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| author | Glenn Johnson <glenn-johnson@uiowa.edu> | 2022-03-21 09:15:27 -0500 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2022-03-21 15:15:27 +0100 |
| commit | 26a62a3258b9d0c039ebdcc537e5b3e5ce12c58a (patch) | |
| tree | d978bb7f17509c93071c1f0b2f0362a0780d3df5 | |
| parent | 732f1dd14d904b1fb0585b6bf8cca3cd90f55011 (diff) | |
| download | spack-26a62a3258b9d0c039ebdcc537e5b3e5ce12c58a.tar.gz spack-26a62a3258b9d0c039ebdcc537e5b3e5ce12c58a.tar.bz2 spack-26a62a3258b9d0c039ebdcc537e5b3e5ce12c58a.tar.xz spack-26a62a3258b9d0c039ebdcc537e5b3e5ce12c58a.zip | |
cnvnator: tweak dependencies (#29600)
- 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
| -rw-r--r-- | var/spack/repos/builtin/packages/cnvnator/package.py | 17 |
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), |