[med-svn] [Git][med-team/vg][master] 3 commits: Added patch to fix include path for vgio's libhandlegraph copy

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / vg


Commits:
c7109a32 by Michael R. Crusoe at 2021-01-21T11:51:22+01:00
Added patch to fix include path for vgio's libhandlegraph copy

- - - - -
ba581dae by Michael R. Crusoe at 2021-01-21T11:51:22+01:00
more cleaning

- - - - -
2c0905c2 by Michael R. Crusoe at 2021-01-21T11:52:47+01:00
TODO: compilation error needs fixing: https://github.com/vgteam/vg/issues/3170

- - - - -


4 changed files:

- debian/changelog
- debian/copyright
- + debian/patches/fix-handlegraph
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -4,6 +4,9 @@ vg (1.30.0+ds-1) UNRELEASED; urgency=medium
   * Re-enable tests on avx.
   * New upstream version
   * Refresh patches. No longer uses rocksdb.
+  * Added patch to fix include path for vgio's libhandlegraph copy
+
+    TODO: compilation error needs fixing: https://github.com/vgteam/vg/issues/3170
 
  -- Michael R. Crusoe <crusoe at debian.org>  Wed, 20 Jan 2021 16:33:05 +0100
 


=====================================
debian/copyright
=====================================
@@ -25,6 +25,7 @@ Files-Excluded: deps/libdeflate
                 deps/libVCFH
                 deps/vcflib
                 deps/sublinear-Li-Stephens/deps/htslib
+                deps/sublinear-Li-Stephens/deps
                 deps/sparsehash
                 deps/sdsl-lite/external
                 deps/sonLib/C/impl/lz4hc.h
@@ -33,7 +34,9 @@ Files-Excluded: deps/libdeflate
                 deps/sonLib/C/impl/lz4hc.c
                 deps/FlameGraph
                 deps/htslib
-                obj/*
+                obj/
+                bin/
+                lib/
 
 Files: *
 Copyright: © 2014, 2010, 2012, 2014-2015 Erik Garrison


=====================================
debian/patches/fix-handlegraph
=====================================
@@ -0,0 +1,15 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: libvgio: fix include path for libhandlegraph
+
+It is odd that this is needed...
+--- vg.orig/deps/libvgio/CMakeLists.txt
++++ vg/deps/libvgio/CMakeLists.txt
+@@ -86,7 +86,7 @@
+   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/libhandlegraph"
+   CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>")
+ ExternalProject_Get_property(handlegraph INSTALL_DIR)
+-set(handlegraph_INCLUDE "${INSTALL_DIR}/include")
++set(handlegraph_INCLUDE "${CMAKE_SOURCE_DIR}/deps/libhandlegraph/src/include")
+ set(handlegraph_LIB "${INSTALL_DIR}/lib")
+ 
+ # Set link directories. We can't use target_link_directories to keep these


=====================================
debian/patches/series
=====================================
@@ -27,3 +27,4 @@ use_packaged_htslib
 simde
 crossbuild
 python3
+fix-handlegraph



View it on GitLab: https://salsa.debian.org/med-team/vg/-/compare/f181c5a15bf3e43dc199e137cd8a5a99844f1247...2c0905c2364639713f7b72fbbe3a7b4403546214

-- 
View it on GitLab: https://salsa.debian.org/med-team/vg/-/compare/f181c5a15bf3e43dc199e137cd8a5a99844f1247...2c0905c2364639713f7b72fbbe3a7b4403546214
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