Andreas Tille pushed to branch master at Debian Med / wise
Commits: 092d2289 by Andreas Tille at 2018-10-04T12:38:22Z debhelper 11 - - - - - d514cba8 by Andreas Tille at 2018-10-04T12:38:35Z Point Vcs fields to salsa.debian.org - - - - - 8468b11e by Andreas Tille at 2018-10-04T12:38:35Z Standards-Version: 4.2.1 - - - - - 139d181b by Andreas Tille at 2018-10-04T12:46:54Z Adapt doc-base control files to doc location by debhelper 11 - - - - - d0642c55 by Andreas Tille at 2018-10-04T12:47:51Z Typo - - - - - bd1f5861 by Andreas Tille at 2018-10-04T12:49:01Z Long description for all packages - - - - - 8a296ca9 by Andreas Tille at 2018-10-04T12:49:47Z Drop unneeded Testsuite: autopkgtest - - - - - be215cf8 by Andreas Tille at 2018-10-04T12:54:46Z Upload to unstable - - - - - 7 changed files: - debian/changelog - debian/compat - debian/control - debian/patches/09_dnal-add-return-statement.patch - debian/wise-doc.doc-base.api - debian/wise-doc.doc-base.dynamite - debian/wise-doc.doc-base.wise Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +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 <[email protected]> Thu, 04 Oct 2018 14:49:55 +0200 + wise (2.4.1-20) unstable; urgency=medium * Moved packaging from SVN to Git ===================================== debian/compat ===================================== @@ -1 +1 @@ -10 +11 ===================================== debian/control ===================================== @@ -5,16 +5,15 @@ Uploaders: Steffen Moeller <[email protected]>, Andreas Tille <[email protected]> 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 ===================================== @@ -1,7 +1,7 @@ Author: Dejan Latinovic <[email protected]> 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 ===================================== @@ -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 ===================================== @@ -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 ===================================== @@ -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/* View it on GitLab: https://salsa.debian.org/med-team/wise/compare/9c695b59c100962c224cef22eac43fe0e951acd6...be215cf805754f75a5bcc045d42a62955bf3c79b -- View it on GitLab: https://salsa.debian.org/med-team/wise/compare/9c695b59c100962c224cef22eac43fe0e951acd6...be215cf805754f75a5bcc045d42a62955bf3c79b You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
