add an option to set the ouput path for log files

[GoogleCodeExporter]

Hi,

It is said in the README file of the distribution 
(jmodeltest-2.1.2-20130103.tar.gz file):
        4.1. Required conditions
-----------------------------------------------------------------------------

In order to run jModelTest there will be some general constraints you have to
satisfy:

- You should run it from the jModelTest root directory (i.e. the directory where
you have unpackaged the distribution).
-----------------------------------------------------------------------------

Can you add and option/argument to change the output path. This way, we will be 
able to install once for many different users. Users usually don't have write 
permission into root/admin installation directories. 

This is the error I got when I tried to run jmodeltest2 as a normal user:
There was a problem building the html log files: 
/home/apps/jmodeltest2/jmodeltest-2.1.2/log/aP6.fas.jmodeltest.1360685129357.htm
l (Permission denied)

Thanks,
François 

Original issue reported on code.google.com by francois...@calculquebec.ca on 13 Feb 2013 at 8:19

[GoogleCodeExporter]

I should update the README file in order to clarify this point. In the newest 
version is not necessary to execute jModelTest from its directory. The error 
you are getting is for writing the html log files but the console output should 
be OK. If not, please let me know.

You can either disable logging or change the log directory to any other with 
permissions in $JMODELTEST_HOME/conf/jmodeltest.conf.

However, for the next release I'm going to add new arguments in order to set 
the logging path and redirect the console output.

Original comment by DiegoDL84 on 20 Feb 2013 at 6:52

• Changed state: Accepted
• Added labels: Component-Docs, Component-UI, Milestone-Release2.2, Type-Enhancement

[GoogleCodeExporter]

This option was added for the next release 2.1.3. Check software updates: 
http://code.google.com/p/jmodeltest2/wiki/Updates

Original comment by DiegoDL84 on 6 Mar 2013 at 12:14

[GoogleCodeExporter]

Original comment by DiegoDL84 on 6 Mar 2013 at 12:14

• Changed state: Verified

[GoogleCodeExporter]

The latest version of jmodeltest2 doesn't allow a user to run more than one job 
on the same machine, because the path for logs is still hardcoded.  An ordinary 
user (assuming the code was installed by root for a pool of users sharing the 
same machine) cannot change the contents of 
$JMODELTEST_HOME/conf/jmodeltest.conf; even if he could we couldn't allow it 
since another user (or the same) may already be using the code.  This path 
OUGHT to be set through a command line argument, just like  -o ; it is the 
simplest, most portable, and best solution to this problem that is stopping 
many of our users from using the code in a shared system at the moment.  We are 
forced to direct them to various machines so that only one instance of the code 
runs on any single machine at any time.  A lot of computing power and 
flexibility is wasted.

Original comment by jacques....@calculquebec.ca on 24 Feb 2014 at 6:46