diff options
| author | George Hartzell <hartzell@alerce.com> | 2020-02-29 20:58:13 -0800 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2020-02-29 22:58:13 -0600 |
| commit | 501fdc75b6ae8e3237438393d5df86a0edfcc2b0 (patch) | |
| tree | 6060eda1fa4dbfda05a9842b4169a4fbb3130068 /var | |
| parent | 5fc43b3b0efcf9bb5820097fcef95e09ec2f5a99 (diff) | |
| download | spack-501fdc75b6ae8e3237438393d5df86a0edfcc2b0.tar.gz spack-501fdc75b6ae8e3237438393d5df86a0edfcc2b0.tar.bz2 spack-501fdc75b6ae8e3237438393d5df86a0edfcc2b0.tar.xz spack-501fdc75b6ae8e3237438393d5df86a0edfcc2b0.zip | |
Update kallisto (with hackery on std_cmake_args) (#15278)
* Filter problematic flag from std_cmake_args
Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args causes
bits of cmake's output to end up in the autoconf-generated configure
script. See https://github.com/spack/spack/issues/15274 and
* Don't build in parallel (sigh)
* Constrain hackery for newer versions...
... to newer versions.
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/kallisto/package.py | 29 |
1 files changed, 29 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/kallisto/package.py b/var/spack/repos/builtin/packages/kallisto/package.py index 337b50f188..d33bd970a2 100644 --- a/var/spack/repos/builtin/packages/kallisto/package.py +++ b/var/spack/repos/builtin/packages/kallisto/package.py @@ -13,8 +13,37 @@ class Kallisto(CMakePackage): homepage = "http://pachterlab.github.io/kallisto" url = "https://github.com/pachterlab/kallisto/archive/v0.43.1.tar.gz" + version('0.46.2', sha256='c447ca8ddc40fcbd7d877d7c868bc8b72807aa8823a8a8d659e19bdd515baaf2') version('0.43.1', sha256='7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400') depends_on('zlib') depends_on('hdf5') depends_on('mpich') + + # htslib isn't built in time to be used.... + parallel = False + + # v0.44.0 vendored a copy of htslib and uses auto* to build + # its configure script. + depends_on('autoconf', type='build', when='@0.44.0:') + depends_on('automake', type='build', when='@0.44.0:') + depends_on('libtool', type='build', when='@0.44.0:') + depends_on('m4', type='build', when='@0.44.0:') + + # Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args + # causes bits of cmake's output to end up in the autoconf-generated + # configure script. + # See https://github.com/spack/spack/issues/15274 and + # https://github.com/pachterlab/kallisto/issues/253 + @property + def std_cmake_args(self): + """Call the original std_cmake_args and then filter the verbose + setting. + """ + a = super(Kallisto, self).std_cmake_args + if (self.spec.version >= Version('0.44.0')): + args = [i for i in a if i != '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON'] + else: + args = a + + return args |