Hello Will,

Thanks again for your reply. Yes I had already tried these but I got the same container.hpp error.

The only thing different in my case is that the names of the directories of the directories are a bit different:

export PBS_PYTHON_INCLUDEDIR=/usr/local/include/
export PBSCONFIG=/usr/local/bin/pbs-config
export LIBTORQUE_DIR=/usr/local/lib/libtorque.so
python scripts/scramble.py -e pbs_python

Any ideas?

Kind regards,
Makis



Date: Wed, 23 Sep 2015 07:06:32 -0700
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble
From: wholtz@lygos.com
To: makis4ever@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org

Hi Makis,

The thread I posted does have the exact same container.hpp error and proposes a solution.

Did you try setting your PBS_PYTHON_INCLUDEDIR to point to your torque/include directory, as mentioned in that thread?

from the thread:
export PBS_PYTHON_INCLUDEDIR=/usr/local/torque/include/
export PBSCONFIG=/usr/local/torque/bin/pbs-config
export LIBTORQUE_DIR=/usr/local/torque/lib/libtorque.so

-Will


On Wed, Sep 23, 2015 at 5:49 AM, Makis Ladoukakis <makis4ever@hotmail.com> wrote:
Hello Will,

Thank you for your reply. I had already checked this thread before as I browsed through the mailing list for "pbs_python" issues. It doesn't have the same errors (can't locate log.h and when i provide it it wants the container.hpp ) and up to one point i've already followed the "rescrambling" of the pbs_python.

Anyone else had any experience with that?

Thank you,
Makis

Date: Tue, 22 Sep 2015 09:35:11 -0700
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble
From: wholtz@lygos.com
To: makis4ever@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org


Here is an old thread that looks rather similar to your problems:

-Will


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


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