./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:
[pkgtools/cwrappers]

Master sites:

Filesize: 1423.456 KB

Version history: (Expand)

CVS history: (Expand)


   2025-11-17 12:01:43 by Thomas Klausner | Files touched by this commit (709) 
Log message: *: switch all sourceforge HOMEPAGEs to https
   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
   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 characters. 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-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.
   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.