Inconsistent file paths for local files in GUI setup

[GoogleCodeExporter]

File paths appear to be set inconsistently in the GUI when convergence analyses 
SSLSAnalysis objects are authored at runtime or loaded from XML. 

When analyses are instantiated, populated and run at runtime, aamlOnTreeOne.ctl 
codeml control file is located in the project working dir, while 
sequence/tree/output files (apart from lnf) are located in locus subdirectory 
(this behaviour is inconsistent perhaps, but at least it works.)

On the other hand, when SSLSAnalysis objects are parsed from XML, the ctl files 
are expected in the locus subdirectory (I think - see below as it's specified 
weirdly); codeml + runCmd.pl don't seem to chdir to the correct location, and 
codeml is unable to find them:

/usr/bin/perl -w runCmd.pl 
/Users/joeparker/a_debug_working_dir/XLOC_000538_Locus_1/. 
/pamlTest/binaries/codeml 
/Users/joeparker/a_debug_working_dir/XLOC_000538_Locus_1/./aamlOnTreeOne.ctl
PamlTestWrapper
    /Users/joeparker/a_debug_working_dir/XLOC_000538_Locus_1/.
    /pamlTest/binaries/codeml
    /Users/joeparker/a_debug_working_dir/XLOC_000538_Locus_1/./aamlOnTreeOne.ctl
dir change to /Users/joeparker/a_debug_working_dir/XLOC_000538_Locus_1/.

runCmd exe:
 /pamlTest/binaries/codeml    
 /Users/joeparker/a_debug_working_dir/XLOC_000538_Locus_1/./aamlOnTreeOne.ctl   
 error when opening file /Users/joeparker/a_debug_working_dir/XLOC_000538_Locus_1/./aamlOnTreeOne.ctl
 tell me the full path-name of the file? 

Original issue reported on code.google.com by joeparke...@gmail.com on 9 Feb 2015 at 7:03

[GoogleCodeExporter]

First thoughts on this - two working dirs needed; the project wdir (absolute 
file path, used when writing subdirectories etc) and the locus sub wdir 
(relative to project wdir - relative pathnames so can be tarred / transferred 
to cluster as a bonus).

NB problem with this would be specifying the binaries location..

Original comment by joeparke...@gmail.com on 9 Feb 2015 at 7:04

[GoogleCodeExporter]

Original comment by joeparke...@gmail.com on 9 Feb 2015 at 7:08

• Changed state: Started

[GoogleCodeExporter]

Update - when adding SSLSAnalysis objects from XML, project working dir 
(GlobalController.model.userWorkDirLocation) is imported / set as locus 
*sub*directory, not overall project wdir.

e.g. wdir should be / is in active runtime (e.g. set in GUI not loaded from 
xml):

/foo/bar/project

but is actually:

/foo/bar/project/locus_ENSG00000123456

Original comment by joeparke...@gmail.com on 9 Feb 2015 at 7:39