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bowtie package: add version 1.2.3 (#12593)

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* Only apply issue-87.patch for versions before 1.2.3
* 1.2.3 builds fine with gcc@8:, but 1.2.2 and 1.2.2_p1 both fail
  (with or without the patch) so the conflict is updated to exclude
  only these two versions.
This commit is contained in:
健美猞猁 2019-08-29 09:46:22 +08:00 committed by Peter Scheibel
parent eee07522fa
commit 85e13ebc03
1 changed files with 6 additions and 6 deletions
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12
var/spack/repos/builtin/packages/bowtie/package.py
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@ -13,6 +13,7 @@ class Bowtie(MakefilePackage):
homepage = "https://sourceforge.net/projects/bowtie-bio/"
url = "https://github.com/BenLangmead/bowtie/archive/v1.2.0.tar.gz"
version('1.2.3', sha256='86402114caeacbb3a3030509cb59f0b7e96361c7b3ee2dd50e2cd68200898823')
# The bowtie project git tagged and GitHub released a v1.2.2,
# discovered/fixed a bug, git tagged a v1.2.2_p1 and moved the
# 1.2.2 release to use it rather than making a new `1.2.2_p1`
@ -29,11 +30,10 @@ class Bowtie(MakefilePackage):
# clearly identical to 1.2.0.
version('1.2', md5='6d97f0ea1a65af11d17cc270cfac4af9', url='https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.0/bowtie-1.2-source.zip')
# Feel free to tighten this. I know that v1.2.2 (aka v1.2.2_p1)
# builds with %gcc@5.5.5 and fails to build with %gcc@8.2.0. I'm
# not sure whether or not it works with other versions in the
# interval.
conflicts('%gcc@8:', when='@1.2.2:')
# 1.2.2 and 1.2.2_p1 fail to build with %gcc@8.3.0
# with and without issue-87 patch
conflicts('%gcc@8:', when='@1.2.2')
conflicts('%gcc@8:', when='@1.2.2_p1')
variant('tbb', default=False, description='Use Intel thread building block')
@ -43,7 +43,7 @@ class Bowtie(MakefilePackage):
# See: https://github.com/BenLangmead/bowtie/issues/87, a
# different fix is in the FreeBSD ports/package tree
# https://svnweb.freebsd.org/ports?view=revision&revision=483954
patch('issue-87.patch', when='%gcc@8.0.0:')
patch('issue-87.patch', when='@:1.2.2 %gcc@8.0.0:')
def edit(self, spec, prefix):
makefile = FileFilter('Makefile')