[1.20beta] Minor bug

[Gaj Stan (BIGCAT)]

Hi Nathan,

I think I may have found a minor bug under Linux / Ubuntu:
- Downloaded a fresh install of GO-Elite from the main website
- Created a new species database (EnsEMBL56Plus for human, mouse and
rat).
- Wanted to update existing databases with WikiPathways content
Error:
---
stan@ntcdata1:~/Desktop/GO-Elite_120beta$ python GO_Elite.py
Traceback (most recent call last):
File "GO_Elite.py", line 1733, in <module>
if use_Tkinter == 'yes': importGOEliteParameters(run_parameter)
File "GO_Elite.py", line 1324, in importGOEliteParameters
parameters = UI.getUserParameters(run_parameter)
File "/home/stan/Desktop/GO-Elite_120beta/UI.py", line 1484, in
getUserParameters
GO_Elite.importGOEliteParameters('skip'); sys.exit()
File "/home/stan/Desktop/GO-Elite_120beta/GO_Elite.py", line 1324,
in importGOEliteParameters
parameters = UI.getUserParameters(run_parameter)
File "/home/stan/Desktop/GO-Elite_120beta/UI.py", line 1615, in
getUserParameters
os.makedirs(filepath(import_dir))
File "/usr/lib/python2.5/os.py", line 164, in makedirs
makedirs(head, mode)
File "/usr/lib/python2.5/os.py", line 164, in makedirs
makedirs(head, mode)
File "/usr/lib/python2.5/os.py", line 171, in makedirs
mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/BuildDBs'
---

I initially thought that there might be some issue with creating the
BuildDBs and wikipathways directory, so I created that one manually,
but to no avail.
Error:
---
stan@ntcdata1:~/Desktop/GO-Elite_120beta$ python GO_Elite.py
Traceback (most recent call last):
File "GO_Elite.py", line 1733, in <module>
if use_Tkinter == 'yes': importGOEliteParameters(run_parameter)
File "GO_Elite.py", line 1324, in importGOEliteParameters
parameters = UI.getUserParameters(run_parameter)
File "/home/stan/Desktop/GO-Elite_120beta/UI.py", line 1615, in
getUserParameters
os.makedirs(filepath(import_dir))
File "/usr/lib/python2.5/os.py", line 164, in makedirs
makedirs(head, mode)
File "/usr/lib/python2.5/os.py", line 164, in makedirs
makedirs(head, mode)
File "/usr/lib/python2.5/os.py", line 171, in makedirs
mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/BuildDBs'
---

All other parts regarding database updates work fine. I've reproduced
this on two different linux machines, one of it being the test-machine
(ntc-calc). You can take a look at the files there (Looking through my
mail archive: I've sent you the login details on 20 November 2009
02:52 GMT+1).

Update 1: I noticed that this problem disappeared when GO-Elite was
started as root user. Probable explanation: directory permission
related?

Update 2: I tried to recreate this on the Windows Platform and there I
don't get the error (WikiPathways content gets downloaded, but after
that the program just quits). The downloaded WP file looks in order.

Best,

-- Stan

[Nathan Salomonis]

Hey Stan,

Thanks for the report. Alex has setup an Ubunto machine that I will try this
on as well as on the webservice machine. If changing the permission on this
directory doesn't work I'll just make sure to include these directories with
the next small release. The next release will fix a bug which I found that
causes the adjusted permutation p-value to be unnecessarily rounded up or
down. This is already fixed on the webservice though.

Since GO-Elite doesn't filter on this p-value, it won't effect the default
results, but it's not great. Also, you will be able to just run the analysis
on just pathways, which should make runtime something like a minute per
dataset.

Best,
Nathan