From 26a62a3258b9d0c039ebdcc537e5b3e5ce12c58a Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Mon, 21 Mar 2022 09:15:27 -0500 Subject: 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 --- var/spack/repos/builtin/packages/cnvnator/package.py | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) (limited to 'var') 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), -- cgit v1.2.3-60-g2f50