diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/orthofinder/package.py | 34 |
1 files changed, 26 insertions, 8 deletions
diff --git a/var/spack/repos/builtin/packages/orthofinder/package.py b/var/spack/repos/builtin/packages/orthofinder/package.py index 4a471da4bd..53969220af 100644 --- a/var/spack/repos/builtin/packages/orthofinder/package.py +++ b/var/spack/repos/builtin/packages/orthofinder/package.py @@ -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 install(self, spec, prefix): - install_tree('.', prefix.bin) + 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) - chmod = which('chmod') - chmod('+x', join_path(prefix.bin, 'orthofinder')) + def install(self, spec, prefix): + 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) + + def setup_run_environment(self, env): + env.prepend_path('PATH', prefix.bin) + env.prepend_path('PATH', prefix.bin.tools) |