[med-svn] r11573 - in trunk/packages/seg/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Thu Jul 5 13:55:25 UTC 2012
Author: lkajan-guest
Date: 2012-07-05 13:55:25 +0000 (Thu, 05 Jul 2012)
New Revision: 11573
Added:
trunk/packages/seg/trunk/debian/ncbi-seg.examples
trunk/packages/seg/trunk/debian/ncbi-seg.install
Removed:
trunk/packages/seg/trunk/debian/seg.examples
trunk/packages/seg/trunk/debian/seg.install
Modified:
trunk/packages/seg/trunk/debian/README.source
trunk/packages/seg/trunk/debian/changelog
trunk/packages/seg/trunk/debian/control
trunk/packages/seg/trunk/debian/patches/autotools
trunk/packages/seg/trunk/debian/patches/seg.pod
trunk/packages/seg/trunk/debian/rules
trunk/packages/seg/trunk/debian/upstream
Log:
changed version to 0.0.20000620; change package and binary name to ncbi-seg; changed get-orig-source back to static version and package name
Modified: trunk/packages/seg/trunk/debian/README.source
===================================================================
--- trunk/packages/seg/trunk/debian/README.source 2012-07-05 11:24:46 UTC (rev 11572)
+++ trunk/packages/seg/trunk/debian/README.source 2012-07-05 13:55:25 UTC (rev 11573)
@@ -1,5 +1,5 @@
-seg for Debian
-==============
+ncbi-seg for Debian
+===================
COPYING
-------
Modified: trunk/packages/seg/trunk/debian/changelog
===================================================================
--- trunk/packages/seg/trunk/debian/changelog 2012-07-05 11:24:46 UTC (rev 11572)
+++ trunk/packages/seg/trunk/debian/changelog 2012-07-05 13:55:25 UTC (rev 11573)
@@ -1,4 +1,4 @@
-seg (1994101801-1) UNRELEASED; urgency=low
+ncbi-seg (0.0.20000620-1) UNRELEASED; urgency=low
* Initial version. (Closes: #680233)
Modified: trunk/packages/seg/trunk/debian/control
===================================================================
--- trunk/packages/seg/trunk/debian/control 2012-07-05 11:24:46 UTC (rev 11572)
+++ trunk/packages/seg/trunk/debian/control 2012-07-05 13:55:25 UTC (rev 11573)
@@ -1,4 +1,4 @@
-Source: seg
+Source: ncbi-seg
Section: science
Priority: extra
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -10,14 +10,14 @@
DM-Upload-Allowed: yes
Homepage: ftp://ftp.ncbi.nih.gov/pub/seg/seg/
-Package: seg
+Package: ncbi-seg
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: masking of segments of low compositional complexity in amino acid sequences
- SEG is a program for identifying and masking segments of low compositional
- complexity in amino acid sequences.
+Description: tool to mask segments of low compositional complexity in amino acid sequences
+ ncbi-seg (a.k.a. SEG) is a program for identifying and masking segments of
+ low compositional complexity in amino acid sequences.
.
- seg divides sequences into contrasting segments of low-complexity and
+ ncbi-seg divides sequences into contrasting segments of low-complexity and
high-complexity. Low-complexity segments defined by the
algorithm represent "simple sequences" or "compositionally-biased regions".
.
@@ -25,12 +25,12 @@
may strip some nucleotide ambiguity codes from nt. sequences as they are being
read.
-Package: seg-dbg
+Package: ncbi-seg-dbg
Section: debug
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, seg (= ${binary:Version})
-Description: debug symbols for seg
- SEG is a program for identifying and masking segments of low compositional
- complexity in amino acid sequences.
+Depends: ${shlibs:Depends}, ${misc:Depends}, ncbi-seg (= ${binary:Version})
+Description: debug symbols for ncbi-seg
+ ncbi-seg (a.k.a. SEG) is a program for identifying and masking segments of
+ low compositional complexity in amino acid sequences.
.
- This package contains detached debug symbols for seg.
+ This package contains detached debug symbols for ncbi-seg.
Copied: trunk/packages/seg/trunk/debian/ncbi-seg.examples (from rev 11572, trunk/packages/seg/trunk/debian/seg.examples)
===================================================================
--- trunk/packages/seg/trunk/debian/ncbi-seg.examples (rev 0)
+++ trunk/packages/seg/trunk/debian/ncbi-seg.examples 2012-07-05 13:55:25 UTC (rev 11573)
@@ -0,0 +1 @@
+prion.fa
Copied: trunk/packages/seg/trunk/debian/ncbi-seg.install (from rev 11572, trunk/packages/seg/trunk/debian/seg.install)
===================================================================
--- trunk/packages/seg/trunk/debian/ncbi-seg.install (rev 0)
+++ trunk/packages/seg/trunk/debian/ncbi-seg.install 2012-07-05 13:55:25 UTC (rev 11573)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share
Modified: trunk/packages/seg/trunk/debian/patches/autotools
===================================================================
--- trunk/packages/seg/trunk/debian/patches/autotools 2012-07-05 11:24:46 UTC (rev 11572)
+++ trunk/packages/seg/trunk/debian/patches/autotools 2012-07-05 13:55:25 UTC (rev 11573)
@@ -3,50 +3,42 @@
From: Laszlo Kajan <lkajan at rostlab.org>
Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-July/016275.html
-Index: seg-1994101801/configure.ac
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ seg-1994101801/configure.ac 2012-07-04 20:31:38.946824368 +0000
+--- /dev/null
++++ b/configure.ac
@@ -0,0 +1,7 @@
-+AC_INIT([seg], [1994101801])
++AC_INIT([ncbi-seg], [0.0.20000620])
+AC_CONFIG_SRCDIR([seg.c])
+AM_INIT_AUTOMAKE
+AC_CONFIG_FILES([Makefile])
+AC_PROG_CC
+
+AC_OUTPUT
-Index: seg-1994101801/Makefile.am
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ seg-1994101801/Makefile.am 2012-07-04 20:31:38.946824368 +0000
+--- /dev/null
++++ b/Makefile.am
@@ -0,0 +1,14 @@
-+man_MANS = seg.1
++man_MANS = ncbi-seg.1
+
-+bin_PROGRAMS = seg
++bin_PROGRAMS = ncbi-seg
+
-+seg_SOURCES = seg.c genwin.c genwin.h lnfac.h
++ncbi_seg_SOURCES = seg.c genwin.c genwin.h lnfac.h
+
+LDADD = -lm
+
-+seg.1: seg.pod
++ncbi-seg.1: ncbi-seg.pod
+ sed -e 's|__datadir__|$(datadir)|g;s|__docdir__|$(docdir)|g;s|__pkgdatadir__|$(pkgdatadir)|g;s|__PREFIX__|$(prefix)|g;s|__sysconfdir__|$(sysconfdir)|g;s|__VERSION__|$(VERSION)|g;' "$<" | \
+ pod2man -c 'User Commands' -r "$(VERSION)" -name $(shell echo "$(basename $@)" | tr '[:lower:]' '[:upper:]') > "$@"
+
+clean-local:
+ rm -f $(man_MANS)
-Index: seg-1994101801/AUTHORS
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ seg-1994101801/AUTHORS 2012-07-04 20:31:38.946824368 +0000
+--- /dev/null
++++ b/AUTHORS
@@ -0,0 +1,4 @@
+John C. Wootton, Scott Federhen
+National Center For Biotechnology Information
+National Library of Medicine
+National Institutes of Health
-Index: seg-1994101801/ChangeLog
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ seg-1994101801/ChangeLog 2012-07-04 20:31:38.950824087 +0000
+--- /dev/null
++++ b/ChangeLog
@@ -0,0 +1,52 @@
+
+This directory contains C language source code for the SEG program of Wootton
@@ -100,16 +92,12 @@
+
+9/30/97
+HMF5 plugged a memory leak.
-Index: seg-1994101801/NEWS
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ seg-1994101801/NEWS 2012-07-04 20:31:38.950824087 +0000
+--- /dev/null
++++ b/NEWS
@@ -0,0 +1 @@
-+2012-07-04 Debianization of seg.
-Index: seg-1994101801/COPYING
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ seg-1994101801/COPYING 2012-07-04 20:32:08.274824880 +0000
++2012-07-04 Debianization of seg as ncbi-seg.
+--- /dev/null
++++ b/COPYING
@@ -0,0 +1,24 @@
+ PUBLIC DOMAIN NOTICE
+ National Center for Biotechnology Information
Modified: trunk/packages/seg/trunk/debian/patches/seg.pod
===================================================================
--- trunk/packages/seg/trunk/debian/patches/seg.pod 2012-07-05 11:24:46 UTC (rev 11572)
+++ trunk/packages/seg/trunk/debian/patches/seg.pod 2012-07-05 13:55:25 UTC (rev 11573)
@@ -3,22 +3,20 @@
From: Laszlo Kajan <lkajan at rostlab.org>
Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-July/016275.html
-Index: seg-1994101801/seg.pod
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ seg-1994101801/seg.pod 2012-07-04 20:45:27.206822408 +0000
+--- /dev/null
++++ b/ncbi-seg.pod
@@ -0,0 +1,290 @@
+=head1 NAME
+
-+seg - segment sequence(s) by local complexity
++ncbi-seg - segment sequence(s) by local complexity
+
+=head1 SYNOPSIS
+
-+seg sequence [ W ] [ K(1) ] [ K(2) ] [ -x ] [ options ]
++ncbi-seg sequence [ W ] [ K(1) ] [ K(2) ] [ -x ] [ options ]
+
+=head1 DESCRIPTION
+
-+seg divides sequences into contrasting segments of low-complexity
++ncbi-seg divides sequences into contrasting segments of low-complexity
+and high-complexity. Low-complexity segments defined by the
+algorithm represent "simple sequences" or "compositionally-biased
+regions".
@@ -30,7 +28,7 @@
+automatically by the algorithm.
+
+The input is a FASTA-formatted sequence file, or a database file
-+containing many FASTA-formatted sequences. seg is tuned for amino
++containing many FASTA-formatted sequences. ncbi-seg is tuned for amino
+acid sequences. For nucleotide sequences, see EXAMPLES OF
+PARAMETER SETS below.
+
@@ -164,7 +162,7 @@
+
+=head1 EXAMPLES OF PARAMETER SETS
+
-+Default parameters are given by 'seg sequence' (equivalent to 'seg
++Default parameters are given by 'ncbi-seg sequence' (equivalent to 'ncbi-seg
+sequence 12 2.2 2.5'). These parameters are appropriate for low-
+complexity masking of many amino acid sequences [with -x option ].
+
@@ -175,26 +173,26 @@
+for BLAST or FASTA searches that compare two amino acid sequence
+databases, the following masking may be applied to both databases:
+
-+ seg database 12 1.8 2.0 -x
++ ncbi-seg database 12 1.8 2.0 -x
+
+=head2 Homopolymer analysis:
+
+To examine all homopolymeric subsequences of length (for example)
+7 or greater:
+
-+ seg sequence 7 0 0
++ ncbi-seg sequence 7 0 0
+
+=head2 Non-globular regions of protein sequences:
+
+Many long non-globular domains may be diagnosed at longer window
+lengths, typically:
+
-+ seg sequence 45 3.4 3.75
++ ncbi-seg sequence 45 3.4 3.75
+
+For some shorter non-globular domains, the following set is
+appropriate:
+
-+ seg sequence 25 3.0 3.3
++ ncbi-seg sequence 25 3.0 3.3
+
+=head2 Nucleotide sequences:
+
@@ -202,7 +200,7 @@
+For masking, the following is approximately equivalent in effect
+to the default parameters for amino acid sequences:
+
-+ seg sequence.na 21 1.4 1.6
++ ncbi-seg sequence.na 21 1.4 1.6
+
+=head1 EXAMPLES
+
@@ -217,7 +215,7 @@
+
+The command line:
+
-+ seg __docdir__/examples/prion.fa
++ ncbi-seg __docdir__/examples/prion.fa
+
+gives the standard output below
+
@@ -246,7 +244,7 @@
+
+The command line:
+
-+ seg __docdir__/examples/prion.fa -x
++ ncbi-seg __docdir__/examples/prion.fa -x
+
+gives the following FASTA-formatted file:-
+
@@ -298,10 +296,8 @@
+IRL Press, Oxford) (In press).
+
+
-Index: seg-1994101801/seg.doc
-===================================================================
---- seg-1994101801.orig/seg.doc 2012-07-04 20:45:24.878825058 +0000
-+++ seg-1994101801/seg.doc 2012-07-04 20:45:27.206822408 +0000
+--- a/seg.doc
++++ b/seg.doc
@@ -13,12 +13,12 @@
seg sequence [ W ] [ K(1) ] [ K(2) ] [ -x ] [ options ]
Modified: trunk/packages/seg/trunk/debian/rules
===================================================================
--- trunk/packages/seg/trunk/debian/rules 2012-07-05 11:24:46 UTC (rev 11572)
+++ trunk/packages/seg/trunk/debian/rules 2012-07-05 13:55:25 UTC (rev 11573)
@@ -6,8 +6,8 @@
export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
-ver := $(shell dpkg-parsechangelog | awk '/^Version/ { print $2 }' | cut -d- -f1 )
-pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+ver := 0.0.20000620
+pkg := ncbi-seg
.PHONY: get-orig-source
get-orig-source:
Deleted: trunk/packages/seg/trunk/debian/seg.examples
===================================================================
--- trunk/packages/seg/trunk/debian/seg.examples 2012-07-05 11:24:46 UTC (rev 11572)
+++ trunk/packages/seg/trunk/debian/seg.examples 2012-07-05 13:55:25 UTC (rev 11573)
@@ -1 +0,0 @@
-prion.fa
Deleted: trunk/packages/seg/trunk/debian/seg.install
===================================================================
--- trunk/packages/seg/trunk/debian/seg.install 2012-07-05 11:24:46 UTC (rev 11572)
+++ trunk/packages/seg/trunk/debian/seg.install 2012-07-05 13:55:25 UTC (rev 11573)
@@ -1,2 +0,0 @@
-usr/bin
-usr/share
Modified: trunk/packages/seg/trunk/debian/upstream
===================================================================
--- trunk/packages/seg/trunk/debian/upstream 2012-07-05 11:24:46 UTC (rev 11572)
+++ trunk/packages/seg/trunk/debian/upstream 2012-07-05 13:55:25 UTC (rev 11573)
@@ -1,4 +1,4 @@
-Name: seg
+Name: ncbi-seg
Reference:
Author: John C. Wootton and Scott Federhen
Title: 'Statistics of local complexity in amino acid sequences and sequence databases.'
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