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authormarcost2 <52476474+marcost2@users.noreply.github.com>2023-10-30 10:19:42 -0300
committerGitHub <noreply@github.com>2023-10-30 14:19:42 +0100
commit9ed9a541c9d7be3729339f810c50496ff6ceb63a (patch)
tree0bedf3a1f69ac6cbae478c030d04c16f9549fab3 /var
parent1ebf1c8d1c87e1d8675353b261b55c9c0c3b1371 (diff)
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freesurfer: fix support for linux (#39864)
* 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
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/freesurfer/package.py25
1 files changed, 23 insertions, 2 deletions
diff --git a/var/spack/repos/builtin/packages/freesurfer/package.py b/var/spack/repos/builtin/packages/freesurfer/package.py
index 4bf4a4a2f5..0e7188db06 100644
--- a/var/spack/repos/builtin/packages/freesurfer/package.py
+++ b/var/spack/repos/builtin/packages/freesurfer/package.py
@@ -3,7 +3,11 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+import glob
+import os
+
from spack.package import *
+from spack.util.environment import EnvironmentModifications
class Freesurfer(Package):
@@ -14,11 +18,11 @@ class Freesurfer(Package):
# A license is required, but is free to obtain.
license_required = True
- license_files = ["./license.txt"]
+ license_files = [".license"]
maintainers("robgics")
- version("7.4.1", sha256="eb6545d1ffdee17a90abd2e7dc444aa1091a6138e257f6f956a7ff214635b092")
+ version("7.4.1", sha256="313a96caeb246c5985f483633b5cf43f86ed8f7ccc6d6acfac8eedb638443010")
version("7.4.0", sha256="6b65c2edf3b88973ced0324269a88966c541f221b799337c6570c38c2f884431")
version("7.3.2", sha256="58518d3ee5abd2e05109208aed2eef145c4e3b994164df8c4e0033c1343b9e56")
version("7.2.0", sha256="4cca78602f898bf633428b9d82cbb9b07e3ab97a86c620122050803779c86d62")
@@ -27,6 +31,9 @@ class Freesurfer(Package):
depends_on("mesa-glu")
depends_on("qt")
+ depends_on("tcsh")
+ depends_on("bc")
+ depends_on("perl")
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(
@@ -34,10 +41,24 @@ class Freesurfer(Package):
)
def setup_run_environment(self, env):
+ source_file = join_path(self.prefix, "SetUpFreeSurfer.sh")
env.prepend_path("PATH", self.prefix.bin)
env.set("FREESURFER_HOME", self.prefix)
env.set("SUBJECTS_DIR", join_path(self.prefix, "subjects"))
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):
+ 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)