[med-svn] [rtax] 01/01: Add Debian dir as provided by Simon Kainz at http://www.familiekainz.at/projekte/linux/rtax/rtax-0.984-all.tgz
Andreas Tille
tille at debian.org
Thu Nov 28 10:08:38 UTC 2013
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository rtax.
commit 60ae02758a56a41a1bde3c14e3b435eaa163c4e9
Author: Andreas Tille <tille at debian.org>
Date: Thu Nov 28 11:12:45 2013 +0100
Add Debian dir as provided by Simon Kainz at http://www.familiekainz.at/projekte/linux/rtax/rtax-0.984-all.tgz
---
debian/README.source | 2 ++
debian/changelog | 10 ++++++
debian/compat | 1 +
debian/control | 17 +++++++++
debian/copyright | 45 ++++++++++++++++++++++++
debian/patches/find_script_path.patch | 47 +++++++++++++++++++++++++
debian/patches/fix-bash-syntax-error.patch | 20 +++++++++++
debian/patches/series | 2 ++
debian/rtax.1 | 56 ++++++++++++++++++++++++++++++
debian/rtax.docs | 1 +
debian/rtax.install | 3 ++
debian/rtax.manpages | 1 +
debian/rules | 5 +++
debian/source/format | 2 ++
debian/upstream | 9 +++++
15 files changed, 221 insertions(+)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..ca68487
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,2 @@
+
+License is contained in the rtax file.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..049f8c8
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,10 @@
+rtax (0.984-1) unstable; urgency=low
+
+ * Initial release. (Closes: #724280)
+ * Removed broken magic to find scripts-subdir,
+ because we know where rtax is installed (set_script_dir.path)
+ * Change interpreter to bash to prevent syntax
+ error warnings (fix-bash-syntax-error.patch)
+ * Added minimal manpage.
+
+ -- Simon Kainz <simon at familiekainz.at> Tue, 27 Nov 2013 09:50:23 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..45a4fb7
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+8
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..37ea8bd
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,17 @@
+Source: rtax
+Maintainer: Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 8)
+Standards-Version: 3.9.4
+Homepage: http://dev.davidsoergel.com/rtax
+
+Package: rtax
+Architecture: all
+Depends: ${misc:Depends},
+ ${perl:Depends}
+Description: Classification of sequence reads of 16S ribosomal RNA gene
+ Short-read technologies for microbial community profiling are increasingly
+ popular, yet previous techniques for assigning taxonomy to paired-end reads
+ perform poorly. RTAX provides rapid taxonomic assignments of paired-end
+ reads using a consensus algorithm.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..82a2528
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,45 @@
+# RTAX: Rapid and accurate taxonomic classification of short paired-end
+# sequence reads from the 16S ribosomal RNA gene.
+#
+# David A. W. Soergel 1*, Rob Knight 2, and Steven E. Brenner 1
+#
+# 1 Department of Plant and Microbial Biology,
+# University of California, Berkeley
+# 2 Howard Hughes Medical Institute and Department of Chemistry
+# and Biochemistry, University of Colorado at Boulder
+# * Corresponding author: soergel at cs.umass.edu
+#
+# http://www.davidsoergel.com/rtax
+#
+# Version 0.984 (August 7, 2013)
+#
+# For usage instructions: just run the script with no arguments
+#
+#
+# Copyright (c) 2011 Regents of the University of California
+#
+# All rights reserved.
+#
+# 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.
+# * Neither the name of the University of California, Berkeley nor the
+# names of its contributors may 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.
diff --git a/debian/patches/find_script_path.patch b/debian/patches/find_script_path.patch
new file mode 100644
index 0000000..ad1b84f
--- /dev/null
+++ b/debian/patches/find_script_path.patch
@@ -0,0 +1,47 @@
+Description: <short summary of the patch>
+As we install the helper scripts using the package management,
+we set scripts hardcoded to /usr/lib/rtax/scripts
+
+ rtax (0.984-1) unstable; urgency=low
+ .
+ * Initial release. (Closes: #724280)
+ * Removed broken magic to find scripts-subdir,
+ because we know where rtax is installed (find_script_path)
+ * Change interpreter to bash to prevent syntax
+ error warnings (fix-bash-syntax-error.patch)
+ * Added minimal manpage.
+Author: Simon Kainz <simon at familiekainz.at>
+Bug-Debian: http://bugs.debian.org/724280
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+--- rtax-0.984.orig/rtax
++++ rtax-0.984/rtax
+@@ -73,15 +73,7 @@ echoerr ''
+
+
+
+-# we want to call subsidiary scripts in the "scripts" subdir, but we don't know where we're installed or what the working directory is.
+-# solution from http://hintsforums.macworld.com/archive/index.php/t-73839.html
+-
+-IFS=$' \t\n'
+-#declare -x PATH=/bin:/usr/bin:/usr/local/bin
+-arg=$0; [[ -L $0 ]] && arg=$(stat -f '%Y' "$0")
+-pth=$(2>/dev/null cd "${arg%/*}" >&2; echo "`pwd -P`/${arg##*/}")
+-par=$(dirname "$pth")
+-scripts="$par/scripts"
++scripts="/usr/lib/rtax/scripts"
+
+ # The above solution works with the widespread GNU Coreutils 5.97. Thanks to Bernd Brandt for this alternate solution for Coreutils 8.5.
+
diff --git a/debian/patches/fix-bash-syntax-error.patch b/debian/patches/fix-bash-syntax-error.patch
new file mode 100644
index 0000000..ccdef78
--- /dev/null
+++ b/debian/patches/fix-bash-syntax-error.patch
@@ -0,0 +1,20 @@
+Description: Change script interpreter to /bin/bash
+ Fixes syntax errors due to differnet if syntax between sh and bash.
+
+Author: Simon Kainz <simon at familiekainz.at>
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Last-Update: 2013-09-12
+
+--- rtax-0.984.orig/greengenes/prepare-greengenes
++++ rtax-0.984/greengenes/prepare-greengenes
+@@ -1,4 +1,4 @@
+-#!/bin/sh
++#!/bin/bash
+
+ cur=`pwd`
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..6981dc4
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+fix-bash-syntax-error.patch
+find_script_path.patch
diff --git a/debian/rtax.1 b/debian/rtax.1
new file mode 100644
index 0000000..dfdbb34
--- /dev/null
+++ b/debian/rtax.1
@@ -0,0 +1,56 @@
+.TH "rtax" 1 "27 Nov 2013"
+.SH "NAME"
+rtax - Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
+.SH "SYNOPSIS"
+.B rtax
+[\fIOPTION\fR]...
+.SH DESCRIPTION
+.PP
+.SH OPTIONS
+.TP 13
+.I \-r refd
+reference database in FASTA format
+.TP 13
+.I \-t taxonomy
+taxonomy file with sequence IDs matching the reference database
+.TP 13
+.I \-a queryA
+FASTA file containing query sequences (single-ended or read 1)
+.TP 13
+.I \-b queryB
+FASTA file containing query sequences (read b, with matching IDs)
+.TP 13
+.I \-x
+Reverse-complement query A sequences (required if they are provided in the reverse sense)
+.TP 13
+.I \-y
+Reverse-complement query B sequences (required if they are provided in the reverse sense)
+.TP 13
+.I \-i regex
+regular expression used to select part of the fasta header to use as the sequence id. Default: "(\\S+)"
+.TP 13
+.I \-l file
+text file containing sequence IDs to process, one per line
+.TP 13
+.I \-d delimiter
+delimiter separating the two reads when provided in a single file
+.TP 13
+.I \-m tempdir
+temporary directory. Will be removed on successful completion, but likely not if there is an error.
+.TP 13
+.I \-f
+for sequences where only one read is available, fall back to single-ended classification. Default: drop these sequences.
+.TP 13
+.I \-g
+for sequences where one read is overly generic, do not fall back to single-ended classification. Default: classify these sequences based on only the more specific read.
+.TP 13
+.I \-o classifications.out
+output path
+.SH EXAMPLES
+A quickstart example can be found here: \fIhttp://dev.davidsoergel.com/trac/rtax/wiki/QuickStart\fR
+.P
+Rtax can also be used within \fIQIIME\fR workflows, se this link for more information: \fIhttp://www.qiime.org/tutorials/rtax.html\fR
+.SH AUTHOR
+This manual page was written by Simon Kainz <simon at familiekainz.at> for the rtax package.
+.P
+Rtax was written by David A. W. Soergel <soergel at cs.umass.edu>.
diff --git a/debian/rtax.docs b/debian/rtax.docs
new file mode 100644
index 0000000..e845566
--- /dev/null
+++ b/debian/rtax.docs
@@ -0,0 +1 @@
+README
diff --git a/debian/rtax.install b/debian/rtax.install
new file mode 100644
index 0000000..804203a
--- /dev/null
+++ b/debian/rtax.install
@@ -0,0 +1,3 @@
+greengenes/* /usr/lib/rtax/greengenes
+scripts/* /usr/lib/rtax/scripts
+rtax /usr/bin
diff --git a/debian/rtax.manpages b/debian/rtax.manpages
new file mode 100644
index 0000000..34777c9
--- /dev/null
+++ b/debian/rtax.manpages
@@ -0,0 +1 @@
+debian/rtax.1
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1330ccd
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,5 @@
+#!/usr/bin/make -f
+%:
+ dh $@
+
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..c3d9f24
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1,2 @@
+3.0 (quilt)
+
diff --git a/debian/upstream b/debian/upstream
new file mode 100644
index 0000000..e6ee6d5
--- /dev/null
+++ b/debian/upstream
@@ -0,0 +1,9 @@
+Name: rtax
+Homepage: http://dev.davidsoergel.com/trac/rtax/
+Bug-Database: http://dev.davidsoergel.com/trac/rtax/report/1
+Bug-Submit: http://dev.davidsoergel.com/trac/rtax/newticket
+Changelog: http://hg.davidsoergel.com/rtax/src/tip/changelog
+Contact: dev at davidsoergel.com
+Cite-As: http://www.nature.com/ismej/journal/vaop/ncurrent/abs/ismej2011208a.html
+Repository: http://hg.davidsoergel.com/rtax
+Repository-Browse: http://hg.davidsoergel.com/rtax/src
\ No newline at end of file
--
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