Commit 927b1a1c authored by Steffen Möller's avatar Steffen Möller

Initial upload

parent 08c3744e
lucy for Debian
--------------
This package was initially selected for Bio-Linux. It is now repackaged
from the sources as a joint effort by Bio-Linux and Debian maintainers.
Uploaded to Debian it will be available across platforms and it shall
also help its integration in workflows.
-- Steffen Moeller <moeller@debian.org> Wed, 05 Sep 2018 14:15:32 +0200
The lucy.ps file is a postscript variant of the man page. Following
Debian's principles this should be removed from the source tree. But
since the packaging does not use the package and only miniscule disk
space is occupied by it, that additional file is tolerated in favour
of avoiding the source to be repackaged.
The patch supports the passing of Debian's default compilation flags.
-- Steffen Moeller <moeller@debian.org> Wed, 05 Sep 2018 15:41:09 +0200
lucy (1.20-1) unstable; urgency=medium
* Initial release (Closes: #908110)
-- Steffen Moeller <moeller@debian.org> Wed, 05 Sep 2018 14:15:32 +0200
Source: lucy
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>
Build-Depends: debhelper (>= 11)
Standards-Version: 4.2.0
Homepage: https://lucy.sourceforge.net
Vcs-Browser: https://salsa.debian.org/med-team/lucy
Vcs-Git: https://salsa.debian.org/med-team/lucy.git
Package: lucy
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: DNA sequence quality and vector trimming tool
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.
.
Lucy was designed and written at The Institute for Genomic Research
(TIGR, now the J. Craig Venter Institute), and it has been used here for
several years to clean sequence data from automated DNA sequencers prior
to sequence assembly and other downstream uses. The quality trimming
portion of lucy makes use of phred quality scores, such as those produced
by many automated sequencers based on the Sanger sequencing method. As
such, lucy’s quality trimming may not be appropriate for sequence
data produced by some of the new “next-generation” sequencers.
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: lucy
Source: https://lucy.sourceforge.net
Files: *
Copyright: 1999-2008 The Institute for Genomic Research (TIGR), Rockville, Maryland, USA
Lucy was written by Hui-Hsien Chou and Michael Holmes at The Institute for
Genomic Research, with help and suggestions from Granger Sutton, Anna Glodek,
John Scott, and Terry Shea. Michael Holmes is currently responsible for lucy.
Please direct any suggestions, bug reports, etc. to mholmes@tigr.org.
License: Artistic-1.0
Files: debian/*
Copyright: 2018 Steffen Moeller <moeller@debian.org>
License: Artistic-1.0
License: Artistic-1.0
This program is free software; you can redistribute it and/or modify it
under the terms of the "Artistic License" which comes with Debian.
.
THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
.
On Debian systems, the complete text of the Artistic License
can be found in "/usr/share/common-licenses/Artistic".
debian/README.Debian
debian/README.source
README.FIRST
HISTORY
Index: lucy-1.20/Makefile
===================================================================
--- lucy-1.20.orig/Makefile
+++ lucy-1.20/Makefile
@@ -1,6 +1,6 @@
-CC = cc
-CFLAGS = -O
-LIBS = -lpthread
+CC ?= cc
+CFLAGS ?= -O
+LIBS += -lpthread
OBJS = lucy.o qual_trim.o abi.o vector.o splice.o poly.o
all: lucy beep
helpingMakefile.patch
#!/usr/bin/make -f
export DH_VERBOSE = 1
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
%:
dh $@
Registry:
- Name: OMICtools
Entry: OMICS_14823
- Name: bio.tools
Entry: lucy
- Name: SciCrunch
Entry: NA
version=4
opts="uversionmangle=s%^.*lucy%%" http://sf.net/lucy/ lucy(.*)\.tar\.gz debian uupdate
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