[med-svn] [Git][med-team/diamond-aligner][master] 5 commits: DEP3 + d/changelog
Andreas Tille
gitlab at salsa.debian.org
Fri Jan 10 12:58:44 GMT 2020
Andreas Tille pushed to branch master at Debian Med / diamond-aligner
Commits:
3269a41c by Andreas Tille at 2020-01-10T13:36:52+01:00
DEP3 + d/changelog
- - - - -
19bc5751 by Andreas Tille at 2020-01-10T13:39:26+01:00
Package diamond was removed from Debian so the name /usr/bin/diamond can be used again
- - - - -
bd8323e4 by Andreas Tille at 2020-01-10T13:49:22+01:00
Upstream version just contains patch from Frédéric Bonnard
- - - - -
a05bde27 by Andreas Tille at 2020-01-10T13:50:28+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit.
- - - - -
8d1cd7d1 by Andreas Tille at 2020-01-10T13:52:59+01:00
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- − debian/README.Debian
- debian/changelog
- debian/links
- − debian/patches/fix-unsigned-char-by-default-arches.patch
- debian/patches/series
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/README.Debian deleted
=====================================
@@ -1,36 +0,0 @@
-diamond for Debian
-------------------
-
-There is a name conflict with
-
- diamond - smart data producer for Graphite graphing package
-
-The short story is: We are facing a name clash in the Free Software
-universe and we have to circumvent this somehow. The Debian Med team
-deals with situation usually the following way:
-
- 1. The diamond executable resides in
- /usr/lib/debian-med/bin/diamond
- and can be either executed there or users can use
- 2. A symlink with the name
- /usr/bin/diamond-aligner
- which can be used alternatively
-
-If you want to use diamond right from the command line just set the
-PATH variable like
-
- export PATH=/usr/lib/debian-med/bin:$PATH
-
-If a user creates a file
-
- ${HOME}/.blends
-
-with the content
-
-# Add Blend names here which should prepend its bin dir to PATH
-debian-med
-
-the med-config package automatically adds this PATH to the users
-environment (when using bash).
-
- -- Andreas Tille <tille at debian.org> Thu, 05 Jan 2017 10:33:38 +0100
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+diamond-aligner (0.9.29+dfsg-2) unstable; urgency=medium
+
+ [ Frédéric Bonnard ]
+ * Upstream 0.9.29 includes patch to build diamond-aligner on any
+ Closes: #942850
+
+ [ Andreas Tille ]
+ * Package diamond was removed from Debian so the name /usr/bin/diamond
+ can be used again
+ * Set upstream metadata fields: Bug-Database, Bug-Submit.
+
+ -- Andreas Tille <tille at debian.org> Fri, 10 Jan 2020 13:50:28 +0100
+
diamond-aligner (0.9.29+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/links
=====================================
@@ -1,3 +1,3 @@
-usr/lib/debian-med/bin/diamond usr/bin/diamond-aligner
-usr/lib/debian-med/share/man/man1/diamond.1 usr/share/man/man1/diamond-aligner.1
+usr/bin/diamond usr/bin/diamond-aligner
+usr/share/man/man1/diamond.1.gz usr/share/man/man1/diamond-aligner.1.gz
=====================================
debian/patches/fix-unsigned-char-by-default-arches.patch deleted
=====================================
@@ -1,18 +0,0 @@
---- a/src/basic/score_matrix.cpp
-+++ b/src/basic/score_matrix.cpp
-@@ -36,7 +36,7 @@
-
- const double INT2_MAX = std::numeric_limits<double>::max();
-
--const char DNA_scores[5 * 5] = {
-+const signed char DNA_scores[5 * 5] = {
- 2, -3, -3, -3, -3,
- -3,2,-3,-3,-3,
- -3,-3,2,-3,-3,
-@@ -317,4 +317,4 @@
- constants[3] = lambda;
- constants[4] = K;
- constants_ = constants;
--}
-\ No newline at end of file
-+}
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,2 @@
avoid_unwanted_optimisation.patch
82feea2aee5c82e283704b9317cb5e8abc625f90.patch
-fix-unsigned-char-by-default-arches.patch
=====================================
debian/rules
=====================================
@@ -13,26 +13,8 @@ MSSSSE3=$(shell if [ `dpkg-architecture -qDEB_BUILD_ARCH` = 'amd64' ] ; then ech
%:
dh $@
-override_dh_install:
- dh_install
- # due to a file name conflict diamond is moved out of the way
- mkdir -p debian/$(DEB_SOURCE)/usr/lib/debian-med/bin/
- mv debian/$(DEB_SOURCE)/usr/bin/diamond debian/$(DEB_SOURCE)/usr/lib/debian-med/bin/
-
-override_dh_installman:
- dh_installman
- # due to a file name conflict diamond.1 is moved out of the way
- mkdir -p debian/$(DEB_SOURCE)/usr/lib/debian-med/share/man/man1/
- mv debian/$(DEB_SOURCE)/usr/share/man/man1/diamond.1 debian/$(DEB_SOURCE)/usr/lib/debian-med/share/man/man1/
- gzip -9 debian/$(DEB_SOURCE)/usr/lib/debian-med/share/man/man1/diamond.1
-
override_dh_compress:
dh_compress --exclude=.pdf
-override_dh_fixperms:
- dh_fixperms
- # strangely the manpage becomes executable ... hmmm
- chmod -x debian/$(DEB_SOURCE)/usr/lib/debian-med/share/man/man1/*
-
build_simple:
MSSSSE3=$(MSSSSE3) build_simple.sh
=====================================
debian/upstream/metadata
=====================================
@@ -10,11 +10,13 @@ Reference:
PMID: 25402007
URL: http://www.nature.com/nmeth/journal/v12/n1/abs/nmeth.3176.html
Registry:
- - Name: OMICtools
- Entry: OMICS_08011
- - Name: bio.tools
- Entry: Diamond
- - Name: SciCrunch
- Entry: SCR_016071
- - Name: conda:bioconda
- Entry: diamond
+- Name: OMICtools
+ Entry: OMICS_08011
+- Name: bio.tools
+ Entry: Diamond
+- Name: SciCrunch
+ Entry: SCR_016071
+- Name: conda:bioconda
+ Entry: diamond
+Bug-Database: https://github.com/bbuchfink/diamond/issues
+Bug-Submit: https://github.com/bbuchfink/diamond/issues/new
View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/compare/6f56988aed2194504aebdc22b63867765cd62d76...8d1cd7d12f792358462f5366feb058b532590a1e
--
View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/compare/6f56988aed2194504aebdc22b63867765cd62d76...8d1cd7d12f792358462f5366feb058b532590a1e
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