Merge remote-tracking branch 'upstream/master' into fix/misc

* upstream/master:
  Update Vagrantfile
  few minor spell fixes
  Fixed missing outputfiles

Author: satra

Vagrantfile

@@ -20,19 +20,19 @@ $script = <<SCRIPT
 # qconf -aattr queue slots "2, [neuro=3]" main.q
 
 # install anaconda
-wget http://repo.continuum.io/miniconda/Miniconda-3.0.0-Linux-x86_64.sh -O miniconda.sh
+wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
 chmod +x miniconda.sh
 ./miniconda.sh -b
 echo "export PATH=$HOME/miniconda/bin:\\$PATH" >> .bashrc
 
 # install nipype dependencies
-$HOME/anaconda/bin/conda update --yes conda
-$HOME/anaconda/bin/conda install --yes pip numpy scipy nose traits networkx
-$HOME/anaconda/bin/conda install --yes dateutil ipython-notebook matplotlib
-$HOME/anaconda/bin/pip install nibabel --use-mirrors
-$HOME/anaconda/bin/pip install https://github.com/RDFLib/rdflib/archive/master.zip
-$HOME/anaconda/bin/pip install https://github.com/satra/prov/archive/enh/rdf.zip
-$HOME/anaconda/bin/pip install https://github.com/nipy/nipype/archive/master.zip
+$HOME/miniconda/bin/conda update --yes conda
+$HOME/miniconda/bin/conda install --yes pip numpy scipy nose traits networkx
+$HOME/miniconda/bin/conda install --yes dateutil ipython-notebook matplotlib
+$HOME/miniconda/bin/pip install nibabel --use-mirrors
+$HOME/miniconda/bin/pip install https://github.com/RDFLib/rdflib/archive/master.zip
+$HOME/miniconda/bin/pip install https://github.com/satra/prov/archive/enh/rdf.zip
+$HOME/miniconda/bin/pip install https://github.com/nipy/nipype/archive/master.zip
 SCRIPT
 
 Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
@@ -42,7 +42,7 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
     engine_config.vm.box = "gridneuro"
     #engine_config.vm.box_url = "http://files.vagrantup.com/precise64.box"
     engine_config.vm.box_url = "https://dl.dropboxusercontent.com/u/363467/precise64_neuro.box"
-    engine_config.vm.network :forwarded_port, guest: 80, host: 8080
+    #engine_config.vm.network :forwarded_port, guest: 80, host: 8080
 
     #engine_config.vm.network :public_network, :bridge => 'en0: Wi-Fi (AirPort)'
     engine_config.vm.network :private_network, ip: "192.168.100.20"

nipype/interfaces/fsl/preprocess.py

@@ -1396,7 +1396,7 @@ def _gen_filename(self, name):
 
 
 class FIRSTInputSpec(FSLCommandInputSpec):
-    in_file = File(exists=True, mandatory=True, position=-2,
+    in_file = File(exists=True, mandatory=True, position=-2, copyfile=False,
                   argstr='-i %s',
                   desc='input data file')
     out_file = File('segmented', usedefault=True, mandatory=True, position=-1,
@@ -1496,12 +1496,12 @@ def _gen_mesh_names(self, name, structures):
             vtks = list()
             for struct in structures:
                 vtk = prefix + '-' + struct + '_first.vtk'
-            vtks.append(op.abspath(vtk))
+                vtks.append(op.abspath(vtk))
             return vtks
         if name == 'bvars':
             bvars = list()
             for struct in structures:
                 bvar = prefix + '-' + struct + '_first.bvars'
-            bvars.append(op.abspath(bvar))
+                bvars.append(op.abspath(bvar))
             return bvars
         return None

nipype/pipeline/plugins/dagman.py

@@ -27,16 +27,16 @@ class CondorDAGManPlugin(GraphPluginBase):
                  submit file
     - override_specs : additional submit specs that are appended to any job's
                  submit file
-    - wrapper_cmd : path to an exectuable that will be started instead of a node
+    - wrapper_cmd : path to an executable that will be started instead of a node
                  script. This is useful for wrapper script that execute certain
                  functionality prior or after a node runs. If this option is
                  given the wrapper command is called with the respective Python
-                 exectuable and the path to the node script as final arguments
+                 executable and the path to the node script as final arguments
     - wrapper_args : optional additional arguments to a wrapper command
     - dagman_args : arguments to be prepended to the arguments of the
                     condor_submit_dag call
     - block : if True the plugin call will block until Condor has finished
-                 prcoessing the entire workflow (default: False)
+                 processing the entire workflow (default: False)
     """
 
     default_submit_template = """