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

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