hlrs-software-stack/spack
7
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity

cnvnator: tweak dependencies (#29600)

Browse source 
- constrain samtools to version 1.13
- replace lzma dependency with xz
- add missing dependencies for libdeflate and openssl
- explicitly set LD_FLAGS for dependencies in makefile
This commit is contained in:
Glenn Johnson 2022-03-21 09:15:27 -05:00 committed by GitHub
parent 732f1dd14d
commit 26a62a3258
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 14 additions and 3 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

17
var/spack/repos/builtin/packages/cnvnator/package.py
View file

@ -15,13 +15,15 @@ class Cnvnator(MakefilePackage):
version('0.3.3', sha256='58c5acf61f9a1e5febf546c196f8917a5e084b729e5c4cfd3eba83471b3fe5c1') version('0.3.3', sha256='58c5acf61f9a1e5febf546c196f8917a5e084b729e5c4cfd3eba83471b3fe5c1')
depends_on('samtools') depends_on('samtools@:1.13')
depends_on('htslib') depends_on('htslib')
depends_on('root') depends_on('root')
depends_on('bzip2') depends_on('bzip2')
depends_on('curl') depends_on('curl')
depends_on('lzma') depends_on('xz')
depends_on('zlib') depends_on('zlib')
depends_on('libdeflate')
depends_on('openssl')
def edit(self, spec, prefix): def edit(self, spec, prefix):
makefile = FileFilter('Makefile') makefile = FileFilter('Makefile')
@ -35,9 +37,18 @@ def edit(self, spec, prefix):
makefile.filter('$(CXX)', '$(CXX) $(CXXFLAGS)', string=True) makefile.filter('$(CXX)', '$(CXX) $(CXXFLAGS)', string=True)
# Replace -I$(SAMDIR) with -I$(SAMINC) # Replace -I$(SAMDIR) with -I$(SAMINC)
makefile.filter('-I$(SAMDIR)', '-I$(SAMINC)', string=True) makefile.filter('-I$(SAMDIR)', '-I$(SAMINC)', string=True)
# Link more libs # 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.*', makefile.filter('^override LIBS.*',
'override LIBS += -lz -lbz2 -lcurl -llzma -lcrypto') 'override LIBS += {0}'.format(' '.join(ldflags)))
def build(self, spec, prefix): def build(self, spec, prefix):
make('ROOTSYS={0}'.format(spec['root'].prefix), make('ROOTSYS={0}'.format(spec['root'].prefix),