Just a heads up, I'm sure we the IUC will have Tool Shed packages prepared for the samtools 1.3 etc release shortly.
However, I'm less clear what Galaxy itself is doing for sorting BAM files - noting the original "samtools sort" API has been withdrawn.
Peter
---------- Forwarded message ---------- From: John Marshall jm18@sanger.ac.uk Date: Wed, Dec 16, 2015 at 12:47 AM Subject: [Samtools-devel] Samtools/BCFtools/HTSlib 1.3 released To: samtools-announce@lists.sourceforge.net Cc: Samtools-help List samtools-help@lists.sourceforge.net, samtools-devel samtools-devel@lists.sourceforge.net
New 1.3 versions of Samtools, BCFtools, and HTSlib have been released. These have numerous bug fixes, improvements, and new commands. The changes are too numerous to list here, but we would particularly like to draw your attention to these three items:
* The old way of invoking the samtools sort subcommand has been superseded since samtools 1.0 and from this release no longer works:
samtools sort [-f] [-o] in.bam out.prefix
If you do use this obsolete way of specifying sort options, samtools will now in most cases fail and give you a hint about the new ways. If you are still using sort ‑f, ‑o, or out.prefix, convert to use -T PREFIX and/or -o FILE instead. See the manual page for details.
* The samtools rmdup command has been restored to its basic functionality. It no longer immediately aborts, but it remains not recommended for most use.
* When HTSlib has been built to use libcurl, most tools can now access remote files over HTTPS and via AWS S3 in addition to the previous HTTP, FTP, and iRODS. See HTSlib's INSTALL and Samtools's README for details.
For further details of these and other changes in these releases, see the release notes for each project linked to at http://www.htslib.org/download/, or see all three together at http://sourceforge.net/projects/samtools/files/samtools/1.3/.
These releases can be found at http://www.htslib.org/. Development and source code of these projects are linked from that web site and can be found in various Git repositories under https://github.com/samtools. Release archives are available at both GitHub and SourceForge.
Installing the tools will also install manual pages for them. Once installed, you should be able to use "man samtools" etc at your command line to find details of new commands and functionality. Manual pages and other documentation are also available online at http://www.htslib.org/doc/.
John
-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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