Author: moeller Date: 2010-06-25 23:01:25 +0000 (Fri, 25 Jun 2010) New Revision: 4935
Added: trunk/packages/python-nast/ trunk/packages/python-nast/trunk/ trunk/packages/python-nast/trunk/debian/ trunk/packages/python-nast/trunk/debian/source/ trunk/packages/python-nast/trunk/debian/watch Removed: trunk/packages/python-nast/trunk/debian/compat trunk/packages/python-nast/trunk/debian/patches/ trunk/packages/python-nast/trunk/debian/python-cogent.doc-base.EX trunk/packages/python-nast/trunk/debian/python-cogent.prerm.debhelper trunk/packages/python-nast/trunk/debian/python-cogent.substvars trunk/packages/python-nast/trunk/debian/watch Modified: trunk/packages/python-nast/trunk/debian/README.source trunk/packages/python-nast/trunk/debian/changelog trunk/packages/python-nast/trunk/debian/control trunk/packages/python-nast/trunk/debian/copyright trunk/packages/python-nast/trunk/debian/docs trunk/packages/python-nast/trunk/debian/pyversions Log: Iinital attempt to package python-nast Modified: trunk/packages/python-nast/trunk/debian/README.source =================================================================== --- trunk/packages/python-cogent/trunk/debian/README.source 2010-06-25 16:33:10 UTC (rev 4931) +++ trunk/packages/python-nast/trunk/debian/README.source 2010-06-25 23:01:25 UTC (rev 4935) @@ -1,8 +1,2 @@ -python-cogent for Debian --------------------------- - -All source is left intact, except for obvious adjustments to the shebang -line to have it point to /usr/bin/python. - - - +python-nast for Debian +---------------------- Modified: trunk/packages/python-nast/trunk/debian/changelog =================================================================== --- trunk/packages/python-cogent/trunk/debian/changelog 2010-06-25 16:33:10 UTC (rev 4931) +++ trunk/packages/python-nast/trunk/debian/changelog 2010-06-25 23:01:25 UTC (rev 4935) @@ -1,6 +1,6 @@ -python-cogent (1.4.1-1) unstable; urgency=low +python-nast (1.1-1) unstable; urgency=low - * Initial release (Closes: #587161) + * Initial release (Closes: #587189) -- Sri Girish Srinivasa Murthy <[email protected]> Fri, 25 Jun 2010 17:23:58 +0200 Deleted: trunk/packages/python-nast/trunk/debian/compat =================================================================== --- trunk/packages/python-cogent/trunk/debian/compat 2010-06-25 16:33:10 UTC (rev 4931) +++ trunk/packages/python-nast/trunk/debian/compat 2010-06-25 23:01:25 UTC (rev 4935) @@ -1 +0,0 @@ -7 Modified: trunk/packages/python-nast/trunk/debian/control =================================================================== --- trunk/packages/python-cogent/trunk/debian/control 2010-06-25 16:33:10 UTC (rev 4931) +++ trunk/packages/python-nast/trunk/debian/control 2010-06-25 23:01:25 UTC (rev 4935) @@ -1,19 +1,38 @@ -Source: python-cogent +Source: python-nast Section: python Priority: extra Maintainer: Sri Girish Srinivasa Murthy <[email protected]> -Build-Depends: debhelper (>= 7), cdbs, python, python-central, python-numpy (>= 1.3.0) +Uploaders: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 7), cdbs, python, python-central, python-cogent Standards-Version: 3.8.4 -Homepage: http://pycogent.sourceforge.net/ +Homepage: http://pynast.sourceforge.net/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/python-nast/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/python-nast/trunk/ -Package: python-cogent +Package: python-nast Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends} -Description: framework for genomic biology - PyCogent is a software library for genomic biology. It is a fully - integrated and thoroughly tested framework for: controlling third-party - applications; devising workflows; querying databases; conducting novel - probabilistic analyses of biological sequence evolution; and generating - publication quality graphics. It is distinguished by many unique built-in - capabilities (such as true codon alignment) and the frequent addition - of entirely new methods for the analysis of genomic data. +Description: alignment of short DNA sequences + The package provices a reimplementation of the Nearest Alignment + Space Termination tool in python. It was prepared for next generation + sequencers. + . + Given a set of sequences and a template alignment, PyNAST will align the + input sequences against the template alignment, and return a multiple + sequence alignment which contains the same number of positions (or + columns) as the template alignment. This facilitates the analysis of new + sequences in the context of existing alignments, and additional data + derived from existing alignments such as phylogenetic trees. Because + any protein or nucleic acid sequences and template alignments can be + provided, PyNAST is not limited to the analysis of 16s rDNA sequences. + . + Since version 1.1, PyNAST no longer exactly matches the output + of the origianl NAST program. Instead it focuses on getting better + alignments. Users who wish to exactly match the results of NAST should + download PyNAST 1.0. + . + PyNAST: a flexible tool for aligning sequences to a template + alignment. J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, + Todd Z. DeSantis, Gary L. Andersen, and Rob Knight. January 15, 2010, + DOI 10.1093/bioinformatics/btp636. Bioinformatics 26: 266-267. + Modified: trunk/packages/python-nast/trunk/debian/copyright =================================================================== --- trunk/packages/python-cogent/trunk/debian/copyright 2010-06-25 16:33:10 UTC (rev 4931) +++ trunk/packages/python-nast/trunk/debian/copyright 2010-06-25 23:01:25 UTC (rev 4935) @@ -1,27 +1,27 @@ This work was packaged for Debian by: - root <r...@unknown> on Fri, 25 Jun 2010 17:23:58 +0200 + Sri Girish Srinivasa Murthy <[email protected]> + and Steffen Moeller <[email protected]> + on Fri, 25 Jun 2010 17:23:58 +0200 -It was downloaded from <http://pycogent.sorceforge.net> +It was downloaded from <http://pynast.sorceforge.net> -Upstream Authors: +Upstream Author: - Gavin Huttley <[email protected]> - Andrew Butterfield - Peter Maxwell - Rob Knight + Greg Caporaso Copyright: - Copyright 2007-2009, The Cogent Project" + Copyright 2010, The PyNAST Project License: - GPL-2+ + GPL-2 The Debian packaging is: - Copyright (C) 2010 root <r...@unknown> + Copyright (C) 2010 Sri Girish Srinivasa Murthy <[email protected]> + and Steffen Moeller <[email protected]> and is licensed under the same copyright, see `/usr/share/common-licenses/GPL-2'. Modified: trunk/packages/python-nast/trunk/debian/docs =================================================================== --- trunk/packages/python-cogent/trunk/debian/docs 2010-06-25 16:33:10 UTC (rev 4931) +++ trunk/packages/python-nast/trunk/debian/docs 2010-06-25 23:01:25 UTC (rev 4935) @@ -1,3 +1,2 @@ -cogent-requirements.txt -NumpyPortingNotes.txt README +doc/* Deleted: trunk/packages/python-nast/trunk/debian/python-cogent.doc-base.EX =================================================================== --- trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base.EX 2010-06-25 16:33:10 UTC (rev 4931) +++ trunk/packages/python-nast/trunk/debian/python-cogent.doc-base.EX 2010-06-25 23:01:25 UTC (rev 4935) @@ -1,20 +0,0 @@ -Document: python-pycogent -Title: Debian python-pycogent Manual -Author: <insert document author here> -Abstract: This manual describes what python-pycogent is - and how it can be used to - manage online manuals on Debian systems. -Section: unknown - -Format: debiandoc-sgml -Files: /usr/share/doc/python-pycogent/python-pycogent.sgml.gz - -Format: postscript -Files: /usr/share/doc/python-pycogent/python-pycogent.ps.gz - -Format: text -Files: /usr/share/doc/python-pycogent/python-pycogent.text.gz - -Format: HTML -Index: /usr/share/doc/python-pycogent/html/index.html -Files: /usr/share/doc/python-pycogent/html/*.html Deleted: trunk/packages/python-nast/trunk/debian/python-cogent.prerm.debhelper =================================================================== --- trunk/packages/python-cogent/trunk/debian/python-cogent.prerm.debhelper 2010-06-25 16:33:10 UTC (rev 4931) +++ trunk/packages/python-nast/trunk/debian/python-cogent.prerm.debhelper 2010-06-25 23:01:25 UTC (rev 4935) @@ -1,45 +0,0 @@ -# Automatically added by dh_pycentral -case "$1" in remove|upgrade) - pkgremove=y -esac -if [ -f /var/lib/pycentral/python-cogent.pkgremove ] || [ -f /var/lib/pycentral/pkgremove ]; then - pkgremove=y -fi -if [ "$pkgremove" = y ]; then -if which python >/dev/null 2>&1 && which pycentral >/dev/null 2>&1; then - pycentral pkgremove python-cogent -else - flist=$(tempfile) - slist=$(tempfile) - dpkg -L python-cogent | tee $flist | \ - while read n; do - case "$n" in - /usr/share/pyshared/*) - n2=${n#/usr/share/pyshared/*} - case "$n" in - *.py) echo "p $n";; - *) [ -d "$n" ] && echo "d $n2" || echo "f $n2" - esac - ;; - *) continue - esac - done > $slist - if [ -s $slist ]; then - for d in /usr/lib/python[0-9].[0-9]/????-packages; do - case "$d" in */python2.1/*|*/python2.2/*) continue; esac - while read t n; do - case "$t" in - p) rm -f $d/$n $d/${n}[co];; - d) rmdir $d/$n 2>/dev/null || true;; - *) rm -f $d/$n - esac - done < $slist - done - fi - awk '/\/usr\/share\/pyshared/ {next} /\.py$/ {print $0"c\n" $0"o"}' $flist \ - | xargs -r rm -f >&2 - rm -f $flist $slist -fi -rm -f /var/lib/pycentral/python-cogent.pkgremove -fi -# End automatically added section Deleted: trunk/packages/python-nast/trunk/debian/python-cogent.substvars =================================================================== --- trunk/packages/python-cogent/trunk/debian/python-cogent.substvars 2010-06-25 16:33:10 UTC (rev 4931) +++ trunk/packages/python-nast/trunk/debian/python-cogent.substvars 2010-06-25 23:01:25 UTC (rev 4935) @@ -1,5 +0,0 @@ -python:Versions=2.6 -python:Provides=python2.6-cogent -python:Depends=python (<< 2.7), python (>= 2.6), python-central (>= 0.6.11) -shlibs:Depends=libc6 (>= 2.3.4) -misc:Depends= Modified: trunk/packages/python-nast/trunk/debian/pyversions =================================================================== --- trunk/packages/python-cogent/trunk/debian/pyversions 2010-06-25 16:33:10 UTC (rev 4931) +++ trunk/packages/python-nast/trunk/debian/pyversions 2010-06-25 23:01:25 UTC (rev 4935) @@ -1 +1 @@ -2.6 +all Deleted: trunk/packages/python-nast/trunk/debian/watch =================================================================== --- trunk/packages/python-cogent/trunk/debian/watch 2010-06-25 16:33:10 UTC (rev 4931) +++ trunk/packages/python-nast/trunk/debian/watch 2010-06-25 23:01:25 UTC (rev 4935) @@ -1,2 +0,0 @@ -version=3 -http://sf.net/pycogent/PyCogent-(.*)\.tar\.gz Copied: trunk/packages/python-nast/trunk/debian/watch (from rev 4932, trunk/packages/python-cogent/trunk/debian/watch) =================================================================== --- trunk/packages/python-nast/trunk/debian/watch (rev 0) +++ trunk/packages/python-nast/trunk/debian/watch 2010-06-25 23:01:25 UTC (rev 4935) @@ -0,0 +1,2 @@ +version=3 +http://sf.net/pynast/PyNAST-([.0-9]+)\.tgz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
