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orthofinder: retrieve sources, overhaul recipes (#22423)

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Desmond Orton 2021-03-23 03:27:52 -05:00 committed by GitHub
parent adf19379cc
commit 6bfc0504cb
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1 changed files with 25 additions and 7 deletions
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var/spack/repos/builtin/packages/orthofinder/package.py
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@ -3,6 +3,8 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
import shutil
from spack import *
@ -18,18 +20,34 @@ class Orthofinder(Package):
in FASTA format."""
homepage = "https://github.com/davidemms/OrthoFinder"
url = "https://github.com/davidemms/OrthoFinder/releases/download/2.5.2/OrthoFinder.tar.gz"
url = "https://github.com/davidemms/OrthoFinder/releases/download/2.5.2/OrthoFinder_source.tar.gz"
version('2.5.2', sha256='23b478996509bbfb2650a14f62744150c51156f7f4244e1168f8491776079829')
version('2.2.0', sha256='7314f3fdfb24d84aa5b9ee27ce9f670df314889c12b8100e4e476c2d21a1c8e7')
version('2.5.2', sha256='e0752b66866e23a11f0592e880fac5f67258f9cf926f926dec8849564c41b8f7')
version('2.2.0', sha256='375f711086b44e2118d7d460821294744245e254e5fa2151dfe73100c0707a8c')
depends_on('py-numpy', type='run')
depends_on('py-scipy', type='run')
depends_on('diamond', type='run')
depends_on('blast-plus', type='run')
depends_on('mcl', type='run')
depends_on('fastme', type='run')
depends_on('py-dlcpar', type='run')
def url_for_version(self, version):
if '@:2.3.6' in self.spec:
url = "https://github.com/davidemms/OrthoFinder/releases/download/{0}/OrthoFinder-{0}_source.tar.gz"
return url.format(version)
else:
url = "https://github.com/davidemms/OrthoFinder/releases/download/{0}/OrthoFinder_source.tar.gz"
return url.format(version)
def install(self, spec, prefix):
install_tree('.', prefix.bin)
if '@2.2.0' in spec:
install_tree('./orthofinder', prefix.bin)
else:
install_tree('.', prefix.bin)
shutil.rmtree(prefix.bin.scripts_of.bin)
os.rename('%s/orthofinder.py' % prefix.bin, '%s/orthofinder' % prefix.bin)
chmod = which('chmod')
chmod('+x', join_path(prefix.bin, 'orthofinder'))
def setup_run_environment(self, env):
env.prepend_path('PATH', prefix.bin)
env.prepend_path('PATH', prefix.bin.tools)