[med-svn] [Git][med-team/sweed][master] Import Debian changes 3.2.1+dfsg-1

Andreas Tille gitlab at salsa.debian.org
Wed Jul 4 07:07:08 BST 2018 

Andreas Tille pushed to branch master at Debian Med / sweed


Commits:
5aa75c85 by Steffen Moeller at 2018-07-04T00:54:44+02:00
Import Debian changes 3.2.1+dfsg-1

sweed (3.2.1+dfsg-1) unstable; urgency=medium

  * Initial release (Closes: #902960)

- - - - -


11 changed files:

- + debian/README.source
- + debian/SweeD.1
- + debian/changelog
- + debian/compat
- + debian/control
- + debian/copyright
- + debian/manpages
- + debian/rules
- + debian/source/format
- + debian/sweed.install
- + debian/upstream/metadata


Changes:

=====================================
debian/README.source
=====================================
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1 @@
+The unfortunate original tarball contained object files.


=====================================
debian/SweeD.1
=====================================
--- /dev/null
+++ b/debian/SweeD.1
@@ -0,0 +1,76 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH SWEED "1" "July 2018" "SweeD " "User Commands"
+.SH NAME
+SweeD \- Assess SNPs for their contribution to genetic drift
+.SH DESCRIPTION
+.IP
+SweeD version 3.1 released by Nikolaos Alachiotis and Pavlos Pavlidis in January 2013.
+.IP
+SweeD | SweeD\-P | SweeD\-C | SweeD\-P\-C
+.HP
+\fB\-name\fR runName
+.HP
+\fB\-input\fR inputFile
+.HP
+\fB\-grid\fR gridNumber
+.IP
+[\-folded]
+[\-monomorphic]
+[\-strictPolymorphic]
+[\-isfs inputSFS]
+[\-osfs outputSFS]
+[\-osf outputSF]
+[\-threads threadNumber]
+[\-checkpoint checkpointInterval]
+[\-eN timeT sizeX]
+[\-G rateG]
+[\-s sequences]
+[\-h|\-help]
+[\-v|version]
+.TP
+\fB\-name\fR <STRING>
+Specifies a name for the run and the output files.
+.TP
+\fB\-input\fR <STRING>
+Specifies the name of the input alignment file.
+Supported file formats: SF (Sweep Finder) format.
+.TP
+\fB\-grid\fR <INTEGER>
+Specifies the number of positions in the alignment where the CLR will be computed.
+.TP
+\fB\-folded\fR
+Considers the SFS folded (the ancestral and derived states can not be distinguished).
+.TP
+\fB\-monomorphic\fR
+Includes the monomorphic sites in the analysis. The default action is to discard them.
+.TP
+\fB\-strictPolymorphic\fR
+Does not include *potential monomorphic* sites in the analysis. These are sites where for some sequences the state is missing and the remaining are monomorphic.
+.TP
+\fB\-isfs\fR <STRING>
+Specifies the name of the input SFS file.
+.TP
+\fB\-osfs\fR <STRING>
+Specifies the name of the output SFS file.
+.TP
+\fB\-osf\fR <STRING>
+Specifies the name of the output SF file.
+.TP
+\fB\-threads\fR <INTEGER>
+Specifies the number of threads.
+.TP
+\fB\-checkpoint\fR <INTEGER>
+Specifies the checkpoint interval in seconds (default: 3600).
+.TP
+\fB\-eN\fR <FLOAT> <FLOAT>
+Sets population size to sizeX*N0 at time timeT, where N0 is the present\-day population size.
+.TP
+\fB\-G\fR <FLOAT>
+Sets the growth rate of the population size at time 0. The growth rate continues to be exponential until
+the \fB\-eN\fR command specifies a constant population size.
+.TP
+\fB\-s\fR <INTEGER>
+Specifies the number of sequences when no input file is provided.
+.TP
+\fB\-h\fR|\-help
+Displays this help message.


=====================================
debian/changelog
=====================================
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+sweed (3.2.1+dfsg-1) unstable; urgency=medium
+
+  * Initial release (Closes: #902960)
+
+ -- Steffen Moeller <moeller at debian.org>  Wed, 04 Jul 2018 00:25:27 +0200


=====================================
debian/compat
=====================================
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+11


=====================================
debian/control
=====================================
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,19 @@
+Source: sweed
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 11)
+Standards-Version: 4.1.3
+Homepage: https://sco.h-its.org/exelixis/web/software/sweed/
+Vcs-Browser: https://salsa.debian.org/med-team/sweed
+Vcs-Git: https://salsa.debian.org/med-team/sweed.git
+
+Package: sweed
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: assessment of SNPs for their evolutionary advantage
+ Biological sequences are available in ever increasing abundance across
+ ever larger populations for ever increasing fractions of the genome. This
+ tool sorts the SNPs for their active or passive contribution to a genetic
+ drift, i.e. to see particular sequences at a higher fraction over time.
+


=====================================
debian/copyright
=====================================
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,28 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SweeD
+Source: https://sco.h-its.org/exelixis/web/software/sweed/index.html
+
+Files: *
+Copyright: 2011-12 Nikolaos Alachiotis and Pavlos Pavlidis
+License: GPL-2.0+
+
+Files: debian/*
+Copyright: 2018 Steffen Moeller <moeller at debian.org>
+License: GPL-2.0+
+
+License: GPL-2.0+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".


=====================================
debian/manpages
=====================================
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/SweeD.1


=====================================
debian/rules
=====================================
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+# See debhelper(7) (uncomment to enable)
+# output every command that modifies files on the build system.
+#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 $@
+
+override_dh_auto_build:
+	$(MAKE) -f Makefile.gcc $*
+
+
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -f *.o *~ SweeD


=====================================
debian/source/format
=====================================
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)


=====================================
debian/sweed.install
=====================================
--- /dev/null
+++ b/debian/sweed.install
@@ -0,0 +1 @@
+SweeD usr/bin


=====================================
debian/upstream/metadata
=====================================
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,21 @@
+Reference:
+ - Author: >
+    Pavlos Pavlidis and Daniel Živković and Alexandros Stamatakis and
+    Nikolaos Alachiotis
+   Title: >
+    SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands
+    of Genomes
+   Journal: Molecular Biology and Evolution
+   Volume: 30
+   Issue: 9
+   Day: 1
+   Month: 9
+   Year: 2013
+   Pages: 2224–2234
+   DOI: 10.1093/molbev/mst112
+   URL: https://academic.oup.com/mbe/article/30/9/2224/999783
+   ePrint: >
+    https://academic.oup.com/mbe/article-pdf/30/9/2224/13175153/mst112.pdf
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_08598



View it on GitLab: https://salsa.debian.org/med-team/sweed/commit/5aa75c857256e069a2b0be8811c1ec70c9e2f153

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