"No such file or directory" in very simple example

Hi everybody,

First of all I would like to congratulate you all for the amazing work you
are doing with the CWL. It really seems a great idea to try to standardize
practices which we are actually reimplementing almost continuously in our
work (I am a bioinformatician).

I am beginning with the tools, just trying to replicate some of the simple
examples (Hello world!) and finding out if I can do something similar with
a command line R script, which is something I am currently very interested
in. I already have the following dummy R script:

```
#!/usr/bin/env Rscript

args = commandArgs(trailingOnly = TRUE)

result = sum(as.numeric(args))

cat(result, '\n')
```

And I have created the following CWL specification:

```
- id: "#sumcmd"
class: CommandLineTool
inputs:
- id: "#a"
type: int
inputBinding: {}
- id: "#b"
type: int
inputBinding: {}
- id: "#output-file"
type: string
outputs:
- id: "#filename"
type: File
outputBinding:
glob: $(inputs['output-file'])
baseCommand: sum.r
stdout: $(inputs['output-file'])
```

If I try to run the tool, it seems fine at first:

```
vagrant@debian-jessie:~$ cwl-runner sum.cwl#sumcmd -h
/usr/local/bin/cwl-runner 1.0.20160222205901
usage: sum.cwl#sumcmd [-h] -a A -b B --output-file OUTPUT_FILE [job_order]

positional arguments:
job_order Job input json file

optional arguments:
-h, --help show this help message and exit
-a A
-b B
--output-file OUTPUT_FILE
```

But when I try to run it with actual arguments:

```
vagrant@debian-jessie:~$ cwl-runner sum.cwl#sumcmd -a 50 -b 49
--output-file foobar.txt
/usr/local/bin/cwl-runner 1.0.20160222205901
Got workflow error
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cwltool/main.py", line 160,
in single_job_executor
for r in jobiter:
File "/usr/local/lib/python2.7/dist-packages/cwltool/draft2tool.py", line
131, in job
j.stdout = builder.do_eval(self.tool["stdout"])
File "/usr/local/lib/python2.7/dist-packages/cwltool/builder.py", line 164
, in do_eval
context=context, pull_image=pull_image)
File "/usr/local/lib/python2.7/dist-packages/cwltool/expression.py", line
135, in do_eval
return sandboxjs.interpolate(ex, jshead(r.get("expressionLib", []),
rootvars))
File "/usr/local/lib/python2.7/dist-packages/cwltool/sandboxjs.py", line
131, in interpolate
e = execjs(scan[w[0]+1:w[1]], jslib)
File "/usr/local/lib/python2.7/dist-packages/cwltool/sandboxjs.py", line
20, in execjs
stderr=subprocess.PIPE)
File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1335, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Workflow error:
[Errno 2] No such file or directory
```

At first I thought this was on me, but then I cloned the example workflows
and tools repository, and tried to execute one of the included tools.

```
vagrant@debian-jessie:~$ cwl-runner workflows/tools/linux-sort.cwl --input
kk.txt --output kk2.txt --key 1
/usr/local/bin/cwl-runner 1.0.20160222205901
Got workflow error
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cwltool/main.py", line 160,
in single_job_executor
for r in jobiter:
File "/usr/local/lib/python2.7/dist-packages/cwltool/draft2tool.py", line
131, in job
j.stdout = builder.do_eval(self.tool["stdout"])
File "/usr/local/lib/python2.7/dist-packages/cwltool/builder.py", line 164
, in do_eval
context=context, pull_image=pull_image)
File "/usr/local/lib/python2.7/dist-packages/cwltool/expression.py", line
135, in do_eval
return sandboxjs.interpolate(ex, jshead(r.get("expressionLib", []),
rootvars))
File "/usr/local/lib/python2.7/dist-packages/cwltool/sandboxjs.py", line
131, in interpolate
e = execjs(scan[w[0]+1:w[1]], jslib)
File "/usr/local/lib/python2.7/dist-packages/cwltool/sandboxjs.py", line
20, in execjs
stderr=subprocess.PIPE)
File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1335, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Workflow error:
[Errno 2] No such file or directory
```

Problem is, I do not have any idea of what is exactly causing the error. I
can see that is related to not finding a file or a directory, but I am not
exactly sure about where to start looking for, because I think I do not
understand what the cwl-runner tool is actually doing.

Any help or hint would be much appreciated.

Regards,
Gustavo.