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Commits on Source (5)
DEP3 + d/changelog
· 3269a41c
Andreas Tille
authored
Jan 10, 2020
3269a41c
Package diamond was removed from Debian so the name /usr/bin/diamond can be used again
· 19bc5751
Andreas Tille
authored
Jan 10, 2020
19bc5751
Upstream version just contains patch from Frédéric Bonnard
· bd8323e4
Andreas Tille
authored
Jan 10, 2020
bd8323e4
Set upstream metadata fields: Bug-Database, Bug-Submit.
· a05bde27
Andreas Tille
authored
Jan 10, 2020
a05bde27
routine-update: Ready to upload to unstable
· 8d1cd7d1
Andreas Tille
authored
Jan 10, 2020
8d1cd7d1
Show whitespace changes
Inline
Side-by-side
debian/README.Debian
deleted
100644 → 0
View file @
6f56988a
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
${HOME}/.blends
with the content
# Add Blend names here which should prepend its bin dir to PATH
debian-med
the med-config package automatically adds this PATH to the users
environment (when using bash).
-- Andreas Tille <tille@debian.org> Thu, 05 Jan 2017 10:33:38 +0100
debian/changelog
View file @
8d1cd7d1
diamond-aligner (0.9.29+dfsg-2) unstable; urgency=medium
[ Frédéric Bonnard ]
* Upstream 0.9.29 includes patch to build diamond-aligner on any
Closes: #942850
[ Andreas Tille ]
* Package diamond was removed from Debian so the name /usr/bin/diamond
can be used again
* Set upstream metadata fields: Bug-Database, Bug-Submit.
-- Andreas Tille <tille@debian.org> Fri, 10 Jan 2020 13:50:28 +0100
diamond-aligner (0.9.29+dfsg-1) unstable; urgency=medium
* Team upload.
...
...
debian/links
View file @
8d1cd7d1
usr/
lib/debian-med/
bin/diamond usr/bin/diamond-aligner
usr/
lib/debian-med/
share/man/man1/diamond.1 usr/share/man/man1/diamond-aligner.1
usr/bin/diamond usr/bin/diamond-aligner
usr/share/man/man1/diamond.1
.gz
usr/share/man/man1/diamond-aligner.1
.gz
debian/patches/fix-unsigned-char-by-default-arches.patch
deleted
100644 → 0
View file @
6f56988a
--- a/src/basic/score_matrix.cpp
+++ b/src/basic/score_matrix.cpp
@@ -36,7 +36,7 @@
const double INT2_MAX = std::numeric_limits<double>::max();
-const char DNA_scores[5 * 5] = {
+const signed char DNA_scores[5 * 5] = {
2, -3, -3, -3, -3,
-3,2,-3,-3,-3,
-3,-3,2,-3,-3,
@@ -317,4 +317,4 @@
constants[3] = lambda;
constants[4] = K;
constants_ = constants;
-}
\ No newline at end of file
+}
debian/patches/series
View file @
8d1cd7d1
avoid_unwanted_optimisation.patch
82feea2aee5c82e283704b9317cb5e8abc625f90.patch
fix-unsigned-char-by-default-arches.patch
debian/rules
View file @
8d1cd7d1
...
...
@@ -13,26 +13,8 @@ MSSSSE3=$(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
View file @
8d1cd7d1
...
...
@@ -18,3 +18,5 @@ Registry:
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