From 2b4bf58e8787a5eaa4e80ed92b89b2144cde961d Mon Sep 17 00:00:00 2001
From: Martin Craig <martin.craig@eng.ox.ac.uk>
Date: Tue, 10 Jul 2018 10:53:18 +0100
Subject: [PATCH] Search for command in all configured FSL locations Previously
this would assume $FSLDEVDIR/bin whenever $FSLDEVDIR was set even if there
was no matching command there, but there was one in $FSLDIR
---
fsl/utils/run.py | 37 ++++++++++++++++++++++++-------------
1 file changed, 24 insertions(+), 13 deletions(-)
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index a8adb80b8..561e2ce23 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -337,27 +337,38 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args):
def runfsl(*args, **kwargs):
- """Call a FSL command and return its output. This function simply prepends
- ``$FSLDIR/bin/`` to the command before passing it to :func:`run`.
+ """Call a FSL command and return its output.
+
+ This function searches for the command in the following
+ locations (ordered by priority):
+
+ 1. ``FSL_PREFIX``
+ 2. ``$FSLDEVDIR/bin``
+ 3. ``$FSLDIR/bin``
+
+ If found, the full path to the command is then passed to :func:`run`.
"""
-
- prefix = None
+ prefixes = []
if FSL_PREFIX is not None:
- prefix = FSL_PREFIX
- elif fslplatform.fsldevdir is not None:
- prefix = op.join(fslplatform.fsldevdir, 'bin')
- elif fslplatform.fsldir is not None:
- prefix = op.join(fslplatform.fsldir, 'bin')
- else:
+ prefixes.append(FSL_PREFIX)
+ if fslplatform.fsldevdir is not None:
+ prefixes.append(op.join(fslplatform.fsldevdir, 'bin'))
+ if fslplatform.fsldir is not None:
+ prefixes.append(op.join(fslplatform.fsldir, 'bin'))
+
+ if not prefixes:
raise FSLNotPresent('$FSLDIR is not set - FSL cannot be found!')
- args = _prepareArgs(args)
- args[0] = op.join(prefix, args[0])
+ args = _prepareArgs(args)
+ for prefix in prefixes:
+ cmdpath = op.join(prefix, args[0])
+ if op.isfile(cmdpath):
+ args[0] = cmdpath
+ break
return run(*args, **kwargs)
-
def wait(job_ids):
"""Proxy for :func:`.fslsub.wait`. """
return fslsub.wait(job_ids)
--
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