[med-svn] [clearcut] 02/12: Clearcut package done. Any remaining references to ParsInsert are due to copy-and-paste lazyness, but I think I got them all.
Andreas Tille
tille at debian.org
Tue Nov 14 07:36:45 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository clearcut.
commit 057869c093b1c105aa3cc37b4cf8580134cf18e6
Author: Tim Booth <tbooth at ceh.ac.uk>
Date: Thu Feb 27 12:03:32 2014 +0000
Clearcut package done. Any remaining references to ParsInsert are
due to copy-and-paste lazyness, but I think I got them all.
---
debian/changelog | 5 ++
debian/clearcut.1 | 82 +++++++++++++++++++++++++++++++++
debian/compat | 1 +
debian/control | 23 ++++++++++
debian/copyright | 91 +++++++++++++++++++++++++++++++++++++
debian/docs | 1 +
debian/examples | 1 +
debian/install | 1 +
debian/manpages | 1 +
debian/patches/mothur_trivial_patch | 15 ++++++
debian/patches/series | 1 +
debian/rules | 14 ++++++
debian/source/format | 1 +
debian/watch | 2 +
14 files changed, 239 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..2a77ef9
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+clearcut (1.0.9-0biolinux1) precise; urgency=low
+
+ * New package to support QIIME
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 21 Feb 2014 18:52:48 +0000
diff --git a/debian/clearcut.1 b/debian/clearcut.1
new file mode 100644
index 0000000..cf009af
--- /dev/null
+++ b/debian/clearcut.1
@@ -0,0 +1,82 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH CLEARCUT "1" "February 2014" "Clearcut Version: 1.0.9" "User Commands"
+.SH NAME
+Clearcut \- Relaxed Neighbor Joining
+.SH SYNOPSIS
+.B clearcut
+--in=<infilename> --out=<outfilename> [\fIoptions\fR]...
+.SH DESCRIPTION
+.SS ""
+.SS "GENERAL OPTIONS:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Display this information.
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+Print the version of this program.
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+More output. (Default: OFF)
+.TP
+\fB\-q\fR, \fB\-\-quiet\fR
+Silent operation. (Default: ON)
+.TP
+\fB\-s\fR, \fB\-\-seed=\fR<seed>
+Explicitly set the PRNG seed to a specific value.
+.TP
+\fB\-r\fR, \fB\-\-norandom\fR
+Attempt joins deterministically. (Default: OFF)
+.TP
+\fB\-S\fR, \fB\-\-shuffle\fR
+Randomly shuffle the distance matrix. (Default: OFF)
+.TP
+\fB\-N\fR, \fB\-\-neighbor\fR
+Use traditional Neighbor\-Joining algorithm. (Default: OFF)
+.SS "INPUT OPTIONS:"
+.TP
+\fB\-I\fR, \fB\-\-stdin\fR
+Read input from STDIN.
+.TP
+\fB\-d\fR, \fB\-\-distance\fR
+Input file is a distance matrix. (Default: ON)
+.TP
+\fB\-a\fR, \fB\-\-alignment\fR
+Input file is a set of aligned sequences. (Default: OFF)
+.TP
+\fB\-D\fR, \fB\-\-DNA\fR
+Input alignment are DNA sequences.
+.TP
+\fB\-P\fR, \fB\-\-protein\fR
+Input alignment are protein sequences.
+.SS "CORRECTION MODEL FOR COMPUTING DISTANCE MATRIX (Default: NO Correction):"
+.TP
+\fB\-j\fR, \fB\-\-jukes\fR
+Use Jukes\-Cantor correction for computing distance matrix.
+.TP
+\fB\-k\fR, \fB\-\-kimura\fR
+Use Kimura correction for distance matrix.
+.SS "OUTPUT OPTIONS:"
+.TP
+\fB\-O\fR, \fB\-\-stdout\fR
+Output tree to STDOUT.
+.HP
+\fB\-m\fR, \fB\-\-matrixout=\fR<file> Output distance matrix to specified file.
+.TP
+\fB\-n\fR, \fB\-\-ntrees=\fR<n>
+Output n trees. (Default: 1)
+.TP
+\fB\-e\fR, \fB\-\-expblen\fR
+Exponential notation for branch lengths. (Default: OFF)
+.TP
+\fB\-E\fR, \fB\-\-expdist\fR
+Exponential notation in distance output. (Default: OFF)
+.SS "EXAMPLES:"
+Compute tree by supplying distance matrix via stdin:
+
+.IP
+clearcut \fB\-\-distance\fR < distances.txt > treefile.tre
+.TP
+Compute tree by supplying an alignment of DNA sequences from a file:
+
+.IP
+clearcut \fB\-\-alignment\fR \fB\-\-DNA\fR \fB\-\-in\fR=\fIalignment\fR.txt \fB\-\-out\fR=\fItreefile\fR.tre
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..35490c2
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,23 @@
+Source: clearcut
+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>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.3
+Homepage: http://bioinformatics.hungry.com/clearcut/
+
+Package: clearcut
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Relaxed Neighbor Joining
+ Clearcut is the reference implementation for the Relaxed Neighbor Joining (RNJ)
+ algorithm by J. Evans, L. Sheneman, and J. Foster from the Initiative
+ for Bioinformatics and Evolutionary Studies (IBEST) at the University of
+ Idaho.
+ .
+ Details of RNJ are published here:
+ .
+ Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining:
+ A Fast Distance-Based Phylogenetic Tree Construction Method,
+ J. Mol. Evol., 62, 785-792
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..ddd3f5e
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,91 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Clearcut
+Upstream-Contact: Luke Sheneman
+Source: http://bioinformatics.hungry.com/clearcut/
+
+Files: *
+Copyright: Copyright (c) 2004, Luke Sheneman
+License:
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ + Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ + Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in
+ the documentation and/or other materials provided with the
+ distribution.
+ + The names of its contributors may not be used to endorse or promote
+ products derived from this software without specific prior
+ written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.
+
+Files: getopt_long.*
+Copyright: (c) 2004 Koji Arai
+License:
+ Permission is hereby granted, free of charge, to any person
+ obtaining a copy of this software and associated documentation files
+ (the "Software"), to deal in the Software without restriction,
+ including without limitation the rights to use, copy, modify, merge,
+ publish, distribute, sublicense, and/or sell copies of the Software,
+ and to permit persons to whom the Software is furnished to do so,
+ subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+
+Files: prng.*
+Copyright: (C) 1997-2002, Makoto Matsumoto <m-mat at math.sci.hiroshima-u.ac.jp>
+ and Takuji Nishimura, All rights reserved.
+License:
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+
+ 3. The names of its contributors may not be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: debian/*
+Copyright: © 2014 Tim Booth <tbooth at ceh.ac.uk>
+License: As above
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..e845566
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..e39721e
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+examples/*
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..0628419
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+clearcut /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/patches/mothur_trivial_patch b/debian/patches/mothur_trivial_patch
new file mode 100644
index 0000000..3581c51
--- /dev/null
+++ b/debian/patches/mothur_trivial_patch
@@ -0,0 +1,15 @@
+The source posted on the Mothur page at http://www.mothur.org/wiki/Download_Clearcut
+is identical to the upstream bar this one change.
+I have not investigated why, but I assume it's there for a reason and
+QIIME says it wants the Mothur version.
+--- a/clearcut.c
++++ b/clearcut.c
+@@ -1494,7 +1494,7 @@
+ }
+
+ NJ_output_tree2(fp, nj_args, tree, tree, dmat);
+- fprintf(fp, " ;\n");
++ fprintf(fp, ";\n");
+
+ if(!nj_args->stdout_flag) {
+ fclose(fp);
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..1c9195f
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+mothur_trivial_patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1a13fef
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
+
+override_dh_compress:
+ dh_compress -X.dist
+
+# Note a manpage was generated using:
+# help2man -N ./clearcut > debian/clearcut.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..01bfcf4
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://bioinformatics.hungry.com/clearcut/clearcut-([0-9.]+).tar.gz
--
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