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Merged
merged 5 commits into from
May 9, 2019
Merged

Packages/paien/tophat #233

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7f8ff68
Add TopHat package release 2.1.1
gio31415 Mar 18, 2019
cd3f3c8
Merge changes from cornalin
rmsds Apr 3, 2019
afd886a
TopHat package release 2.1.2
gio31415 Apr 26, 2019
f26d472
tophat conflicts with gcc@6: (#234)
rmsds May 9, 2019
98fe4e3
Merge branch 'releases/paien' into packages/paien/tophat
rmsds May 9, 2019
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18 changes: 16 additions & 2 deletions var/spack/repos/builtin/packages/tophat/package.py
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Expand Up @@ -26,21 +26,35 @@


class Tophat(AutotoolsPackage):
"""Spliced read mapper for RNA-Seq."""
"""TopHat is a fast splice junction read mapper for RNA-Seq.

It aligns RNA-Seq reads to mammalian-sized genomes using the ultra
high-throughput short read aligner Bowtie, and then analyzes the
the mapping results to identify splice junctions between exons."""

homepage = "http://ccb.jhu.edu/software/tophat/index.shtml"
url = "https://github.com/infphilo/tophat/archive/v2.1.1.tar.gz"

version('2.1.2', 'db844fd7f53c519e716cd6222e6195b2')
version('2.1.1', 'ffd18de2f893a95eb7e9d0c5283d241f')

depends_on('autoconf', type='build')
depends_on('automake', type='build')
# 2.1.1 only builds with [email protected]. There's a patch here:
# https://github.com/spack/spack/pull/8244, which was incorporated
# upstream in 2.1.2, which is known to build with 1.16.1 and 1.15.1.
depends_on('automake', type='build')
depends_on('[email protected]', when='@:2.1.1', type='build')
depends_on('libtool', type='build')
depends_on('m4', type='build')

depends_on('[email protected]:')
depends_on('bowtie2', type='run')

# uses make_pair which changed signature with C++14
# a patch exists: https://github.com/DaehwanKimLab/tophat/pull/38
# but there might be unexpected side effects
conflicts('%gcc@6:')

parallel = False

def configure_args(self):
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