./biology/mummer, System for aligning whole genome sequences

[ CVSweb ] [ Homepage ] [ RSS ] [ Required by ] [ Add to tracker ]

Branch: CURRENT, Version: 3.20nb10, Package name: mummer-3.20nb10, Maintainer: pkgsrc-users

Mummer is a system for aligning whole genome sequences. Using an efficient
data structure called a suffix tree, the system is able rapidly to align
sequences containing millions of nucleotides whether in complete or draft
form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s
of contigs from a shotgun sequencing project with ease, and will align them to
another set of contigs or a genome using the NUCmer program included with the
system.


Required to run:
[lang/perl5]

Required to build:
[pkgtools/cwrappers]

Master sites:

Filesize: 3081.49 KB

Version history: (Expand)

CVS history: (Expand)


   2022-06-28 13:38:00 by Thomas Klausner | Files touched by this commit (3952) 
Log message:
*: recursive bump for perl 5.36
   2021-10-26 12:03:45 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes
   2021-10-07 15:19:44 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Remove SHA1 hashes for distfiles
   2021-05-24 21:56:06 by Thomas Klausner | Files touched by this commit (3575) 
Log message:
*: recursive bump for perl 5.34
   2020-08-31 20:13:29 by Thomas Klausner | Files touched by this commit (3631) 
Log message:
*: bump PKGREVISION for perl-5.32.
   2020-01-26 06:26:29 by Roland Illig | Files touched by this commit (189) 
Log message:
all: migrate some SourceForge homepage URLs back from https to http

https://mail-index.netbsd.org/pkgsrc-changes/2020/01/18/msg205146.html

In the above commit, the homepage URLs were migrated from http to https,
assuming that SourceForge would use the same host names for both http and
https connections. This assumption was wrong. Their documentation at
https://sourceforge.net/p/forge/documentation/Custom%20VHOSTs/ states
that the https URLs use the domain sourceforge.io instead.

To make the homepages from the above commit reachable again, pkglint has
been extended to check for reachable homepages. This check is only
enabled when the --network command line option is given.

Each of the homepages that referred to https://$project.sourceforge.net
before was migrated to https://$project.sourceforge.io (27), and if that
was not reachable, to the fallback URL http://$project.sourceforge.net
(163).
   2020-01-19 00:36:14 by Roland Illig | Files touched by this commit (3046) 
Log message:
all: migrate several HOMEPAGEs to https

pkglint --only "https instead of http" -r -F

With manual adjustments afterwards since pkglint 19.4.4 fixed a few
indentations in unrelated lines.

This mainly affects projects hosted at SourceForce, as well as
freedesktop.org, CTAN and GNU.
   2019-08-11 15:25:21 by Thomas Klausner | Files touched by this commit (3557) 
Log message:
Bump PKGREVISIONs for perl 5.30.0