[med-svn] [Git][med-team/bowtie][master] 8 commits: routine-update: Add salsa-ci file

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / bowtie


Commits:
0c6c1352 by Andreas Tille at 2020-09-15T08:59:34+02:00
routine-update: Add salsa-ci file

- - - - -
8e6c7bb9 by Andreas Tille at 2020-09-15T08:59:34+02:00
routine-update: Rules-Requires-Root: no

- - - - -
6b2f344d by Andreas Tille at 2020-09-15T08:59:44+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

- - - - -
a5c81795 by Andreas Tille at 2020-09-15T09:06:30+02:00
Seems seqan-rename-ChunkPool.patch was not finished since there is a build error

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56a58b4d by Andreas Tille at 2020-09-15T09:19:05+02:00
Drop seqan-dev from Build-Depends and deactivate patch to rename ChunkPool and popCount from seqan

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b63942ff by Andreas Tille at 2020-09-15T09:38:25+02:00
Point dh_install to binaries available in usr/local/bin

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eda38d7a by Andreas Tille at 2020-09-15T09:49:32+02:00
Also install -debug version of the binaries since these were in previous packages as well ... but why????

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8dc9e138 by Andreas Tille at 2020-09-15T09:58:27+02:00
Upload to unstable

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7 changed files:

- debian/bowtie.install
- debian/changelog
- debian/control
- debian/patches/seqan-rename-ChunkPool.patch
- debian/patches/series
- + debian/salsa-ci.yml
- debian/upstream/metadata


Changes:

=====================================
debian/bowtie.install
=====================================
@@ -1,5 +1,3 @@
-bowtie		usr/bin
-bowtie-align*	usr/bin
-bowtie-build*	usr/bin
-bowtie-inspect*  usr/bin
+usr/local/bin	usr
 debian/tests/[er]*	usr/share/doc/bowtie/tests
+bowtie-*-debug	usr/bin


=====================================
debian/changelog
=====================================
@@ -1,10 +1,16 @@
-bowtie (1.3.0+dfsg-1) UNRELEASED; urgency=medium
+bowtie (1.3.0+dfsg-1) unstable; urgency=medium
 
   * New upstream version (upstream has adopted several patches)
   * Standards-Version: 4.5.0 (routine-update)
   * debhelper-compat 13 (routine-update)
-
- -- Andreas Tille <tille at debian.org>  Tue, 15 Sep 2020 08:16:20 +0200
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse.
+  * Drop seqan-dev from Build-Depends
+  * Point dh_install to binaries available in usr/local/bin
+
+ -- Andreas Tille <tille at debian.org>  Tue, 15 Sep 2020 09:50:29 +0200
 
 bowtie (1.2.3+dfsg-4) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -11,7 +11,6 @@ Build-Depends: debhelper-compat (= 13),
                help2man,
                libtbb-dev,
                python3,
-               seqan-dev,
                zlib1g-dev,
                libclone-perl,
                libtest-deep-perl,
@@ -20,6 +19,7 @@ Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/bowtie
 Vcs-Git: https://salsa.debian.org/med-team/bowtie.git
 Homepage: http://bowtie-bio.sourceforge.net/
+Rules-Requires-Root: no
 
 Package: bowtie
 Architecture: alpha any-amd64 arm64 mips64el ppc64 ppc64el s390x sparc64 riscv64


=====================================
debian/patches/seqan-rename-ChunkPool.patch
=====================================
@@ -140,6 +140,15 @@ Last-Update: 2013-04-18
  			BitPairReference* refs,
  			EList<BTRefString >& os,
  			bool maqPenalty,
+@@ -597,7 +597,7 @@ public:
+ 			RangeCache* cacheFw,
+ 			RangeCache* cacheBw,
+ 			uint32_t cacheLimit,
+-			ChunkPool *pool,
++			bowtieChunkPool *pool,
+ 			BitPairReference* refs,
+ 			EList<BTRefString >& os,
+ 			bool reportSe,
 @@ -1372,7 +1372,7 @@ private:
  	RangeCache *cacheFw_;
  	RangeCache *cacheBw_;


=====================================
debian/patches/series
=====================================
@@ -3,8 +3,8 @@ strip_html5shiv.patch
 spelling.patch
 no_hash_style_both_for_mips.patch
 use-dpkg-buildflags.patch
-seqan-rename-ChunkPool.patch
-seqan-popcount.patch
+# seqan-rename-ChunkPool.patch
+# seqan-popcount.patch
 reproducible.patch
 build-as-Cpp03.patch
 simple-test


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/BenLangmead/bowtie/issues
+Bug-Submit: https://github.com/BenLangmead/bowtie/issues/new
 Reference:
   author: "Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg\n"
   title: "Ultrafast and memory-efficient alignment of short DNA sequences to the human\
@@ -18,3 +20,5 @@ Registry:
   Entry: bowtie
 - Name: conda:bioconda
   Entry: bowtie
+Repository: https://github.com/BenLangmead/bowtie.git
+Repository-Browse: https://github.com/BenLangmead/bowtie



View it on GitLab: https://salsa.debian.org/med-team/bowtie/-/compare/5944e054c3300c591655f0f33534952438cf10e6...8dc9e138ac757d83873085e78c9985d951d8b288

-- 
View it on GitLab: https://salsa.debian.org/med-team/bowtie/-/compare/5944e054c3300c591655f0f33534952438cf10e6...8dc9e138ac757d83873085e78c9985d951d8b288
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