./biology/lucy, Sequence Cleanup Program

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Branch: CURRENT, Version: 1.20, Package name: lucy-1.20, Maintainer: dprice

A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA
sequence fragments for sequence assembly,possibly using the TIGR
Assembler. The cleanup process includes quality assessment,
confidence reassurance, vector trimming and vector removal. The
primary advantage of Lucy over other similar utilities is that it is a
fully integrated, stand alone program.

Required to build:

Master sites:

SHA1: 890006f550efd06745e7156359ee8b519d3b5f62
RMD160: de6f9a787f9bd63b8d297beb2ecdc9793e3c183d
Filesize: 1423.456 KB

Version history: (Expand)

CVS history: (Expand)

   2020-05-20 08:09:10 by Roland Illig | Files touched by this commit (52)
Log message:
mark packages that fail with -Werror=char-subscripts

These packages are susceptible to bugs when confronted with non-ASCII

See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=94182.

It takes some time to analyze and fix these individually, therefore they
are only marked as "needs work".
   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-ch … 05146.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/documen … %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
   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.
   2015-11-02 19:42:23 by Alistair G. Crooks | Files touched by this commit (38)
Log message:
Add SHA512 digests for distfiles for biology category.

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.
   2014-10-09 16:07:17 by Thomas Klausner | Files touched by this commit (1163)
Log message:
Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles.
   2012-09-11 22:32:15 by Aleksej Saushev | Files touched by this commit (31)
Log message:
"user-destdir" is default these days
   2010-09-19 09:13:37 by OBATA Akio | Files touched by this commit (2) | Package updated
Log message:
Update lucy to 1.20.
Based on PR#43777 by Kamel Derouiche, with some clean up by me.

Version 1.20, 9/3/2008.  This version fixes a bug that caused lucy
to fail when there was too much information on the FASTA header lines
in the input files.  Lucy had a 256 character buffer for reading
lines from the input files.  If any FASTA header lines were longer
than 256 characters, the remaining characters would get read as part
of the FASTA sequence.  The solution implemented in this version is
simply to increase the buffer size to 4096 characters.  While that
still leaves the potential for the same error to occur with extremely
long header lines, the limitation that this entails seems reasonable,
and this should fix the problem for all pratical purposes.

Version 1.19, 12/30/2003.  This version fixes a bug that could cause
sequences to be rejected incorrectly in the vector detection step
(phase 6).  Because of the way that lucy compares "tags" in the
target sequence with "tags" in the vector sequence, some bases in
the target sequence could get counted more than once in the tally
of bases that match the vector sequence.  In rare instances, this
could cause the sequence to exceed the minimum threshold for
rejection, as a result of random sequence similarity.

The reporting of the CLB range in the -debug output file has also
been changed.  If the CLB range begins with the first base of the
sequence, then the left coordinate of the CLB range will be reported
as 1 (instead of 0).  The range "CLB 0 0" still indicates an empty
CLB range.
   2009-06-14 19:34:35 by Joerg Sonnenberger | Files touched by this commit (21)
Log message:
Remove @dirrm entries from PLISTs