[med-svn] [Git][med-team/sra-sdk][master] 2 commits: fix_libngs_linkage.patch (new): Substitute ngs-c++ for absent ngs.

[Aaron M. Ucko (@ucko)]

Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk


Commits:
648f0b0d by Aaron M. Ucko at 2021-10-14T16:23:45-04:00
fix_libngs_linkage.patch (new): Substitute ngs-c++ for absent ngs.

- - - - -
8b630244 by Aaron M. Ucko at 2021-10-14T16:27:48-04:00
debian/rules: Stop renaming kget now that it's retired altogether.

The historical rename addressed a file conflict, #851219.

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/fix_libngs_linkage.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,11 +1,18 @@
 sra-sdk (2.11.2+dfsg-1) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * Fix watchfile to detect new versions on github
   * New upstream version
   * Standards-Version: 4.6.0 (routine-update)
   * Bump versioned Build-Depends: libngs-sdk-dev (>= 2.11.2)
 
- -- Andreas Tille <tille at debian.org>  Wed, 13 Oct 2021 15:54:35 +0200
+  [ Aaron M. Ucko ]
+  * d/p/fix_libngs_linkage.patch (new): Substitute ngs-c++ library for
+    absent ngs library.
+  * debian/rules: Stop renaming kget (to avoid a file conflict, #851219)
+    now that it's retired altogether.
+
+ -- Aaron M. Ucko <ucko at debian.org>  Thu, 14 Oct 2021 16:27:47 -0400
 
 sra-sdk (2.10.9+dfsg-2) unstable; urgency=medium
 


=====================================
debian/patches/fix_libngs_linkage.patch
=====================================
@@ -0,0 +1,38 @@
+Author: Aaron M. Ucko <ucko at debian.org>
+Last-Changed: Thu, 14 Oct 2021 16:23:45 -0400
+Description: Substitute ngs-c++ library for absent ngs library.
+
+Index: b/tools/vdb-sql/Makefile
+===================================================================
+--- a/tools/vdb-sql/Makefile
++++ b/tools/vdb-sql/Makefile
+@@ -80,7 +80,7 @@ VDB_SQL_SRC = \
+ 
+ VDB_SQL_LIB = \
+ 	-svdb-sqlite \
+-	-sngs \
++	-sngs-c++ \
+ 	-sncbi-vdb \
+ 	-lm \
+ 	-lpthread
+@@ -100,7 +100,7 @@ FASTCONV_LIB = \
+ 	-skapp \
+ 	-stk-version \
+ 	-svdb-sqlite \
+-	-sngs \
++	-sngs-c++ \
+ 	-sncbi-vdb \
+ 	-lm \
+ 	-lpthread
+Index: b/tools/ngs-pileup/Makefile
+===================================================================
+--- a/tools/ngs-pileup/Makefile
++++ b/tools/ngs-pileup/Makefile
+@@ -73,7 +73,6 @@ NGS_PILEUP_OBJ = \
+ NGS_PILEUP_LIBS = \
+ 	-sncbi-ngs-c++    \
+ 	-sngs-c++         \
+-	-sngs         \
+ 	-sncbi-vdb \
+ 	-skapp \
+ 	-stk-version \


=====================================
debian/patches/series
=====================================
@@ -20,3 +20,4 @@ python3
 use_exposed_headers.patch
 #reenable_legacy_schema_in_sra_load.patch
 skip_broken_loaders.patch
+fix_libngs_linkage.patch


=====================================
debian/rules
=====================================
@@ -68,8 +68,6 @@ override_dh_install:
 	dh_install
 	# remove susipcious file which is not executable and conflicts with package magic
 	rm -f debian/*/usr/bin/magic
-	# rename kget which conflicts with kget download manager (see #851219)
-	mv debian/$(pkg)/usr/bin/kget debian/$(pkg)/usr/bin/vdb-get
 	# Formally supply a standard installation ID to satisfy sratools
 	echo '/LIBS/GUID = "$(DEBIAN_GUID)"' >debian/$(pkg)/etc/ncbi/debian.kfg
 



View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/dc201cc5cb985642eed919d69867b80feb7b9ce9...8b630244e7e1071868df80ea76b80b9a14bb6db1

-- 
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/dc201cc5cb985642eed919d69867b80feb7b9ce9...8b630244e7e1071868df80ea76b80b9a14bb6db1
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