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Re: [COMBINE-lab/RapMap] rapmap v0.6.0

Okay, now that we are on the same page we can address the main issue: in Debian we have been only packaging RapMap in the service of salmon, using the salmon tagged releases and version numbers.

We have not yet packaged sailfish, though bcbio uses it, so we have a new reason to package it soon.

Michael R. Crusoe

On Tue, Feb 5, 2019, 17:39 Rob Patro <rob.patro@cs.stonybrook.edu> wrote:
Hi Michael,

  Indeed, Andreas is right.  The tagging scheme for RapMap is as follows.  Versions of the code that are used as a library for salmon (or sailfish), are tagged as such.  That is, they have the `salmon-` prefix before the version.  This ensures that each release of salmon or sailfish is tied to a specific commit of rapmap for reproducible builds.  However, the master branch has versions tagged without any prefix (apart from `v`).  That being said, one of the main points of the recent release was to sync-up with all of the recent developments made in the develop-salmon branch, so that the next release on that branch `salmon-0.13.0` should be essentially the same as what was released in v0.6.0.

On Feb 5, 2019, 4:57 AM -0500, Andreas Tille <tille@debian.org>, wrote:

On Tue, Feb 05, 2019 at 11:17:25AM +0200, Michael Crusoe wrote:
We packaged rapmap for Debian because we were packaging salmon as well.
Looks like we adopted the numbering of the salmon-v* release of rapmap
(recently 0.12) so this 0.6.0 release will currently be ignored as it is
numerically smaller.

Is that okay with you? What would you like done in the future?

As far as I understood (which does not mean that it is correct) new
rapmap releases are featuring a 'salmon-' prefix and are closely related
to salmon releases. This understanding is in fact in contrast to the
recent rapmap 0.6.0 release and is not visible for our scanner for new
releases that is at version 0.12 as Michael said.

Kind regards


În mar., 5 feb. 2019 la 06:59, Rob Patro <notifications@github.com> a scris:

This release brings the master branch and tagged release up to date with
many of the bug fixes, developments and improvements that have been going
into the develop-salmon branch in support of salmon development. Among
the most important new features in this release is the ability to have
rapmap apply *selective-alignment* to improve the sensitivity and
specificity of the mappings. For more details on *selective-alignment*
and mapping validation, refer to the release notes of salmon
<https://github.com/COMBINE-lab/salmon/releases/tag/v0.12.0> --- and
specifically options related to the --validateMappings. This release also
adds the ability to optionally write out unmapped reads in the output SAM
with the -u flag.

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Michael R. Crusoe
Co-founder & Lead, Common Workflow Language project
Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
+1 480 627 9108 / +370 653 11125


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