[phenixbb] Problem getting Phenix and Rosetta working together
nechols at lbl.gov
Fri Feb 1 09:22:27 PST 2013
---------- Forwarded message ----------
From: Dale Tronrud <dale at daletronrud.com>
To: phenixbb at phenix-online.org
Date: Fri, 01 Feb 2013 08:24:53 -0800
Subject: Re: [phenixbb] Problem getting Phenix and Rosetta working together
I was right! The source of the problem was in the stupid/silly
category. I had left the "export" out. I didn't notice the problem
since my test scripts didn't include the "-f" option, like yours, so
they were reading the init scripts every time. Thanks for pointing
me to your scripts so I could figure this out.
On 1/31/2013 2:11 PM, Terwilliger, Thomas C wrote:
> Hi Dale,
> I think the check that is giving you the error is:
> if (! $?PHENIX_ROSETTA_PATH) then
> echo "Skipping phenix rosetta tests: rosetta build not available."
> goto skip
> This is located in
> I'm puzzled how that can give you the error message you are getting unless the environment is different in the script you are running from your shell, but maybe now with the location of this file you can track it down?
> All the best,
> Tom T
> On Jan 31, 2013, at 3:01 PM, Dale Tronrud wrote:
>> I would like to get mr_rosetta running on my CentOS 6.3 64 bit
>> computer but I can't seem to get them connected. I'm probably
>> doing something stupid/silly but I'm stumped.
>> I've downloaded, installed and compiled rosetta3.4 in the folder
>> /usr/local/rosetta3.4. There are a bunch of files in rosetta_source/bin
>> and they are executable. However, typing the following commands
>> shows my problem.
>> [dale at athena tln]$ echo $PHENIX_ROSETTA_PATH
>> [dale at athena tln]$ ls -l $PHENIX_ROSETTA_PATH
>> total 156
>> drwxr-xr-x. 10 root root 4096 Mar 20 2012 Antibody
>> drwxr-xr-x. 3 root root 4096 Jul 26 2011 foldit-3.4
>> -rw-r--r--. 1 root root 1115 Mar 25 2012 new_apps.note
>> drwxr-xr-x. 25 root root 4096 Mar 20 2012 protocol_capture
>> -rw-r--r--. 1 root root 460 Mar 25 2012 README.Copyrights
>> -rw-r--r--. 1 root root 12 Mar 25 2012 README.version
>> -rw-r--r--. 1 root root 3345 Mar 25 2012 release.note
>> drwxr-xr-x. 19 root root 106496 Mar 25 2012 rosetta3.4_user_guide
>> drwxr-xr-x. 9 root root 4096 Mar 25 2012 rosetta_database
>> drwxr-xr-x. 61 root root 4096 Mar 20 2012 rosetta_demos
>> drwxr-xr-x. 11 root root 4096 Jan 30 15:27 rosetta_source
>> drwxr-xr-x. 7 root root 4096 Mar 27 2012 rosetta_tests
>> drwxr-xr-x. 13 root root 4096 Mar 20 2012 rosetta_tools
>> [dale at athena tln]$ phenix_regression.wizards.test_command_line_rosetta_quick
>> Skipping phenix rosetta tests: rosetta build not available.
>> I can try "mr_rosetta" itself but it just tells me that I need to
>> set PHENIX_ROSETTA_PATH.
>> What, in particular, is Phenix looking for to determine that
>> Rosetta is installed?
>> Dale Tronrud
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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