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

Lampredi2 – off-campus access – for Macs

 Uncategorized  No Responses »
Oct 212013
 

This option will provide Mac users with a full graphical Linux desktop environment. There is a separate guide for those that require command line only access.

* Prerequisites

(1) You need to download Microsoft’s *new* version of Microsoft Remote Desktop (version 8.0)

(2) A working Internet connection. Please NOTE: The quality of your connection is determined by your Internet Service Provider. Contact your ISP if you are not happy with the consistent quality of the connection between yourself and the University. Your external connection is not the responsibility of either the University or the IGM.

* NOTE!

You should not run jobs on the login or head node

Graphical/Interactive software, like The Integrative Genomics Viewer, require that you run it via a QRSH session. Indeed, if you are in any doubt that your commands will place stress on the login node, simply issue qrsh at the terminal, and then try your commands from there.

When finished with your session, please log out correctly – most users forget to do this correctly.

________________________________________________

* Download and Install the newest version of Microsoft’s Remote Desktop 8 for Mac

You can find this via the App Store:

Apple menu
App Store
In the search field, type microsoft remote
Click the install button next to “Microsoft Remote Desktop” icon

* Launch Microsoft Remote Desktop

Microsoft Remote Desktop blank configuration

Microsoft Remote Desktop blank configuration

________________________________________________

Let’s add the most important part first, the settings needed for the Newcastle University Terminal Services Gateway. Click on the Preferences icon.

Click on + icon
Gateway name = newcastle university
Server = tsgateway.ncl.ac.uk
User name = your ISS username. As suggested, use the CAMPUS\ format e.g my ISS username is nas18 but here I must enter CAMPUS\nas18
Password = your ISS password

Remote Desktop Terminal Services Gateway settings

Remote Desktop Terminal Services Gateway settings

Close this windows

________________________________________________

Click the “+ New” icon

Connection name = anything, eg lampredi2 off-campus
PC name = lampredi2.ncl.ac.uk
Gateway = Newcastle university
Username = your lampredi2 username (do NOT use campus/ format here)
Password = your lampredi2 password
Resolution = experiment but 1024×768 or 1280×1024 seem sensible

Remote Desktop configuration

Remote Desktop configuration

Close this window

________________________________________________

To connect to lampredi2, simply double-click on “lampredi2 off-campus”, from the list under “My Desktops”.

When finished with your remote session, please click on System (menu bar on lampredi2) and choose Log Out.

Remote Desktop ready to connect

Remote Desktop ready to connect

 Posted by at 12:10 pm

HPC – Lampredi – software update – GATK & GATKQUEUE 2.7.2

 Uncategorized  No Responses »
Oct 022013
 

GATK 2.7.2 and GATKQUEUE 2.7.2 have been added to lampredi2. Details are:

$module load apps/gatk/2.7.2/noarch
apps/gatk/2.7.2/noarch
|
OK

$ ls $GATKDIR
bin GenomeAnalysisTK.jar resources

———————————————————————————-

$ module whatis apps/gatk/2.7.2/noarch
apps/gatk/2.7.2 :

Title: Genome Analysis Toolkit
Summary: Software package developed at the Broad Institute to analyse next-generation resequencing data
License: Free for non-commercial use; registration required; see http://j.mp/TTba2N
Group: Bioinformatics
URL: http://www.broadinstitute.org/gatk/index.php

Name: gatk
Version: 2.7.2
Module: apps/gatk/2.7.2/noarch
Module path: /opt/gridware/etc/modules/apps/gatk/2.7.2/noarch
Package path: /opt/gridware/pkg/apps/gatk/2.7.2/noarch

Repository: git+http://download.alces-software.com/git/packager-base@0fda8da
Package: ext/gatk/2.7.2@9df24753
Last update: 2013-10-01

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-01T15:50:24
Build parameters: tarball=/opt/gridware/ext/GenomeAnalysisTK-2.7-2.tar.bz2
Compiler: N/A

For further information, execute:

module help apps/gatk/2.7.2/noarch

———————————————————————————-

$ module help apps/gatk/2.7.2/noarch

----------- Module Specific Help for 'apps/gatk/2.7.2/noarch' ---------------------------

======== Genome Analysis Toolkit ========
Software package developed at the Broad Institute to
analyse next-generation resequencing data
========================================

This module sets up your environment for the use of the 'gatk'
application. This module sets up version '2.7.2' 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/gatk/2.7.2/noarch
-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/gatk/2.7.2/noarch:

module-whatis

Title: Genome Analysis Toolkit
Summary: Software package developed at the Broad Institute to analyse next-generation resequencing data
License: Free for non-commercial use; registration required; see http://j.mp/TTba2N
Group: Bioinformatics
URL: http://www.broadinstitute.org/gatk/index.php

Name: gatk
Version: 2.7.2
Module: apps/gatk/2.7.2/noarch
Module path: /opt/gridware/etc/modules/apps/gatk/2.7.2/noarch
Package path: /opt/gridware/pkg/apps/gatk/2.7.2/noarch

Repository: git+http://download.alces-software.com/git/packager-base@0fda8da
Package: ext/gatk/2.7.2@9df24753
Last update: 2013-10-01

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-01T15:50:24
Build parameters: tarball=/opt/gridware/ext/GenomeAnalysisTK-2.7-2.tar.bz2
Compiler: N/A

For further information, execute:

module help apps/gatk/2.7.2/noarch

module-conflict apps/gatk
module-conflict apps/gatklite
setenv GATKDIR /opt/gridware/pkg/apps/gatk/2.7.2/noarch
setenv GATKBIN /opt/gridware/pkg/apps/gatk/2.7.2/noarch/bin
setenv GATK_JAVA_MEM_MX 2g
setenv GATK_JAVA_TMPDIR /tmp
setenv GATK_JAVA_OPTS -Xmx$GATK_JAVA_MEM_MX -Djava.io.tmpdir=$GATK_JAVA_TMPDIR
prepend-path PATH /opt/gridware/pkg/apps/gatk/2.7.2/noarch/bin
——————————————————————-

GATKQUEUE 2.7.2

$ module load apps/gatkqueue/2.7.2/noarch
apps/gatkqueue/2.7.2/noarch
| -- apps/gatk/2.7.2/noarch
| * --> OK
|
OK

$ ls $GATKQUEUEDIR
bin java Queue.jar resources

———————————————————————————-

$ module whatis apps/gatkqueue/2.7.2/noarch
apps/gatkqueue/2.7.2/noarch:

Title: Genome Analysis Toolkit Queue
Summary: Command-line scripting framework for defining multi-stage genomic analysis pipelines
License: Free for non-commercial use; registration required; see http://j.mp/TTba2N
Group: Bioinformatics
URL: http://www.broadinstitute.org/gatk/index.php

Name: gatkqueue
Version: 2.7.2
Module: apps/gatkqueue/2.7.2/noarch
Module path: /opt/gridware/etc/modules/apps/gatkqueue/2.7.2/noarch
Package path: /opt/gridware/pkg/apps/gatkqueue/2.7.2/noarch

Repository: git+http://download.alces-software.com/git/packager-base@0fda8da
Package: ext/gatkqueue/2.7.2@95ff256d
Last update: 2013-10-01

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-01T15:50:50
Build parameters: tarball=/opt/gridware/ext/Queue-2.7-2.tar.bz2
Compiler: N/A
Dependencies: apps/gatk/2.7.2/noarch (using: apps/gatk/2.7.2/noarch)

For further information, execute:

module help apps/gatkqueue/2.7.2/noarch

———————————————————————————-

$ module help apps/gatkqueue/2.7.2/noarch

----------- Module Specific Help for 'apps/gatkqueue/2.7.2/noarch' ---------------------------

======== Genome Analysis Toolkit Queue ========
Command-line scripting framework for defining multi-stage
genomic analysis pipelines
==============================================

This module sets up your environment for the use of the 'gatkqueue'
application. This module sets up version '2.7.2' 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/gatkqueue/2.7.2/noarch
-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/gatkqueue/2.7.2/noarch:

module-whatis

Title: Genome Analysis Toolkit Queue
Summary: Command-line scripting framework for defining multi-stage genomic analysis pipelines
License: Free for non-commercial use; registration required; see http://j.mp/TTba2N
Group: Bioinformatics
URL: http://www.broadinstitute.org/gatk/index.php

Name: gatkqueue
Version: 2.7.2
Module: apps/gatkqueue/2.7.2/noarch
Module path: /opt/gridware/etc/modules/apps/gatkqueue/2.7.2/noarch
Package path: /opt/gridware/pkg/apps/gatkqueue/2.7.2/noarch

Repository: git+http://download.alces-software.com/git/packager-base@0fda8da
Package: ext/gatkqueue/2.7.2@95ff256d
Last update: 2013-10-01

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-01T15:50:50
Build parameters: tarball=/opt/gridware/ext/Queue-2.7-2.tar.bz2
Compiler: N/A
Dependencies: apps/gatk/2.7.2/noarch (using: apps/gatk/2.7.2/noarch)

For further information, execute:

module help apps/gatkqueue/2.7.2/noarch

module-prereq apps/gatk/2.7.2/noarch
module-conflict apps/gatkqueue
setenv GATKQUEUEDIR /opt/gridware/pkg/apps/gatkqueue/2.7.2/noarch
setenv GATKQUEUEEXAMPLES /opt/gridware/pkg/apps/gatkqueue/2.7.2/noarch/resources
setenv GATKQUEUEBIN /opt/gridware/pkg/apps/gatkqueue/2.7.2/noarch/bin
setenv GATKQUEUE_JAVA_MEM_MX 2g
setenv GATKQUEUE_JAVA_TMPDIR /tmp
setenv GATKQUEUE_JAVA_OPTS -Xmx$GATKQUEUE_JAVA_MEM_MX -Djava.io.tmpdir=$GATKQUEUE_JAVA_TMPDIR
prepend-path PATH /opt/gridware/pkg/apps/gatkqueue/2.7.2/noarch/bin
——————————————————————-

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

IGM IT
igmithelp@ncl.ac.uk
x8625

HPC – Lampredi – software update – HLA*IMP

 Uncategorized  No Responses »
Oct 012013
 

The HLA*IMP software has been amended, in order to accommodate the temp folder that the software likes to use. The previous version required root access to this internal folder, something that is not a good idea on a shared cluster.

The workaround is to create your own temp folder, issued just before you run the software. The precise command is mentioned below.

Unless stated otherwise, this temp folder would be created on your lampredi2 home folder, and should be a one-off process. If you wanted to set a temp folder elsewhere e.g. within the lustre storage then that is possible too.

This temp folder is where the graphs, and other files, are stored during the software run. They don’t appear to be particularly large (your lampredi2 home folder does have a quota level set at 20GB, in order to prevent jobs being run from the login/head node).

https://oxfordhla.well.ox.ac.uk/hla/static/tutorialIMP2.pdf

For our purposes, we are assuming that you will take a copy of the two example data files, mentioned in the tutorial, and will copy them to your lustre area first.

(1)
Log into lampredi2 using Microsoft Remote Desktop Connection (Windows),
CoRD (Mac) or TS Client (Linux – there’s a myriad of names for this
client, depending on the distro you use).

(2)
Click on the Terminal icon and issue the commands:

$ qrsh
$ module load apps/hlaimpbe
$ module load apps/hlaimpfe

Here we issue the new command to create a temp folder that the software can use:

$ mkdir -p $HLAIMPFE_USERTMP

If we are following the tutorial, we can copy the example data we need to our lustre storage. I’m going to use a folder called “hla_test” on my lustre storage area.

$ mkdir -p ~/lustre/hla_test | cp $HLAIMPFEDIR/share/PnP2Pipeline/interface/examples/* ~/lustre/hla_test

(3)
Now we can run the HLA software using:

$ interface.pl

You can follow the tutorial at page 3 on the PDF document. You just need to browse to /users/your_home_folder/lustre/hla_test folder when locating your main data file. Remember that this is also the same as using ~/lustre/hla_test and /mnt/lustre/users/your_home_folder/hla_test

It might seem cumbersome using the example data in this way but it actually avoids us having to “fight” with the GUI, when it comes to declaring where data is to be located.

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

IGM IT
igmithelp@ncl.ac.uk
x8625

HPC – Lampredi – software update – Trinity 20130814

 Uncategorized  No Responses »
Oct 012013
 

Trinity has been updated to version 2013-08-14. Details are:

$ module load apps/trinity/20130814
apps/trinity/20130814/gcc-4.4.6
| -- libs/gcc/system
| * --> OK
|
OK

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

$ ls $TRINITYDIR
Analysis docs install_tests.sh notes PerlLibAdaptors sample_data util
Butterfly galaxy-plugin LICENSE.txt perl README Trinity.pl
Chrysalis Inchworm Makefile PerlLib Release.Notes trinity-plugins

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

$ module whatis apps/trinity/20130814
apps/trinity/20130814:

Title: trinity
Summary: A novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
License: BSD
Group: Bioinformatics
URL: http://trinityrnaseq.sourceforge.net/

Name: trinity
Version: 20130814
Module: apps/trinity/20130814/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/trinity/20130814/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@0fda8da
Package: apps/trinity/20130814@8c2c4fe7
Last update: 2013-10-01

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-01T12:04:20
Build modules: apps/cpanminus/1.5017/noarch
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/trinity/20130814/gcc-4.4.6

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

$ module help apps/trinity/20130814/gcc-4.4.6

----------- Module Specific Help for 'apps/trinity/20130814/gcc-4.4.6' -----------

======== trinity ========
A novel method for the efficient and robust de novo
reconstruction of transcriptomes from RNA-seq data
========================

This module sets up your environment for the use of the 'trinity'
application. This module sets up version '20130814' 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/trinity/20130814/gcc-4.4.6
-------------------------------------------------------------------
/opt/gridware/etc/modules/apps/trinity/20130814/gcc-4.4.6:

module-whatis

Title: trinity
Summary: A novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
License: BSD
Group: Bioinformatics
URL: http://trinityrnaseq.sourceforge.net/

Name: trinity
Version: 20130814
Module: apps/trinity/20130814/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/trinity/20130814/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@0fda8da
Package: apps/trinity/20130814@8c2c4fe7
Last update: 2013-10-01

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-01T12:04:20
Build modules: apps/cpanminus/1.5017/noarch
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/trinity/20130814/gcc-4.4.6

module-prereq libs/gcc/system
module-conflict apps/trinity
setenv TRINITYDIR /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6
setenv TRINITYBIN /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6
prepend-path PERL5LIB /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6/perl/lib/perl5
prepend-path MANPATH /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6/perl/man
prepend-path PATH /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6/perl/bin
prepend-path PATH /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6/util
prepend-path PATH /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6
----------------------------------------------------------------------------------

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

IGM IT
igmithelp@ncl.ac.uk
x8625