MitoSeek has been updated to version 1.2, as of 24/02/2014
This is a software tool to reliably and easily extract mitochondrial genome information from exome sequencing data.
https://github.com/riverlee/MitoSeek
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$ module load apps/mitoseek/1.2
apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18
| — libs/gcc/system
| * –> OK
| — apps/perl/5.16.1/gcc-4.4.6
| | — libs/gcc/system … SKIPPED (already loaded)
| * –> OK
| — apps/samtools/0.1.18/gcc-4.4.6
| | — libs/gcc/system … SKIPPED (already loaded)
| * –> OK
|
OK
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$ module whatis apps/mitoseek/1.2
apps/mitoseek/1.2 :
Title: MitoSeek
Summary: Extraction of mitochondrial genome information from exome sequencing data
License: GPLv2
Group: Bioinformatics
URL: https://github.com/riverlee/MitoSeek
Name: mitoseek
Version: 1.2
Module: apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18
Module path: /opt/gridware/etc/modules/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18
Package path: /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18
Repository: file:/opt/gridware/etc/repos/local
Package: apps/mitoseek/1.2@6ea5eade
Last update: 2014-02-24
Builder: root@headnode1.lampredi.cluster.local
Build date: 2014-02-24T11:08:18
Build modules: apps/perl/5.16.1/gcc-4.4.6, apps/samtools/0.1.18/gcc-4.4.6, 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, 2×4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)
apps/perl/5.16.1/gcc-4.4.6 (using: apps/perl/5.16.1/gcc-4.4.6)
apps/samtools/0.1.18/gcc-4.4.6 (using: apps/samtools/0.1.18/gcc-4.4.6)
For further information, execute:
module help apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18
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$ module help apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18
———– Module Specific Help for ‘apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18’ —————————
======== MitoSeek ========
Extraction of mitochondrial genome information from exome
sequencing data
=========================
This module sets up your environment for the use of the ‘mitoseek’
application. This module sets up version ‘1.2’ of the
application.
>> SYNOPSIS <<
MitoSeek is an open-source software tool to reliably and easily
extract mitochondrial genome information from exome sequencing data.
MitoSeek evaluates mitochondrial genome alignment quality, estimates
relative mitochondrial copy numbers, and detects heteroplasmy,
somatic mutation, and structural variance of the mitochondrial
genome.
>> LICENSING <<
This package is made available subject to the following license(s):
GPLv2
Please refer to the website for further details regarding licensing.
>> FURTHER INFORMATION <<
More information about this software can be found at the website:
https://github.com/riverlee/MitoSeek
For further details regarding this module, including the environment
modifications it will apply, execute:
module show apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18
>> GET STARTED <<
Please refer to the website for further details on usage of this
package.
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$ module show apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18
——————————————————————-
/opt/gridware/etc/modules/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18:
module-whatis
Title: MitoSeek
Summary: Extraction of mitochondrial genome information from exome sequencing data
License: GPLv2
Group: Bioinformatics
URL: https://github.com/riverlee/MitoSeek
Name: mitoseek
Version: 1.2
Module: apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18
Module path: /opt/gridware/etc/modules/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18
Package path: /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18
Repository: file:/opt/gridware/etc/repos/local
Package: apps/mitoseek/1.2@6ea5eade
Last update: 2014-02-24
Builder: root@headnode1.lampredi.cluster.local
Build date: 2014-02-24T11:08:18
Build modules: apps/perl/5.16.1/gcc-4.4.6, apps/samtools/0.1.18/gcc-4.4.6, 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, 2×4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)
apps/perl/5.16.1/gcc-4.4.6 (using: apps/perl/5.16.1/gcc-4.4.6)
apps/samtools/0.1.18/gcc-4.4.6 (using: apps/samtools/0.1.18/gcc-4.4.6)
For further information, execute:
module help apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18
module-prereq libs/gcc/system
module-prereq apps/perl/5.16.1/gcc-4.4.6
module-prereq apps/samtools/0.1.18/gcc-4.4.6
module-conflict apps/mitoseek
setenv MITOSEEKDIR /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18
setenv MITOSEEKBIN /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18/bin
setenv MITOSEEKDOC /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18/doc
prepend-path PERL5LIB /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18/perl/lib/perl5
prepend-path MANPATH /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18/perl/man
prepend-path PATH /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18/bin
prepend-path PATH /opt/gridware/pkg/apps/mitoseek/1.2/gcc-4.4.6+perl-5.16.1+samtools-0.1.18/perl/bin
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