freesurfer: fix support for linux (spack#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

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")
@@ -27,17 +31,34 @@ 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(
             version, version
         )
 
     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)