext/strelka/@f8d32f14
Last update: 2013-10-31

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-31T12:46:53
Build parameters: tarball=/opt/gridware/ext/strelka_workflow-1.0.12.tar.gz
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, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/strelka/1.0.12/gcc-4.4.6

——————————————————————-

$ module help apps/strelka/1.0.12/gcc-4.4.6

----------- Module Specific Help for 'apps/strelka/1.0.12/gcc-4.4.6' ---------------------------

======== Strelka ========
Somatic variant calling workflow for matched tumor-normal
samples
========================

This module sets up your environment for the use of the 'strelka'
application. This module sets up version '1.0.12' of the
application.

>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<

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

——————————————————————-

$ module show apps/strelka/1.0.12/gcc-4.4.6
-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/strelka/1.0.12/gcc-4.4.6:

module-whatis

Title: Strelka
Summary: Somatic variant calling workflow for matched tumor-normal samples
License: NONFREE - Illumina Open Source Source License
Group: Bioinformatics
URL: https://sites.google.com/site/strelkasomaticvariantcaller/

Name: strelka
Version: 1.0.12
Module: apps/strelka/1.0.12/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/strelka/1.0.12/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@8cca844
Package: ext/strelka/@f8d32f14
Last update: 2013-10-31

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-31T12:46:53
Build parameters: tarball=/opt/gridware/ext/strelka_workflow-1.0.12.tar.gz
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, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/strelka/1.0.12/gcc-4.4.6

module-prereq libs/gcc/system
module-conflict apps/strelka
setenv STRELKADIR /opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6
setenv STRELKABIN /opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin
prepend-path PATH /opt/gridware/pkg/apps/strelka/1.0.12/gcc-4.4.6/bin


——————————————————————-

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

IGM IT
igmithelp@ncl.ac.uk
x8625

HPC – Lampredi – software update – FamSeq 1.0.0-2

 Uncategorized  No Responses »
Oct 282013
 

FamSeq 1.0.0-2 has been added to lampredi2. Details are:

$ module load apps/famseq
apps/famseq/1.0.0-2/gcc-4.4.6
| -- libs/gcc/system
| * --> OK
|
OK

[...@node05(lampredi) ~]$ ls $FAMSEQDIR
bin doc sample

[...@node05(lampredi) ~]$ ls $FAMSEQDIR/doc
manual.pdf

[...@node05(lampredi) ~]$ FamSeq

Program: FamSeq (Sequence calling using pedigree information)
Version: 0.0.1

Usage: FamSeq [options]

Input type: vcf input vcf file
LK input likelihood file

——————————————————————-

$ module whatis apps/famseq
apps/famseq :

Title: FamSeq
Summary: A computational tool for calculating probability of variants in family-based sequencing data
License: Public Domain
Group: Bioinformatics
URL: http://odin.mdacc.tmc.edu/~wwang7/FamSeqIndex.html

Name: famseq
Version: 1.0.0-2
Module: apps/famseq/1.0.0-2/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/famseq/1.0.0-2/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@ea64008
Package: apps/famseq/1.0.0-2@61f6fd9a
Last update: 2013-10-28

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-28T14:52:15
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, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/famseq/1.0.0-2/gcc-4.4.6

——————————————————————-

$ module help apps/famseq/1.0.0-2/gcc-4.4.6

----------- Module Specific Help for 'apps/famseq/1.0.0-2/gcc-4.4.6' ---------------------------

======== FamSeq ========
A computational tool for calculating probability of
variants in family-based sequencing data
=======================

This module sets up your environment for the use of the 'famseq'
application. This module sets up version '1.0.0-2' of the
application.

>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<

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

——————————————————————-

$ module show apps/famseq/1.0.0-2/gcc-4.4.6
-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/famseq/1.0.0-2/gcc-4.4.6:

module-whatis

Title: FamSeq
Summary: A computational tool for calculating probability of variants in family-based sequencing data
License: Public Domain
Group: Bioinformatics
URL: http://odin.mdacc.tmc.edu/~wwang7/FamSeqIndex.html

Name: famseq
Version: 1.0.0-2
Module: apps/famseq/1.0.0-2/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/famseq/1.0.0-2/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@ea64008
Package: apps/famseq/1.0.0-2@61f6fd9a
Last update: 2013-10-28

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-28T14:52:15
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, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/famseq/1.0.0-2/gcc-4.4.6

module-prereq libs/gcc/system
module-conflict apps/famseq
setenv FAMSEQDIR /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6
setenv FAMSEQBIN /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6/bin
setenv FAMSEQDOC /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6/doc
setenv FAMSEQSAMPLE /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6/sample
prepend-path PATH /opt/gridware/pkg/apps/famseq/1.0.0-2/gcc-4.4.6/bin

——————————————————————-

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

IGM IT
igmithelp@ncl.ac.uk
x8625

HPC – Lampredi – software update – Polymutt 0.15

 Uncategorized  No Responses »
Oct 282013
 

Polymutt 0.15 has been added to lampredi2. Details are:

$ module load apps/polymutt
apps/polymutt/0.15/gcc-4.4.6
| -- libs/gcc/system
| * --> OK
|
OK

$ ls -l $POLYMUTTDIR
total 12
drwxr-xr-x 2 root root 4096 Oct 28 14:47 bin
drwxr-xr-x 2 root root 4096 Oct 28 14:47 doc
drwxr-xr-x 2 root root 4096 Oct 28 14:47 example

$ polymutt --help

The following parameters are in effect:
pedfile : (-pname)
datfile : (-dname)
glfIndexFile : (-gname)
posterior cutoff : 0.50 (-c99.999)

Additional Options
Alternative input file : --in_vcf [], --mixed_vcf_records
Scaled mutation rate : --theta [1.0e-03], --indel_theta [1.0e-04]
Prior of ts/tv ratio : --poly_tstv [2.00]
Non-autosome labels : --chrX [X], --chrY [Y], --MT [MT]
de novo mutation : --denovo, --rate_denovo [1.5e-08],
[snip]

[...@node06(lampredi) ~]$ $POLYMUTTEXAMPLE/run.sh

The following parameters are in effect:
pedfile : test.ped (-pname)
datfile : test.dat (-dname)
glfIndexFile : test.gif (-gname)
posterior cutoff : 0.90 (-c99.999)
[snip]
Analysis started on Mon Oct 28 14:58:35 2013

Summary of reference -- 1
Total Entry Count: 81016
Total Base Cout: 81016
Non-Polymorphic Count: 72880
Transition Count: 5373
Transversion Count: 2763
Other Polymorphism Count: 0
Filter counts:
minMapQual 0
minTotalDepth 0
maxTotalDepth 0
Hard to call: 0
Skipped bases: 0
Analysis ended on Mon Oct 28 14:58:42 2013

Running time is 7 seconds
[snip]

———————————————————————————-

$ module whatis apps/polymutt
apps/polymutt :

Title: Polymutt
Summary: Calls single nucleotide variants and detects de novo point mutation events in families for next-generation sequencing data
License: NONFREE - modification granted; distribution of modifications prohibited
Group: Bioinformatics
URL: http://genome.sph.umich.edu/wiki/Polymutt

Name: polymutt
Version: 0.15
Module: apps/polymutt/0.15/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/polymutt/0.15/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/polymutt/0.15/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@ea64008
Package: apps/polymutt/0.15@b8b7f565
Last update: 2013-10-28

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-28T14:47:12
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, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/polymutt/0.15/gcc-4.4.6

———————————————————————————-

$ module help apps/polymutt/0.15/gcc-4.4.6

----------- Module Specific Help for 'apps/polymutt/0.15/gcc-4.4.6' ---------------------------

======== Polymutt ========
Calls single nucleotide variants and detects de novo point
mutation events in families for next-generation sequencing
data
=========================

This module sets up your environment for the use of the 'polymutt'
application. This module sets up version '0.15' of the
application.

>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<

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

———————————————————————————-

$ module show apps/polymutt/0.15/gcc-4.4.6

/opt/gridware/etc/modules/apps/polymutt/0.15/gcc-4.4.6:

module-whatis

Title: Polymutt
Summary: Calls single nucleotide variants and detects de novo point mutation events in families for next-generation sequencing data
License: NONFREE - modification granted; distribution of modifications prohibited
Group: Bioinformatics
URL: http://genome.sph.umich.edu/wiki/Polymutt

Name: polymutt
Version: 0.15
Module: apps/polymutt/0.15/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/polymutt/0.15/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/polymutt/0.15/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@ea64008
Package: apps/polymutt/0.15@b8b7f565
Last update: 2013-10-28

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-28T14:47:12
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, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/polymutt/0.15/gcc-4.4.6

module-prereq libs/gcc/system
module-conflict apps/polymutt
setenv POLYMUTTDIR /opt/gridware/pkg/apps/polymutt/0.15/gcc-4.4.6
setenv POLYMUTTBIN /opt/gridware/pkg/apps/polymutt/0.15/gcc-4.4.6/bin
setenv POLYMUTTDOC /opt/gridware/pkg/apps/polymutt/0.15/gcc-4.4.6/doc
setenv POLYMUTTEXAMPLE /opt/gridware/pkg/apps/polymutt/0.15/gcc-4.4.6/example
prepend-path PATH /opt/gridware/pkg/apps/polymutt/0.15/gcc-4.4.6/bin

———————————————————————————-

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

IGM IT
igmithelp@ncl.ac.uk
x8625

 Posted by at 3:25 pm

2014 IGM Hot Desking PCs

 Uncategorized  No Responses »
Oct 252013
 

2014 IGM Hot Desk PCs

University Common Desktop
Windows 7, 64bit
Office 2010, Lync 2013
Excel 2003 (for some generic software)
Turning Point (interactive PowerPoint presentations for use in ISS Lecture Theatres, including IGM LT)
Internet Explorer / Chrome – University supported web browsers
7zip – handles zip, 7z, rar and gz compressed formats
Adobe Acrobat Reader 11, Flash 12, Shockwave 11 (all Adobe updates handled by ISS)

Fiji / ImageJ (complete with IGM requested plug-ins)
Axiovision 64bit (last edition of this software)
ZEN Blue and Black editions  (the Axiovision replacement)
Nikon Elements Viewer
Paint.Net
Irfanview

BioEdit
SDS 2.4.1
GeneSnap – old geldoc reader
LSI Image Browser
Ape – A Plasmid Editor
Unipro UGENE
MEGA 6
Chromas Lite

Java 7 (updates handled by ISS)
J-dotter
Haploview
Integrative Genomics Viewer 2GB version

Exceed 9 (not needed when accessing IGM based Linux servers)
Communication/Remote Access tools – SSH, PuTTY, Nx, FTP client, wget, bitser

Endnote X7
LabVIEW 2012
Maple 15
MatLab 2013
MiniTab 16
Sigmaplot 11
SPSS 21

R 3 32bit
Perl 5
Python 2.7
Tinn-R

 Posted by at 11:40 am
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