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debian/changelog
View file @ be215cf8
wise (2.4.1-21) unstable; urgency=medium
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Long description for all packages
* Drop unneeded Testsuite: autopkgtest
-- Andreas Tille <tille@debian.org> Thu, 04 Oct 2018 14:49:55 +0200
wise (2.4.1-20) unstable; urgency=medium
* Moved packaging from SVN to Git
......
debian/control
View file @ be215cf8
......@@ -5,16 +5,15 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Testsuite: autopkgtest
Build-Depends: debhelper (>= 10),
Build-Depends: debhelper (>= 11~),
texlive-latex-base,
texlive-extra-utils,
hevea,
docbook-to-man,
libglib2.0-dev
Standards-Version: 4.1.0
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/wise.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/wise.git
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/wise
Vcs-Git: https://salsa.debian.org/med-team/wise.git
Homepage: http://www.ebi.ac.uk/~birney/wise2/
Package: wise
......@@ -54,6 +53,29 @@ Depends: ${misc:Depends}
Recommends: wise (= ${source:Version}),
xpdf-reader | pdf-viewer
Description: documentation for the wise package
Wise2 is a package focused on comparisons of biopolymers, commonly DNA
and protein sequences. There are many other packages which do
this, probably the best known being BLAST package (from NCBI) and the
Fasta package (from Bill Pearson). There are other packages, such as
the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
on hidden Markov models (HMMs) of biopolymers.
.
Wise2's particular forte is the comparison of DNA sequence at the level
of its protein translation. This comparison allows the simultaneous
prediction of say gene structure with homology based alignment.
.
Wise2 also contains other algorithms, such as the venerable Smith-Waterman
algorithm, or more modern ones such as Stephen Altschul's generalised
gap penalties, or even experimental ones developed in house, such as
dba. The development of these algorithms is due to the ease of developing
such algorithms in the environment used by Wise2.
.
Wise2 has also been written with an eye for reuse and maintainability.
Although it is a pure C package you can access its functionality
directly in Perl. Parts of the package (or the entire package) can
be used by other C or C++ programs without namespace clashes as all
externally linked variables have the unique identifier Wise2 prepended.
.
This package contains the documentation for Wise2, a package focused on
comparisons of biopolymers, commonly DNA and protein sequences.
......@@ -63,5 +85,28 @@ Section: doc
Depends: ${misc:Depends}
Recommends: wise (= ${source:Version})
Description: data files for the wise package
Wise2 is a package focused on comparisons of biopolymers, commonly DNA
and protein sequences. There are many other packages which do
this, probably the best known being BLAST package (from NCBI) and the
Fasta package (from Bill Pearson). There are other packages, such as
the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
on hidden Markov models (HMMs) of biopolymers.
.
Wise2's particular forte is the comparison of DNA sequence at the level
of its protein translation. This comparison allows the simultaneous
prediction of say gene structure with homology based alignment.
.
Wise2 also contains other algorithms, such as the venerable Smith-Waterman
algorithm, or more modern ones such as Stephen Altschul's generalised
gap penalties, or even experimental ones developed in house, such as
dba. The development of these algorithms is due to the ease of developing
such algorithms in the environment used by Wise2.
.
Wise2 has also been written with an eye for reuse and maintainability.
Although it is a pure C package you can access its functionality
directly in Perl. Parts of the package (or the entire package) can
be used by other C or C++ programs without namespace clashes as all
externally linked variables have the unique identifier Wise2 prepended.
.
This package contains data files for Wise2, a package focused on
comparisons of biopolymers, commonly DNA and protein sequences.
debian/patches/09_dnal-add-return-statement.patch
View file @ be215cf8
Author: Dejan Latinovic <Dejan.Latinovic@imgtec.com>
Last-Update: Mon, 4 Aug 2014 17:10:38 +0000
Bug-Debian: http://bugs.debian.org/751277
Desription: Make sure dnal has a valid return value
Description: Make sure dnal has a valid return value
This affects a bug reported against python-biopython.
--- wise-2.4.1.orig/src/models/dnal.c
......
debian/wise-doc.doc-base.api
View file @ be215cf8
......@@ -5,8 +5,8 @@ Abstract: This manual describes the wise API.
Section: Science/Biology
Format: PDF
Files: /usr/share/doc/wise-doc/api.pdf.gz
Files: /usr/share/doc/wise/api.pdf.gz
Format: HTML
Index: /usr/share/doc/wise-doc/api/api.html
Files: /usr/share/doc/wise-doc/api/*
Index: /usr/share/doc/wise/api/api.html
Files: /usr/share/doc/wise/api/*
debian/wise-doc.doc-base.dynamite
View file @ be215cf8
......@@ -6,8 +6,8 @@ Abstract: This manual describes the dynamite code generating
Section: Science/Biology
Format: PDF
Files: /usr/share/doc/wise-doc/dynamite.pdf.gz
Files: /usr/share/doc/wise/dynamite.pdf.gz
Format: HTML
Index: /usr/share/doc/wise-doc/dynamite/dynamite.html
Files: /usr/share/doc/wise-doc/dynamite/*
Index: /usr/share/doc/wise/dynamite/dynamite.html
Files: /usr/share/doc/wise/dynamite/*
debian/wise-doc.doc-base.wise
View file @ be215cf8
......@@ -5,8 +5,8 @@ Abstract: This manual describes wise program usages.
Section: Science/Biology
Format: PDF
Files: /usr/share/doc/wise-doc/wise2.pdf.gz
Files: /usr/share/doc/wise/wise2.pdf.gz
Format: HTML
Index: /usr/share/doc/wise-doc/wise2/wise2.html
Files: /usr/share/doc/wise-doc/wise2/*
Index: /usr/share/doc/wise/wise2/wise2.html
Files: /usr/share/doc/wise/wise2/*