Re: [galaxy-dev] pbs_python can't be installed via scramble

Hello Will, The second command returns the container.hpp inside the directory of the torque source which i used to install it: find / -name container.hpp /home/user/torque-5.1.1.2-1_18e4a5f1/src/include/container.hpp I noticed there is also a log.h file there. the first command doesn't return anything (I've search manually too, nothing inside /usr/local/include/). How do I fix this? Shall I change the export command of PBS_PYTHON_INCLUDEDIR? Thank you, Makis Date: Thu, 24 Sep 2015 08:31:07 -0700 Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble From: wholtz(a)lygos.com To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.galaxyproject.org And does find /usr/local/include -name container.hppor find / -name container.hppreturn torque/src/include/container.hpp ? My guess is you installed binaries for Torque, but the scrambling requires the Torque source (or at least the header files form Torque). -Will On Thu, Sep 24, 2015 at 1:16 AM, Makis Ladoukakis <makis4ever(a)hotmail.com&gt; wrote: 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(a)lygos.com To: makis4ever(a)hotmail.com CC: galaxy-dev(a)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(a)hotmail.com&gt; 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(a)lygos.com To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.galaxyproject.org Here is an old thread that looks rather similar to your problems:https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/... -Will On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis <makis4ever(a)hotmail.com&gt; 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(a)lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). 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