On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis <makis4ever@hotmail.com> wrote:

Hello everyone,

I'm trying to set up a Galaxy instance on a multi-core server in my university so according to the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS

I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of pbs_python

and tried to setup pbs_python via scramble:

LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python

When I did that I got the error:

Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable)
Traceback (most recent call last):
File "scripts/scramble.py", line 50, in <module>
    egg.scramble()
File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble
    self.run_scramble_script()
File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in run_scramble_script
    raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) )
galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.4.0

so I did some digging around and found that the file I need is in

/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/

(please correct me if I am wrong)

So I tried again using:

PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python

but then I got the error:

In file included from src/C++/pbs_ifl.h:90:0,
                 from src/C++/pbs_wrap.cxx:2978:
/usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No such file or directory
#include "container.hpp"

Can someone help me please?

Kind regards,
Makis

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers).

Please consider the environment before printing this email.