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bcl2fastq needs with working_dir: after changes in #5776 (#5803)

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#5776  cleaned up the way the the current working directory is
managed (less magic state).

bcl2fastq is packaged like a russian doll, rather than an archive file
that contains the source, there's a zip file that contains a tar.gz
file that contains the source.  The package definition has a bit of
extra code that unpacks the inner tarball.

That extra bit of code now needs to explicitly arrange to be in the
correct directory before it does its work.
This commit is contained in:
George Hartzell 2017-10-18 23:59:25 -07:00 committed by Massimiliano Culpo
parent 4774c9887e
commit b46f1e3605
1 changed files with 14 additions and 10 deletions
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24
var/spack/repos/builtin/packages/bcl2fastq2/package.py
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@ -85,16 +85,20 @@ def do_stage(self, mirror_only=False):
def unpack_it(self, f): def unpack_it(self, f):
def wrap(): def wrap():
f() # call the original expand_archive() f() # call the original expand_archive()
if os.path.isdir('bcl2fastq'): with working_dir(self.stage.path):
tty.msg("The tarball has already been unpacked") if os.path.isdir('bcl2fastq'):
else: tty.msg("The tarball has already been unpacked")
tty.msg("Unpacking bcl2fastq2 tarball") else:
tarball = 'bcl2fastq2-v{0}.tar.gz'.format(self.version.dotted) tty.msg("Unpacking bcl2fastq2 tarball")
shutil.move(join_path('spack-expanded-archive', tarball), '.') tty.msg("cwd sez: {0}".format(os.getcwd()))
os.rmdir('spack-expanded-archive') tarball = 'bcl2fastq2-v{0}.tar.gz'.format(
tar = which('tar') self.version.dotted)
tar('-xf', tarball) shutil.move(join_path('spack-expanded-archive', tarball),
tty.msg("Finished unpacking bcl2fastq2 tarball") '.')
os.rmdir('spack-expanded-archive')
tar = which('tar')
tar('-xf', tarball)
tty.msg("Finished unpacking bcl2fastq2 tarball")
return wrap return wrap
def install(self, spec, prefix): def install(self, spec, prefix):