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/
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$ 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 $FASTXBIN
fasta_clipping_histogram.pl fastx_barcode_splitter.pl
fasta_formatter fastx_clipper
fasta_nucleotide_changer fastx_collapser
fastq_masker fastx_nucleotide_distribution_graph.sh
fastq_quality_boxplot_graph.sh fastx_nucleotide_distribution_line_graph.sh
fastq_quality_converter fastx_quality_stats
fastq_quality_filter fastx_renamer
fastq_quality_trimmer fastx_reverse_complement
fastq_to_fasta fastx_trimmer
fastx_artifacts_filter fastx_uncollapser
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$ 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
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$ 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.
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$ 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
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