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-rw-r--r--var/spack/repos/builtin/packages/cnvnator/package.py17
1 files changed, 14 insertions, 3 deletions
diff --git a/var/spack/repos/builtin/packages/cnvnator/package.py b/var/spack/repos/builtin/packages/cnvnator/package.py
index 56359c291a..42ee4fbf03 100644
--- a/var/spack/repos/builtin/packages/cnvnator/package.py
+++ b/var/spack/repos/builtin/packages/cnvnator/package.py
@@ -15,13 +15,15 @@ class Cnvnator(MakefilePackage):
version('0.3.3', sha256='58c5acf61f9a1e5febf546c196f8917a5e084b729e5c4cfd3eba83471b3fe5c1')
- depends_on('samtools')
+ depends_on('samtools@:1.13')
depends_on('htslib')
depends_on('root')
depends_on('bzip2')
depends_on('curl')
- depends_on('lzma')
+ depends_on('xz')
depends_on('zlib')
+ depends_on('libdeflate')
+ depends_on('openssl')
def edit(self, spec, prefix):
makefile = FileFilter('Makefile')
@@ -35,9 +37,18 @@ class Cnvnator(MakefilePackage):
makefile.filter('$(CXX)', '$(CXX) $(CXXFLAGS)', string=True)
# Replace -I$(SAMDIR) with -I$(SAMINC)
makefile.filter('-I$(SAMDIR)', '-I$(SAMINC)', string=True)
+
# Link more libs
+ ldflags = [
+ spec['zlib'].libs.ld_flags,
+ spec['bzip2'].libs.ld_flags,
+ spec['curl'].libs.ld_flags,
+ spec['xz'].libs.ld_flags,
+ spec['libdeflate'].libs.ld_flags,
+ spec['openssl'].libs.ld_flags,
+ ]
makefile.filter('^override LIBS.*',
- 'override LIBS += -lz -lbz2 -lcurl -llzma -lcrypto')
+ 'override LIBS += {0}'.format(' '.join(ldflags)))
def build(self, spec, prefix):
make('ROOTSYS={0}'.format(spec['root'].prefix),