bowtie-software
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bowtie-software [2014/10/17 08:02] – joguya | bowtie-software [2014/10/30 17:01] – [v 2.2.2] joguya | ||
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===== Bowtie 1 ===== | ===== Bowtie 1 ===== | ||
+ | ==== v1.0.1 ==== | ||
+ | * Version: 1.0.1 | ||
+ | * Link: http:// | ||
+ | |||
+ | === Usage === | ||
+ | * show all versions of bowtie< | ||
+ | |||
+ | ---------------------------------------------------------------------------------------------- / | ||
+ | bowtie/ | ||
+ | </ | ||
+ | * load a specific version, e.g. v1.1.1: < | ||
+ | * get quick help:< | ||
+ | |||
==== v1.1.1 ==== | ==== v1.1.1 ==== | ||
+ | * Version: 1.1.1 | ||
+ | * Added: October, 2014 | ||
+ | * Link: http:// | ||
+ | * Changelog: | ||
+ | * Fixed a compiling linkage problem related with Mavericks OSX. | ||
+ | * Improved performance for cases where the reference contains ambiguous or masked nucleobases represented by Ns. | ||
+ | * Some minor automatic tests updates. | ||
=== Usage === | === Usage === | ||
* show all versions of bowtie< | * show all versions of bowtie< | ||
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* Bowtie2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. | * Bowtie2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. | ||
* Bowtie2 supports gapped, local, and paired-end alignment modes. | * Bowtie2 supports gapped, local, and paired-end alignment modes. | ||
+ | ==== v 2.2.2 ==== | ||
+ | * Version 2.2.2 | ||
+ | * Link: http:// | ||
+ | |||
+ | |||
+ | === Usage === | ||
+ | * show all versions of bowtie2< | ||
+ | |||
+ | ---------------------------------------------------------------------------------------------- / | ||
+ | bowtie2/ | ||
+ | </ | ||
+ | * load specific version, e.g. v2.2.2:< | ||
+ | * get help:< | ||
==== v 2.2.3 ==== | ==== v 2.2.3 ==== | ||
+ | * Version 2.2.3 | ||
+ | * Added: October, 2014 | ||
+ | * Link: http:// | ||
+ | * Changelog: | ||
+ | * Fixed a bug that made loading an index into memory crash sometimes. | ||
+ | * Fixed a silent failure to warn the user in case the -x option is missing. | ||
+ | * Updated al, un, al-conc and un-conc options to avoid confusion in cases where the user does not provide a base file name. | ||
+ | * Fixed a spurious assert that made bowtie2-inspect debug fail. | ||
+ | |||
=== Usage === | === Usage === | ||
* show all versions of bowtie2< | * show all versions of bowtie2< | ||
Line 66: | Line 108: | ||
* load specific version, e.g. v2.2.3:< | * load specific version, e.g. v2.2.3:< | ||
* get help:< | * get help:< | ||
+ | |||
+ | === Installation === | ||
+ | * bowtie2 is precompiled already, so all you have to do is copy the binaries to export-apps< | ||
+ | unzip bowtie2-2.2.3-linux-x86_64.zip | ||
+ | sudo mkdir / | ||
+ | sudo cp -rv bowtie2-2.2.3/ | ||
+ | |||
+ | * create module file:< | ||
+ | ##################################################################### | ||
+ | ## | ||
+ | ## bowtie2 Modulefile | ||
+ | ## by James Oguya, j.oguya@cgiar.org | ||
+ | ## October, 2014 | ||
+ | ## | ||
+ | |||
+ | set appname | ||
+ | set version | ||
+ | set prefix | ||
+ | set exec_prefix | ||
+ | set url " | ||
+ | set msg " | ||
+ | |||
+ | proc ModulesHelp { } { | ||
+ | puts stderr " | ||
+ | } | ||
+ | |||
+ | module-whatis | ||
+ | |||
+ | conflict | ||
+ | |||
+ | prepend-path | ||
+ | * as always, push to github & let ansible take care of teh rest!< |
bowtie-software.txt · Last modified: 2020/04/27 11:13 by aorth