[med-svn] r18744 - in trunk/packages: . fasta3 fasta3/trunk fasta3/trunk/debian fasta3/trunk/debian/patches fasta3/trunk/debian/source
Steffen Möller
moeller at moszumanska.debian.org
Mon Feb 9 15:22:49 UTC 2015
Author: moeller
Date: 2015-02-09 15:22:48 +0000 (Mon, 09 Feb 2015)
New Revision: 18744
Added:
trunk/packages/fasta3/
trunk/packages/fasta3/trunk/
trunk/packages/fasta3/trunk/debian/
trunk/packages/fasta3/trunk/debian/README.Debian
trunk/packages/fasta3/trunk/debian/README.source
trunk/packages/fasta3/trunk/debian/changelog
trunk/packages/fasta3/trunk/debian/compat
trunk/packages/fasta3/trunk/debian/control
trunk/packages/fasta3/trunk/debian/copyright
trunk/packages/fasta3/trunk/debian/docs
trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX
trunk/packages/fasta3/trunk/debian/fasta3.install
trunk/packages/fasta3/trunk/debian/patches/
trunk/packages/fasta3/trunk/debian/patches/Makefile.patch
trunk/packages/fasta3/trunk/debian/patches/series
trunk/packages/fasta3/trunk/debian/rules
trunk/packages/fasta3/trunk/debian/source/
trunk/packages/fasta3/trunk/debian/source/format
trunk/packages/fasta3/trunk/debian/watch
Log:
Initial packaging of fasta3 - non-free, sadly
Sometimes one wonders what we are still missing.
Anyway, the packaging seems functional, at least
for amd64 this should all just be fine.
I would not mind somebody adopting this work
for me - will add the hardening and lto, but
yet have no exact clue about how to integrate
the automated testing for instance.
The copyright file is not yet completed. Will
do that, too.
Cheers,
Steffen
Property changes on: trunk/packages/fasta3/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/fasta3/trunk/debian/README.Debian
===================================================================
--- trunk/packages/fasta3/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/fasta3/trunk/debian/README.Debian 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1,6 @@
+fasta for Debian
+----------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 09 Feb 2015 15:04:28 +0100
Added: trunk/packages/fasta3/trunk/debian/README.source
===================================================================
--- trunk/packages/fasta3/trunk/debian/README.source (rev 0)
+++ trunk/packages/fasta3/trunk/debian/README.source 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1,10 @@
+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 <moeller at debian.org> Mon, 09 Feb 2015 15:04:28 +0100
+
Added: trunk/packages/fasta3/trunk/debian/changelog
===================================================================
--- trunk/packages/fasta3/trunk/debian/changelog (rev 0)
+++ trunk/packages/fasta3/trunk/debian/changelog 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1,5 @@
+fasta3 (36.3.7a-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 09 Feb 2015 15:04:28 +0100
Added: trunk/packages/fasta3/trunk/debian/compat
===================================================================
--- trunk/packages/fasta3/trunk/debian/compat (rev 0)
+++ trunk/packages/fasta3/trunk/debian/compat 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1 @@
+9
Added: trunk/packages/fasta3/trunk/debian/control
===================================================================
--- trunk/packages/fasta3/trunk/debian/control (rev 0)
+++ trunk/packages/fasta3/trunk/debian/control 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1,58 @@
+Source: fasta3
+Section: non-free/science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Homepage: http://fasta.bioch.virginia.edu
+#Vcs-Git: git://anonscm.debian.org/collab-maint/fasta.git
+#Vcs-Browser: http://anonscm.debian.org/?p=collab-maint/fasta.git;a=summary
+
+Package: fasta3
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: tools for searching collections of biological sequences
+ The FASTA programs find regions of local or global similarity between
+ Protein or DNA sequences, either by searching Protein or DNA databases,
+ or by identifying local duplications within a sequence. Other
+ programs provide information on the statistical significance of an
+ alignment. Like BLAST, FASTA can be used to infer functional and
+ evolutionary relationships between sequences as well as help identify
+ members of gene families.
+ .
+ * Protein
+ .
+ - Protein-protein FASTA
+ - Protein-protein Smith-Waterman (ssearch)
+ - Global Protein-protein (Needleman-Wunsch) (ggsearch)
+ - Global/Local protein-protein (glsearch)
+ - Protein-protein with unordered peptides (fasts)
+ - Protein-protein with mixed peptide sequences (fastf)
+ .
+ * Nucleotide
+ .
+ - Nucleotide-Nucleotide (DNA/RNA fasta)
+ - Ordered Nucleotides vs Nucleotide (fastm)
+ - Un-ordered Nucleotides vs Nucleotide (fasts)
+ .
+ * Translated
+ .
+ - Translated DNA (with frameshifts, e.g. ESTs)
+ vs Proteins (fastx/fasty)
+ - Protein vs Translated DNA (with frameshifts)
+ (tfastx/tfasty)
+ - Peptides vs Translated DNA (tfasts)
+ .
+ * Statistical Significance
+ .
+ - Protein vs Protein shuffle (prss)
+ - DNA vs DNA shuffle (prss)
+ - Translated DNA vs Protein shuffle (prfx)
+ .
+ * Local Duplications
+ .
+ - Local Protein alignments (lalign)
+ - Plot Protein alignment "dot-plot" (plalign)
+ - Local DNA alignments (lalign)
+ - Plot DNA alignment "dot-plot" (plalign)
+
Added: trunk/packages/fasta3/trunk/debian/copyright
===================================================================
--- trunk/packages/fasta3/trunk/debian/copyright (rev 0)
+++ trunk/packages/fasta3/trunk/debian/copyright 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1,43 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: FASTA
+Source: http://faculty.virginia.edu/wrpearson/fasta/fasta3/
+
+Files: *
+Copyright: 1996, 1997, 1998, 1999, 2014 by William R. Pearson and
+ The Rector & Visitors of the University of Virginia
+License: Apache-2.0
+
+Files: src/karlin.c
+Copyright: 1980, 1983 Stephen Altschul
+License: Apache-2.0
+
+Files: src/global_sse2.c
+Copyright: 2010 Michael Farrar <farrar.michael at gmail.com>
+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 farrar.michael at gmail.com.
+ .******************************************************************/
+
+Files: debian/*
+Copyright: 2015 Steffen Moeller <moeller at debian.org>
+License: Apache-2.0
+
+License: Apache-2.0
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+ .
+ http://www.apache.org/licenses/LICENSE-2.0
+ .
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+ .
+ On Debian systems, the complete text of the Apache version 2.0 license
+ can be found in "/usr/share/common-licenses/Apache-2.0".
Added: trunk/packages/fasta3/trunk/debian/docs
===================================================================
--- trunk/packages/fasta3/trunk/debian/docs (rev 0)
+++ trunk/packages/fasta3/trunk/debian/docs 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1,2 @@
+README
+doc/*
Added: trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX
===================================================================
--- trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX (rev 0)
+++ trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1,20 @@
+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
Added: trunk/packages/fasta3/trunk/debian/fasta3.install
===================================================================
--- trunk/packages/fasta3/trunk/debian/fasta3.install (rev 0)
+++ trunk/packages/fasta3/trunk/debian/fasta3.install 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1 @@
+bin/[a-z]* usr/bin
Added: trunk/packages/fasta3/trunk/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/fasta3/trunk/debian/patches/Makefile.patch (rev 0)
+++ trunk/packages/fasta3/trunk/debian/patches/Makefile.patch 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1,12 @@
+Index: fasta3-36.3.7a/make/Makefile
+===================================================================
+--- fasta3-36.3.7a.orig/make/Makefile
++++ fasta3-36.3.7a/make/Makefile
+@@ -34,6 +34,7 @@
+ THR_LIBS = -lpthread
+ THR_CC =
+
++BIN = ../bin
+ XDIR = /seqprg/bin
+
+ DROPGSW_NA_O = dropgsw2.o wm_align.o calcons_sw.o
Added: trunk/packages/fasta3/trunk/debian/patches/series
===================================================================
--- trunk/packages/fasta3/trunk/debian/patches/series (rev 0)
+++ trunk/packages/fasta3/trunk/debian/patches/series 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1 @@
+Makefile.patch
Added: trunk/packages/fasta3/trunk/debian/rules
===================================================================
--- trunk/packages/fasta3/trunk/debian/rules (rev 0)
+++ trunk/packages/fasta3/trunk/debian/rules 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1,32 @@
+#!/usr/bin/make -f
+#DH_VERBOSE = 1
+
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+ARCH=`dpkg-architecture -qDEB_TARGET_GNU_CPU`
+
+#MAKEFILE="../make/Makefile"
+#
+#ifeq (x86_64,$(ARCH))
+MAKEFILE="../make/Makefile.linux64"
+#endif
+
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+# package maintainers to append CFLAGS
+#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
+# package maintainers to append LDFLAGS
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ cd src && $(MAKE) -f $(MAKEFILE)
+
+override_dh_auto_clean:
+ cd src && $(MAKE) -f $(MAKEFILE) clean-up
+
+
+
Property changes on: trunk/packages/fasta3/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/fasta3/trunk/debian/source/format
===================================================================
--- trunk/packages/fasta3/trunk/debian/source/format (rev 0)
+++ trunk/packages/fasta3/trunk/debian/source/format 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/fasta3/trunk/debian/watch
===================================================================
--- trunk/packages/fasta3/trunk/debian/watch (rev 0)
+++ trunk/packages/fasta3/trunk/debian/watch 2015-02-09 15:22:48 UTC (rev 18744)
@@ -0,0 +1,2 @@
+version=3
+http://faculty.virginia.edu/wrpearson/fasta/fasta3/fasta-(3.*)\.tar\.gz
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