[med-svn] [parsinsert] 02/15: New package wanted by QIIME 1.8.0
Andreas Tille
tille at debian.org
Tue Aug 22 11:07:11 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository parsinsert.
commit 4b32968fb3683f7520a7f3cb5c33a77ff9b802cf
Author: Tim Booth <tbooth at ceh.ac.uk>
Date: Thu Feb 27 15:33:03 2014 +0000
New package wanted by QIIME 1.8.0
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 16 ++++++++++++++++
debian/copyright | 27 +++++++++++++++++++++++++++
debian/install | 1 +
debian/manpages | 1 +
debian/parsinsert.1 | 40 ++++++++++++++++++++++++++++++++++++++++
debian/rules | 20 ++++++++++++++++++++
debian/source/format | 1 +
debian/watch | 2 ++
10 files changed, 114 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..4feae65
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+parsinsert (1.04-0biolinux1) precise; urgency=low
+
+ * New package to support QIIME
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 16 Aug 2013 12:09:01 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..82112af
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,16 @@
+Source: parsinsert
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>
+Standards-Version: 3.9.3
+Build-Depends: debhelper (>= 9)
+Homepage: http://sourceforge.net/projects/parsinsert/
+
+Package: parsinsert
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Parsimonious Insertion of unclassified sequences into phylogenetic trees
+ ParsInsert efficiently produces both a phylogenetic tree and taxonomic
+ classification for sequences for microbial community sequence analysis. This
+ is a C++ implementation of the Parsimonious Insertion algorithm.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..0295ef9
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,27 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ParsInsert
+Upstream-Contact: David Knox <david.knox at colorado.edu>
+Source: http://parsinsert.sourceforge.net
+
+Files: *
+Copyright: © 2007-2011 David Knox
+License: GPL-3
+ This program 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 3 of the License, or
+ (at your option) any later version.
+ .
+ This program 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.
+ .
+ On Debian systems, the full text of the GNU General Public License version 3
+ can be found in the file `/usr/share/common-licenses/GPL-3'.
+
+Files: debian/*
+Copyright: © 2014 Tim Booth <tbooth at ceh.ac.uk>
+License: GPL-3
+ On Debian systems, the full text of the GNU General Public License version 3
+ can be found in the file `/usr/share/common-licenses/GPL-3'.
+
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..cd544e9
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+parsinsert /usr/bin
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/parsinsert.1 b/debian/parsinsert.1
new file mode 100644
index 0000000..7c6f8e4
--- /dev/null
+++ b/debian/parsinsert.1
@@ -0,0 +1,40 @@
+.\" DO MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH PARSINSERT "1" "February 2014" "parsinsert 1.04" "User Commands"
+.SH NAME
+ParsInsert \- Parsimonious Insertion of unclassified sequences into phylogenetic tree
+.SH DESCRIPTION
+.PP
+\fBparsinsert [options] <insert_sequences>\fR
+.PP
+Perform Insertion of Sequences into Given Tree
+.HP
+\fB\-m\fR <mask file> \- read mask from this file
+.TP
+\fB\-s\fR <tree sequences> \- read core tree sequences from this file
+(default: PI_Tree.fasta)
+.TP
+\fB\-t\fR <tree file> \- read core tree from this file
+(default: PI_Tree.tree)
+.HP
+\fB\-x\fR <tree taxonomy> \- read core tree taxomony from this file
+.TP
+\fB\-o\fR <output file> \- output taxonomy for each insert sequence to this file
+(default: PI_Results.log)
+.HP
+\fB\-l\fR [\-|<log file>] \- create log file (default is ParsInsert.log)
+.HP
+\fB\-n\fR# \- number of best matches to display
+.HP
+\fB\-c\fR# \- percent threshold cutoff
+.HP
+\fB\-p\fR \- print node comments in newick file
+.HP
+\fB\-D\fR# \- print branch lengths using # decimal places
+tree sequence file: PI_Tree.fasta
+.SH LICENSE
+Copyright (C) 2007\-2011 David Knox
+
+This program comes with ABSOLUTELY NO WARRANTY
+
+This is free software, and you are welcome to redistribute under certain
+conditions \- see /usr/share/common-licenses/GPL-3.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..7887994
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,20 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ dh_auto_build
+ mv ParsInsert parsinsert
+
+
+override_dh_auto_clean:
+ mv parsinsert ParsInsert || true
+ dh_auto_clean
+
+# Note a manpage was generated using:
+# help2man -N ./parsinsert --version-string=1.04 > debian/parsinsert.1
+# But this was then manually edited, so it is not rebuilt automatically.
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..71d631b
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/parsinsert/ParsInsert\.([\d\.]+)\.tgz
--
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