Commit 2b4bf58e authored by Martin Craig's avatar Martin Craig
Browse files

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 $FSLDIR
parent 8c5f54fb
......@@ -337,27 +337,38 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args):
def runfsl(*args, **kwargs):
"""Call a FSL command and return its output. This function simply prepends
``$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):
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')
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
return run(*args, **kwargs)
def wait(job_ids):
"""Proxy for :func:`.fslsub.wait`. """
return fslsub.wait(job_ids)
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