Hi Peter,

thanks for forwarding.
Afaik, we are using the pysam API for sorting extracting metadata since a few releases.
So hopefully this will not be a problem.


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files - noting the original "samtools sort" API has been withdrawn.


---------- Forwarded message ----------
From: John Marshall <j...@sanger.ac.uk>
Date: Wed, Dec 16, 2015 at 12:47 AM
Subject: [Samtools-devel] Samtools/BCFtools/HTSlib 1.3 released
To: samtools-annou...@lists.sourceforge.net
Cc: Samtools-help List <samtools-h...@lists.sourceforge.net>,
samtools-devel <samtools-de...@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superseded since samtools 1.0 and from this release no longer works: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

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

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


  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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