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commit 057869c093b1c105aa3cc37b4cf8580134cf18e6 Author: Tim Booth <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Tim Booth <[email protected]> +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 <[email protected]> + 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 <[email protected]> +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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/clearcut.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
