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authorsnehring <snehring@users.noreply.github.com>2022-04-29 17:06:47 -0500
committerGitHub <noreply@github.com>2022-04-29 16:06:47 -0600
commit06b5217c019cf4c3e686eb14ca1a35c02e25d3ff (patch)
treee945adee02639a5b6cf1e00e98a781cb2bc6b902
parent52bf7f41576d78d7f8bca0441e40428c047a0d6f (diff)
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hapcut2: adding new version 1.3.1 (#30383)
-rw-r--r--var/spack/repos/builtin/packages/hapcut2/package.py24
1 files changed, 21 insertions, 3 deletions
diff --git a/var/spack/repos/builtin/packages/hapcut2/package.py b/var/spack/repos/builtin/packages/hapcut2/package.py
index 81b354eacf..beae641608 100644
--- a/var/spack/repos/builtin/packages/hapcut2/package.py
+++ b/var/spack/repos/builtin/packages/hapcut2/package.py
@@ -13,15 +13,33 @@ class Hapcut2(MakefilePackage):
homepage = "https://github.com/vibansal/HapCUT2"
git = "https://github.com/vibansal/HapCUT2.git"
+ maintainers = ['snehring']
+ version('v1.3.1', commit='c6481d5fd0618dc3e82b2eb8c2b4835d9a4f6da7')
version('2017-07-10', commit='2966b94c2c2f97813b757d4999b7a6471df1160e',
- submodules=True)
+ submodules=True, deprecated=True)
- depends_on('zlib', type='link')
+ depends_on('htslib@1.3:')
+ depends_on('curl')
+ depends_on('openssl')
+ depends_on('xz')
+ depends_on('bzip2')
+ depends_on('zlib')
+
+ @when('@v1.3.1:')
+ def edit(self, spec, prefix):
+ filter_file('CC=.*$', '', 'Makefile')
+ filter_file('CFLAGS=.*$', 'CFLAGS=-Wall -g -O3 -D_GNU_SOURCE', 'Makefile')
+ with working_dir('hairs-src'):
+ filter_file(r'(keyvalue\* keypointer;)', 'extern \\1',
+ 'hashtable.h')
+ filter_file(r'(keypointer = ht->blist\[hash\];)', 'keyvalue* \\1',
+ 'hashtable.c')
def install(self, spec, prefix):
mkdirp(prefix.bin)
with working_dir('build'):
- install('extractFOSMID', prefix.bin)
+ if self.spec.satisfies('@2017-07-10'):
+ install('extractFOSMID', prefix.bin)
install('extractHAIRS', prefix.bin)
install('HAPCUT2', prefix.bin)