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freesurfer: fix support for linux (#39864)

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* Load the script file during enviroment setup so that all the enviroment variables are set properly
* Patch csh/tcsh so that it uses spacks via env
* Update SHA for latest version
* Extend shebang to perl and fix up the regex
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marcost2 2023-10-30 10:19:42 -03:00 committed by GitHub
parent 1ebf1c8d1c
commit 9ed9a541c9
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1 changed files with 23 additions and 2 deletions
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25
var/spack/repos/builtin/packages/freesurfer/package.py
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@ -3,7 +3,11 @@
# #
# SPDX-License-Identifier: (Apache-2.0 OR MIT) # SPDX-License-Identifier: (Apache-2.0 OR MIT)
import glob
import os
from spack.package import * from spack.package import *
from spack.util.environment import EnvironmentModifications
class Freesurfer(Package): class Freesurfer(Package):
@ -14,11 +18,11 @@ class Freesurfer(Package):
# A license is required, but is free to obtain. # A license is required, but is free to obtain.
license_required = True license_required = True
license_files = ["./license.txt"] license_files = [".license"]
maintainers("robgics") maintainers("robgics")
version("7.4.1", sha256="eb6545d1ffdee17a90abd2e7dc444aa1091a6138e257f6f956a7ff214635b092") version("7.4.1", sha256="313a96caeb246c5985f483633b5cf43f86ed8f7ccc6d6acfac8eedb638443010")
version("7.4.0", sha256="6b65c2edf3b88973ced0324269a88966c541f221b799337c6570c38c2f884431") version("7.4.0", sha256="6b65c2edf3b88973ced0324269a88966c541f221b799337c6570c38c2f884431")
version("7.3.2", sha256="58518d3ee5abd2e05109208aed2eef145c4e3b994164df8c4e0033c1343b9e56") version("7.3.2", sha256="58518d3ee5abd2e05109208aed2eef145c4e3b994164df8c4e0033c1343b9e56")
version("7.2.0", sha256="4cca78602f898bf633428b9d82cbb9b07e3ab97a86c620122050803779c86d62") version("7.2.0", sha256="4cca78602f898bf633428b9d82cbb9b07e3ab97a86c620122050803779c86d62")
@ -27,6 +31,9 @@ class Freesurfer(Package):
depends_on("mesa-glu") depends_on("mesa-glu")
depends_on("qt") depends_on("qt")
depends_on("tcsh")
depends_on("bc")
depends_on("perl")
def url_for_version(self, version): def url_for_version(self, version):
return "https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/{0}/freesurfer-linux-centos7_x86_64-{1}.tar.gz".format( return "https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/{0}/freesurfer-linux-centos7_x86_64-{1}.tar.gz".format(
@ -34,10 +41,24 @@ def url_for_version(self, version):
) )
def setup_run_environment(self, env): def setup_run_environment(self, env):
source_file = join_path(self.prefix, "SetUpFreeSurfer.sh")
env.prepend_path("PATH", self.prefix.bin) env.prepend_path("PATH", self.prefix.bin)
env.set("FREESURFER_HOME", self.prefix) env.set("FREESURFER_HOME", self.prefix)
env.set("SUBJECTS_DIR", join_path(self.prefix, "subjects")) env.set("SUBJECTS_DIR", join_path(self.prefix, "subjects"))
env.set("FUNCTIONALS_DIR", join_path(self.prefix, "sessions")) env.set("FUNCTIONALS_DIR", join_path(self.prefix, "sessions"))
env.append_path("PERL5LIB", join_path(self.prefix, "mni/share/perl5"))
env.append_path("PATH", join_path(self.prefix, "mni/bin"))
env.extend(EnvironmentModifications.from_sourcing_file(source_file))
def install(self, spec, prefix): def install(self, spec, prefix):
scripts = ["sources.csh", "SetUpFreeSurfer.csh"]
scripts.extend(glob.glob("bin/*"))
scripts.extend(glob.glob("subjects/**/*", recursive=True))
scripts.extend(glob.glob("fsfast/bin/*", recursive=True))
scripts.extend(glob.glob("mni/bin/*", recursive=True))
for s in scripts:
if os.path.isfile(s):
filter_file(r"(\/usr)?(\/local?)\/bin\/tcsh", "/usr/bin/env -S tcsh", s)
filter_file(r"(\/usr)?(\/local?)\/bin\/csh", "/usr/bin/env -S csh", s)
filter_file(r"(\/usr)?(\/local)?\/bin\/perl", "/usr/bin/env -S perl", s)
install_tree(".", prefix) install_tree(".", prefix)