update version, replace some submodules

PetrKralCZ · Sep 19, 2023 · 8c12c84 · 8c12c84
1 parent ccc2aff
commit 8c12c84
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diff --git a/.../easyconfigs/v/vg/vg-1.48.0-foss-2022a.eb → .../easyconfigs/v/vg/vg-1.50.1-foss-2022a.eb b/.../easyconfigs/v/vg/vg-1.48.0-foss-2022a.eb → .../easyconfigs/v/vg/vg-1.50.1-foss-2022a.eb
@@ -1,7 +1,7 @@
 easyblock = 'MakeCp'
 
 name = 'vg'
-version = '1.48.0'
+version = '1.50.1'
 
 homepage = 'https://github.com/vgteam/vg'
 description = """variation graph data structures, interchange formats,
@@ -16,13 +16,21 @@ sources = [{
         'repo_name': '%(namelower)s',
         'tag': 'v%(version)s',
         'recursive': True,
+        'recurse_submodules': [
+            '!vcflib',
+            '!deps/htslib',
+            '!deps/tabixpp',
+        ],
         'keep_git_dir': True,
+        'extra_config_params': [
+            'submodule."deps/elfutils".url=https://sourceware.org/git/elfutils.git',
+        ]
     }
 }]
 patches = ['%(name)s-%(version)s_dep_fix.patch']
 checksums = [
     None,
-    '1ca9dd7c0f493ea41a7e5948f176a38176910b58419b06c96b868e975bd22f7d',  # vg-1.48.1_dep_fix.patch
+    '4db8da4c7b4ed3c846f03ddab47a5b99345edc7db398882b12bcebc4a0ee3fc0',  # vg-1.50.1_dep_fix.patch
 ]
 
 builddependencies = [
@@ -55,8 +63,17 @@ dependencies = [
     ('pkg-config', '0.29.2'),
     ('XZ', '5.2.5'),
     ('nodejs', '16.15.1'),
+
+    ('vcflib', '1.0.9', '-R-4.2.1'),
+    ('HTSlib', '1.15.1'),
+    ('tabixpp', '1.1.2'),
 ]
 
+prebuildopts = 'mkdir lib && '
+prebuildopts += 'ln -s $EBROOTVCFLIB/lib/libvcflib.a lib/ && '
+prebuildopts += 'ln -s $EBROOTHTSLIB/lib/libhts.a lib/ && '
+prebuildopts += 'ln -s $EBROOTTABIXPP/lib/libtabixpp.a lib/ && '
+
 files_to_copy = ['bin']
 
 sanity_check_paths = {

diff --git a/.../easyconfigs/v/vg/vg-1.48.0_dep_fix.patch → .../easyconfigs/v/vg/vg-1.50.1_dep_fix.patch b/.../easyconfigs/v/vg/vg-1.48.0_dep_fix.patch → .../easyconfigs/v/vg/vg-1.50.1_dep_fix.patch
@@ -2,8 +2,8 @@ We only have protobuf and jansson as dynamic libraries.
 
 Author: Petr Král (INUITS)
 diff -u vg/Makefile.orig vg/Makefile
---- vg/Makefile.orig    2023-05-29 13:19:44.616487099 +0200
-+++ vg/Makefile 2023-05-29 13:21:19.283804216 +0200
+--- Makefile.orig       2023-09-13 14:23:25.431047504 +0200
++++ Makefile    2023-09-13 14:25:13.638368889 +0200
 @@ -45,11 +45,11 @@
  # What pkg-config-controlled system dependencies should we use compile and link flags from?
  # Use PKG_CONFIG_PATH to point the build system at the right versions of these, if they aren't picked up automatically.