FASTX-Toolkit 0.0.13 has been added to the cluster (24\/02\/2014)<\/p>\n
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA\/FASTQ files preprocessing. apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6<\/p>\n | — libs\/gcc\/system … SKIPPED (already loaded)<\/p>\n OK<\/p>\n $ ls $FASTXDIR<\/p>\n bin\u00a0 share<\/p>\n ls $FASTXBIN<\/p>\n fasta_clipping_histogram.pl \u00a0 \u00a0 fastx_barcode_splitter.pl<\/p>\n fasta_formatter \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 fastx_clipper<\/p>\n fasta_nucleotide_changer\u00a0 \u00a0 \u00a0 \u00a0 fastx_collapser<\/p>\n fastq_masker\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 fastx_nucleotide_distribution_graph.sh<\/p>\n fastq_quality_boxplot_graph.sh\u00a0 fastx_nucleotide_distribution_line_graph.sh<\/p>\n fastq_quality_converter \u00a0 \u00a0 \u00a0 \u00a0 fastx_quality_stats<\/p>\n fastq_quality_filter\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 fastx_renamer<\/p>\n fastq_quality_trimmer \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 fastx_reverse_complement<\/p>\n fastq_to_fasta\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 fastx_trimmer<\/p>\n fastx_artifacts_filter\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 fastx_uncollapser<\/p>\n ——————————————————————-<\/p>\n $ module whatis apps\/fastx<\/p>\n apps\/fastx : Summary: A collection of command line tools for Short-Reads FASTA\/FASTQ files preprocessing<\/p>\n License: AGPLv3+<\/p>\n Group: Bioinformatics<\/p>\n URL: http:\/\/hannonlab.cshl.edu\/fastx_toolkit\/<\/p>\n Name: fastx<\/p>\n Version: 0.0.13<\/p>\n Module: apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6<\/p>\n Module path: \/opt\/gridware\/etc\/modules\/apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6<\/p>\n Package path: \/opt\/gridware\/pkg\/apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6<\/p>\n <\/p>\n Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@0d67d87<\/p>\n Package: apps\/fastx\/0.0.13@3f151052<\/p>\n Last update: 2012-09-09<\/p>\n <\/p>\n Builder: root@headnode1.lampredi.cluster.local<\/p>\n Build date: 2014-02-24T10:41:52<\/p>\n Build modules: libs\/gtextutils\/0.6\/gcc-4.4.6<\/p>\n Compiler: compilers\/gcc\/system<\/p>\n System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64<\/p>\n Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)<\/p>\n Dependencies: libs\/gcc\/system (using: libs\/gcc\/system)<\/p>\n <\/p>\n For further information, execute:<\/p>\n module help apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6<\/p>\n ——————————————————————-<\/p>\n $ module help apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6<\/p>\n <\/p>\n ———– Module Specific Help for ‘apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6’ —————————<\/p>\n <\/p>\n <\/p>\n ======== fastx ========<\/p>\n A collection of command line tools for Short-Reads<\/p>\n FASTA\/FASTQ files preprocessing<\/p>\n ======================<\/p>\n <\/p>\n This module sets up your environment for the use of the ‘fastx’<\/p>\n application. This module sets up version ‘0.0.13’ of the<\/p>\n application.<\/p>\n <\/p>\n <\/p>\n >> SYNOPSIS <<<\/p>\n <\/p>\n The FASTX-Toolkit is a collection of command line tools for<\/p>\n Short-Reads FASTA\/FASTQ files preprocessing.<\/p>\n <\/p>\n Next-Generation sequencing machines usually produce FASTA or FASTQ<\/p>\n files, containing multiple short-reads sequences (possibly with<\/p>\n quality information).<\/p>\n <\/p>\n The main processing of such FASTA\/FASTQ files is mapping (aka<\/p>\n aligning) the sequences to reference genomes or other databases<\/p>\n using specialized programs. Example of such mapping programs are:<\/p>\n Blat, SHRiMP, LastZ, MAQ and many many others.<\/p>\n <\/p>\n However, it is sometimes more productive to preprocess the<\/p>\n FASTA\/FASTQ files before mapping the sequences to the genome –<\/p>\n manipulating the sequences to produce better mapping results. The<\/p>\n FASTX-Toolkit tools perform some of these preprocessing tasks.<\/p>\n <\/p>\n <\/p>\n >> LICENSING <<<\/p>\n <\/p>\n This package is made available subject to the following license(s):<\/p>\n <\/p>\n AGPLv3+<\/p>\n <\/p>\n Please refer to the website for further details regarding licensing.<\/p>\n <\/p>\n <\/p>\n >> FURTHER INFORMATION <<<\/p>\n <\/p>\n More information about this software can be found at the website:<\/p>\n <\/p>\n http:\/\/hannonlab.cshl.edu\/fastx_toolkit\/<\/p>\n <\/p>\n For further details regarding this module, including the environment<\/p>\n modifications it will apply, execute:<\/p>\n <\/p>\n module show apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6<\/p>\n <\/p>\n <\/p>\n >> GET STARTED <<<\/p>\n <\/p>\n Please refer to the website for further details on usage of this<\/p>\n package.<\/p>\n ——————————————————————-<\/p>\n $ module show apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6<\/p>\n \/opt\/gridware\/etc\/modules\/apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6:<\/p>\n module-whatis<\/p>\n <\/p>\n Title: fastx<\/p>\n Summary: A collection of command line tools for Short-Reads FASTA\/FASTQ files preprocessing<\/p>\n License: AGPLv3+<\/p>\n Group: Bioinformatics<\/p>\n URL: http:\/\/hannonlab.cshl.edu\/fastx_toolkit\/<\/p>\n <\/p>\n Name: fastx<\/p>\n Version: 0.0.13<\/p>\n Module: apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6<\/p>\n Module path: \/opt\/gridware\/etc\/modules\/apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6<\/p>\n Package path: \/opt\/gridware\/pkg\/apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6<\/p>\n <\/p>\n Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@0d67d87<\/p>\n Package: apps\/fastx\/0.0.13@3f151052<\/p>\n Last update: 2012-09-09<\/p>\n <\/p>\n Builder: root@headnode1.lampredi.cluster.local<\/p>\n Build date: 2014-02-24T10:41:52<\/p>\n Build modules: libs\/gtextutils\/0.6\/gcc-4.4.6<\/p>\n Compiler: compilers\/gcc\/system<\/p>\n System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64<\/p>\n Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)<\/p>\n Dependencies: libs\/gcc\/system (using: libs\/gcc\/system)<\/p>\n <\/p>\n For further information, execute:<\/p>\n module help apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6<\/p>\n <\/p>\n module-prereq libs\/gcc\/system<\/p>\n module-conflict apps\/fastx<\/p>\n setenv FASTXDIR \/opt\/gridware\/pkg\/apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6<\/p>\n setenv FASTXBIN \/opt\/gridware\/pkg\/apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6\/bin<\/p>\n setenv FASTXLIB \/opt\/gridware\/pkg\/apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6\/lib<\/p>\n prepend-path GDFONTPATH \/usr\/share\/fonts\/dejavu<\/p>\n setenv GNUPLOT_DEFAULT_GDFONT DejaVuSans<\/p>\n prepend-path PATH \/opt\/gridware\/pkg\/apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6\/bin<\/p>\n prepend-path LD_LIBRARY_PATH \/opt\/gridware\/pkg\/apps\/fastx\/0.0.13\/gcc-4.4.6+gtextutils-0.6\/lib<\/p>\n \u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n Lampredi HPC IGM IT 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\u00a0 share ls $FASTXBIN fasta_clipping_histogram.pl \u00a0 \u00a0 fastx_barcode_splitter.pl fasta_formatter \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 […]<\/a><\/p>\n","protected":false},"author":1149,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[11,10,9,21],"class_list":["post-312","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-cluster","tag-hpc","tag-lampredi","tag-lampredi2","category-1-id","post-seq-1","post-parity-odd","meta-position-corners","fix"],"_links":{"self":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/312","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/users\/1149"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=312"}],"version-history":[{"count":10,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/312\/revisions"}],"predecessor-version":[{"id":333,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/312\/revisions\/333"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=312"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=312"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=312"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
\nhttp:\/\/hannonlab.cshl.edu\/fastx_toolkit\/<\/a>
\n-------------------------------------------------------------------<\/span><\/code><\/p>\n$ module load apps\/fastx<\/span><\/code><\/p>\n
\nTitle: fastx<\/p>\n
\nigm-lampredi-users@ncl.ac.uk<\/p>\n
\nigmithelp@ncl.ac.uk
\nx8625<\/p>\n","protected":false},"excerpt":{"rendered":"