Author: moeller Date: 2015-02-10 09:47:21 +0000 (Tue, 10 Feb 2015) New Revision: 18748
Added: trunk/packages/fasta3/trunk/debian/fasta3.doc-base trunk/packages/fasta3/trunk/debian/fasta3.manpages Removed: trunk/packages/fasta3/trunk/debian/README.Debian trunk/packages/fasta3/trunk/debian/README.source trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX Modified: trunk/packages/fasta3/trunk/debian/changelog trunk/packages/fasta3/trunk/debian/copyright trunk/packages/fasta3/trunk/debian/docs trunk/packages/fasta3/trunk/debian/patches/Makefile.patch trunk/packages/fasta3/trunk/debian/rules Log: fasta3 - almost ready to upload Deleted: trunk/packages/fasta3/trunk/debian/README.Debian =================================================================== --- trunk/packages/fasta3/trunk/debian/README.Debian 2015-02-09 18:18:47 UTC (rev 18747) +++ trunk/packages/fasta3/trunk/debian/README.Debian 2015-02-10 09:47:21 UTC (rev 18748) @@ -1,6 +0,0 @@ -fasta for Debian ----------------- - -<possible notes regarding this package - if none, delete this file> - - -- Steffen Moeller <[email protected]> Mon, 09 Feb 2015 15:04:28 +0100 Deleted: trunk/packages/fasta3/trunk/debian/README.source =================================================================== --- trunk/packages/fasta3/trunk/debian/README.source 2015-02-09 18:18:47 UTC (rev 18747) +++ trunk/packages/fasta3/trunk/debian/README.source 2015-02-10 09:47:21 UTC (rev 18748) @@ -1,10 +0,0 @@ -fasta for Debian ----------------- - -<this file describes information about the source package, see Debian policy -manual section 4.14. You WILL either need to modify or delete this file> - - - - -- Steffen Moeller <[email protected]> Mon, 09 Feb 2015 15:04:28 +0100 - Modified: trunk/packages/fasta3/trunk/debian/changelog =================================================================== --- trunk/packages/fasta3/trunk/debian/changelog 2015-02-09 18:18:47 UTC (rev 18747) +++ trunk/packages/fasta3/trunk/debian/changelog 2015-02-10 09:47:21 UTC (rev 18748) @@ -1,5 +1,5 @@ fasta3 (36.3.7a-1) unstable; urgency=low - * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP> + * Initial release (Closes: #coming) - -- Steffen Moeller <[email protected]> Mon, 09 Feb 2015 15:04:28 +0100 + -- Steffen Moeller <[email protected]> Tue, 10 Feb 2015 10:46:55 +0100 Modified: trunk/packages/fasta3/trunk/debian/copyright =================================================================== --- trunk/packages/fasta3/trunk/debian/copyright 2015-02-09 18:18:47 UTC (rev 18747) +++ trunk/packages/fasta3/trunk/debian/copyright 2015-02-10 09:47:21 UTC (rev 18748) @@ -7,21 +7,29 @@ The Rector & Visitors of the University of Virginia License: Apache-2.0 +Files: src/wm_align.c +Copyright: William R. Pearson, University of Virginia + Webb Miller, Penn State University +License: Apache-2.0 + Files: src/karlin.c -Copyright: 1980, 1983 Stephen Altschul +Copyright: 1990, 1993 Stephen Altschul, NCBI License: Apache-2.0 -Files: src/global_sse2.c -Copyright: 2010 Michael Farrar <[email protected]> -License: - /****************************************************************** - . Copyright 2010 by Michael Farrar. All rights reserved. - . This program may not be sold or incorporated into a commercial product, - . in whole or in part, without written consent of Michael Farrar. For - . further information regarding permission for use or reproduction, please - . contact: Michael Farrar at [email protected]. - .******************************************************************/ +Files: src/smith_waterman_altivec.c +Copyright: 2004, Erik Lindahl <[email protected]> + Stockholm Bioinformatics Center, 2004 +License: Apache-2.0 +Files: src/glo[bc]al_sse2.[ch] + src/smith_waterman_sse2.c +Copyright: 2006,2010 Michael Farrar <[email protected]> +License: Academics-only + This program may not be sold or incorporated into a commercial product, + in whole or in part, without written consent of Michael Farrar. For + further information regarding permission for use or reproduction, please + contact: Michael Farrar at [email protected]. + Files: debian/* Copyright: 2015 Steffen Moeller <[email protected]> License: Apache-2.0 Modified: trunk/packages/fasta3/trunk/debian/docs =================================================================== --- trunk/packages/fasta3/trunk/debian/docs 2015-02-09 18:18:47 UTC (rev 18747) +++ trunk/packages/fasta3/trunk/debian/docs 2015-02-10 09:47:21 UTC (rev 18748) @@ -1,2 +1,5 @@ README -doc/* +doc/readme* +doc/README* +doc/changes* +doc/fasta_guide.pdf Deleted: trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX =================================================================== --- trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX 2015-02-09 18:18:47 UTC (rev 18747) +++ trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX 2015-02-10 09:47:21 UTC (rev 18748) @@ -1,20 +0,0 @@ -Document: fasta -Title: Debian fasta Manual -Author: <insert document author here> -Abstract: This manual describes what fasta is - and how it can be used to - manage online manuals on Debian systems. -Section: unknown - -Format: debiandoc-sgml -Files: /usr/share/doc/fasta/fasta.sgml.gz - -Format: postscript -Files: /usr/share/doc/fasta/fasta.ps.gz - -Format: text -Files: /usr/share/doc/fasta/fasta.text.gz - -Format: HTML -Index: /usr/share/doc/fasta/html/index.html -Files: /usr/share/doc/fasta/html/*.html Copied: trunk/packages/fasta3/trunk/debian/fasta3.doc-base (from rev 18744, trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX) =================================================================== --- trunk/packages/fasta3/trunk/debian/fasta3.doc-base (rev 0) +++ trunk/packages/fasta3/trunk/debian/fasta3.doc-base 2015-02-10 09:47:21 UTC (rev 18748) @@ -0,0 +1,15 @@ +Document: fasta3 +Title: The FASTA program package +Author: William R. Pearson +Abstract: This documentation describes the version 36 of the FASTA program + package (see W. R. Pearson and D. J. Lipman (1988), "Improved Tools for + Biological Sequence Analysis", PNAS 85:2444-2448. W. R. Pearson (1996) + "Effective protein sequence comparison" Meth. Enzymol. 266:227-258; + and Pearson et. al. (1997) Genomics 46:24-36 [18]. Version 3 of the + FASTA packages contains many programs for searching DNA and protein + databases and for evaluating statistical significance from randomly + shuffled sequences. +Section: Science/Biology + +Format: pdf +Files: /usr/share/doc/fasta3/fasta_guide.pdf Added: trunk/packages/fasta3/trunk/debian/fasta3.manpages =================================================================== --- trunk/packages/fasta3/trunk/debian/fasta3.manpages (rev 0) +++ trunk/packages/fasta3/trunk/debian/fasta3.manpages 2015-02-10 09:47:21 UTC (rev 18748) @@ -0,0 +1,6 @@ +doc/fasta36.1 +doc/fastf3.1 +doc/fasts3.1 +doc/map_db.1 +doc/prss3.1 +doc/ps_lav.1 Modified: trunk/packages/fasta3/trunk/debian/patches/Makefile.patch =================================================================== --- trunk/packages/fasta3/trunk/debian/patches/Makefile.patch 2015-02-09 18:18:47 UTC (rev 18747) +++ trunk/packages/fasta3/trunk/debian/patches/Makefile.patch 2015-02-10 09:47:21 UTC (rev 18748) @@ -10,3 +10,38 @@ XDIR = /seqprg/bin DROPGSW_NA_O = dropgsw2.o wm_align.o calcons_sw.o +Index: fasta3-36.3.7a/make/Makefile.linux64_sse2 +=================================================================== +--- fasta3-36.3.7a.orig/make/Makefile.linux64_sse2 ++++ fasta3-36.3.7a/make/Makefile.linux64_sse2 +@@ -12,7 +12,7 @@ + + SHELL=/bin/bash + +-CC = gcc -g -O -msse2 ++CC = gcc -g -O -msse2 $(CPPFLAGS) + #CC= gcc -pg -g -O -msse2 -ffast-math + #CC = gcc -g -DDEBUG -msse2 + +@@ -25,7 +25,7 @@ + + # standard options + +-CFLAGS= -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 ++CFLAGS+= -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 + # -I/usr/include/mysql -DMYSQL_DB + # -DSUPERFAMNUM -DSFCHAR="'|'" + +Index: fasta3-36.3.7a/make/Makefile36m.common +=================================================================== +--- fasta3-36.3.7a.orig/make/Makefile36m.common ++++ fasta3-36.3.7a/make/Makefile36m.common +@@ -34,7 +34,7 @@ + # and "-L/usr/lib64/mysql -lmysqlclient -lz" in LIB_M + # some systems may also require a LD_LIBRARY_PATH change + +-LIB_M= -lm -lz ++LIB_M= $(LDFLAGS) -lm -lz + #LIB_M= -L/usr/lib64/mysql -lmysqlclient -lz -lm + NCBL_LIB=ncbl2_mlib.o + #NCBL_LIB=ncbl2_mlib.o mysql_lib.o Modified: trunk/packages/fasta3/trunk/debian/rules =================================================================== --- trunk/packages/fasta3/trunk/debian/rules 2015-02-09 18:18:47 UTC (rev 18747) +++ trunk/packages/fasta3/trunk/debian/rules 2015-02-10 09:47:21 UTC (rev 18748) @@ -12,7 +12,9 @@ MAKEFILE="../make/Makefile.linux64" #endif -#export DEB_BUILD_MAINT_OPTIONS = hardening=+all +export DEB_BUILD_MAINT_OPTIONS = hardening=+all +CFLAGS+=-flto +LDFLAGS+=-flto # package maintainers to append CFLAGS #export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic @@ -26,7 +28,8 @@ cd src && $(MAKE) -f $(MAKEFILE) override_dh_auto_clean: - cd src && $(MAKE) -f $(MAKEFILE) clean-up + if [ -d src ]; then cd src && $(MAKE) -f $(MAKEFILE) clean-up; fi +override_dh_compress: + dh_compress --exclude=.pdf - _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
