Re: [galaxy-dev] More problems installing Galaxy

2016-11-18 Thread Hernán Piqueras 
Hi Dannon


Thank you for the response. I have tried your suggestion, if I unalias 
everything this is the output:


bash-4.1$ virtualenv -p /usr/local/bin/python2.7 .venv
Traceback (most recent call last):
  File "/usr/bin/virtualenv", line 7, in 
from virtualenv import main
ImportError: No module named virtualenv


If I keep the alias, i.e.:


bash-4.1$ alias
alias easy_install='/usr/local/bin/easy_install-2.7'
alias pip='/usr/local/bin/pip2.7'
alias python='/usr/local/bin/python2.7'
alias virtualenv='/usr/local/bin/virtualenv-2.7'

then execute:

bash-4.1$ virtualenv -p /usr/local/bin/python2.7 .venv
Already using interpreter /usr/local/bin/python2.7
New python executable in .venv/bin/python2.7
Not overwriting existing python script .venv/bin/python (you must use 
.venv/bin/python2.7)
Installing setuptools.done.
Installing pip...done.


the output is pretty much the same as above:


bash-4.1$ sh galaxy/run.sh
+ shopt -s expand_aliases
+ source /home/galaxy/.bashrc
++ alias python=/usr/local/bin/python2.7
++ alias virtualenv=/usr/local/bin/virtualenv-2.7
++ alias pip=/usr/local/bin/pip2.7
++ alias easy_install=/usr/local/bin/easy_install-2.7
++ dirname galaxy/run.sh
+ cd galaxy
+ '[' -z '' ']'
+ GALAXY_LOCAL_ENV_FILE=./config/local_env.sh
+ '[' -f ./config/local_env.sh ']'
+ . ./config/local_env.sh
+ :
+ case "$1" in
+ break
+ ./scripts/common_startup.sh
+ shopt -s expand_aliases
+ source /home/galaxy/.bashrc
++ alias python=/usr/local/bin/python2.7
++ alias virtualenv=/usr/local/bin/virtualenv-2.7
++ alias pip=/usr/local/bin/pip2.7
++ alias easy_install=/usr/local/bin/easy_install-2.7
+ SET_VENV=1
+ /usr/local/bin/python2.7 -V
+ grep -q -e Anaconda -e 'Continuum Analytics'
+ CONDA_ALREADY_INSTALLED=0
+ DEV_WHEELS=0
+ FETCH_WHEELS=1
+ CREATE_VENV=1
+ REPLACE_PIP=1
+ COPY_SAMPLE_FILES=1
+ SAMPLES='
config/migrated_tools_conf.xml.sample
config/shed_tool_conf.xml.sample
config/shed_tool_data_table_conf.xml.sample
config/shed_data_manager_conf.xml.sample
lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
tool-data/shared/ucsc/builds.txt.sample
tool-data/shared/ucsc/manual_builds.txt.sample
tool-data/shared/ucsc/ucsc_build_sites.txt.sample
tool-data/shared/igv/igv_build_sites.txt.sample
tool-data/shared/rviewer/rviewer_build_sites.txt.sample
static/welcome.html.sample
'
+ RMFILES='
lib/pkg_resources.pyc
'
+ '[' 1 -eq 1 ']'
+ for sample in '$SAMPLES'
+ file=config/migrated_tools_conf.xml
+ '[' '!' -f config/migrated_tools_conf.xml -a -f 
config/migrated_tools_conf.xml.sample ']'
+ for sample in '$SAMPLES'
+ file=config/shed_tool_conf.xml
+ '[' '!' -f config/shed_tool_conf.xml -a -f config/shed_tool_conf.xml.sample 
']'
+ for sample in '$SAMPLES'
+ file=config/shed_tool_data_table_conf.xml
+ '[' '!' -f config/shed_tool_data_table_conf.xml -a -f 
config/shed_tool_data_table_conf.xml.sample ']'
+ for sample in '$SAMPLES'
+ file=config/shed_data_manager_conf.xml
+ '[' '!' -f config/shed_data_manager_conf.xml -a -f 
config/shed_data_manager_conf.xml.sample ']'
+ for sample in '$SAMPLES'
+ file=lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml
+ '[' '!' -f lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml -a -f 
lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample ']'
+ for sample in '$SAMPLES'
+ file=tool-data/shared/ucsc/builds.txt
+ '[' '!' -f tool-data/shared/ucsc/builds.txt -a -f 
tool-data/shared/ucsc/builds.txt.sample ']'
+ for sample in '$SAMPLES'
+ file=tool-data/shared/ucsc/manual_builds.txt
+ '[' '!' -f tool-data/shared/ucsc/manual_builds.txt -a -f 
tool-data/shared/ucsc/manual_builds.txt.sample ']'
+ for sample in '$SAMPLES'
+ file=tool-data/shared/ucsc/ucsc_build_sites.txt
+ '[' '!' -f tool-data/shared/ucsc/ucsc_build_sites.txt -a -f 
tool-data/shared/ucsc/ucsc_build_sites.txt.sample ']'
+ for sample in '$SAMPLES'
+ file=tool-data/shared/igv/igv_build_sites.txt
+ '[' '!' -f tool-data/shared/igv/igv_build_sites.txt -a -f 
tool-data/shared/igv/igv_build_sites.txt.sample ']'
+ for sample in '$SAMPLES'
+ file=tool-data/shared/rviewer/rviewer_build_sites.txt
+ '[' '!' -f tool-data/shared/rviewer/rviewer_build_sites.txt -a -f 
tool-data/shared/rviewer/rviewer_build_sites.txt.sample ']'
+ for sample in '$SAMPLES'
+ file=static/welcome.html
+ '[' '!' -f static/welcome.html -a -f static/welcome.html.sample ']'
+ for rmfile in '$RMFILES'
+ '[' -f lib/pkg_resources.pyc ']'
+ : config/galaxy.ini
+ '[' '!' -f config/galaxy.ini ']'
+ '[' '!' -f config/galaxy.ini ']'
+ : .venv
+ '[' 1 -eq 1 -a 1 -eq 1 ']'
+ '[' '!' -d .venv ']'
+ '[' 1 -eq 1 ']'
+ '[' -d .venv ']'
+ printf 'Activating virtualenv at .venv\n'
Activating virtualenv at .venv
+ . .venv/bin/activate
++ deactivate nondestructive
++ unset pydoc
++ '[' -n '' ']'
++ '[' -n '' ']'
++ '[' -n /bin/bash -o -n '' ']'
++ hash -r
++ '[' -n '' ']'
++ unset VIRTUAL_ENV
++ '[' '!' nondestructive = nondestructive ']'
++ VIRTUAL_ENV=/home/galaxy/galaxy/.venv
++

Re: [galaxy-dev] Using pbs-python with glibc version 2.12

2016-11-18 Thread Nate Coraor 
Hi David,

It looks like this is an issue with pbs_python and Torque 4.x. There's a
workaround available:

https://oss.trac.surfsara.nl/pbs_python/ticket/40

--nate

On Fri, Nov 18, 2016 at 6:06 AM, David Lee  wrote:

> Hi Nate,
>
> Thanks for your help. I now get the following error message:
>
>
> (.venv)[galaxy@newblue3 ~]$ python
> Python 2.7.5 (default, Oct 16 2013, 10:52:17)
> [GCC 4.4.7 20120313 (Red Hat 4.4.7-3)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import pbs
> Traceback (most recent call last):
>   File "", line 1, in 
>   File "/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/
> python2.7/site-packages/pbs/pbs.py", line 26, in 
> _pbs = swig_import_helper()
>   File "/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/
> python2.7/site-packages/pbs/pbs.py", line 22, in swig_import_helper
> _mod = imp.load_module('_pbs', fp, pathname, description)
> ImportError: /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/
> python2.7/site-packages/pbs/_pbs.so: undefined symbol: _Z13log_availablei
> >>>
>
>
> David
>
> On 17 November 2016 at 17:13, Nate Coraor  wrote:
>
>> Hi David,
>>
>> It sounds like you may have installed the version of pbs-python currently
>> in PyPI, which includes a copy of the Torque C library that is not
>> "manylinux"-safe (it is not backwards compatible to older systems). The
>> solution here is to install pbs-python from its source distribution:
>>
>> 1. Activate Galaxy's virtualenv: `. /panfs/panasas01/dedicated-
>> galaxy/galaxy/galaxy/.venv/bin/activate`
>> 2. `pip uninstall pbs-python`
>> 3. Download/unpack the source tarball from ftp://ftp.surfsara.nl/pub
>> /outgoing/pbs_python.tar.gz
>> 4. In the pbs_python source: `./configure --prefix=/panfs/panasas01/dedi
>> cated-galaxy/galaxy/galaxy/.venv`
>> 5. `make install`
>>
>> --nate
>>
>> On Thu, Nov 17, 2016 at 11:08 AM, David Lee 
>> wrote:
>>
>>> Hi,
>>>
>>>
>>> I'm trying to install Galaxy version 16.07 on a cluster with the PBS job
>>> scheduler that is using glibc version 2.12. The following error message
>>> suggests that pbs-python needs at least glibc version 2.14 -
>>>
>>>
>>>
>>> assert pbs is not None, PBS_IMPORT_MESSAGE
>>>
>>> AssertionError: The Python pbs-python package is required to use this
>>> feature, please install it or correct the following error:
>>>
>>> ImportError /lib64/libc.so.6: version `GLIBC_2.14' not found (required
>>> by /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/py
>>> thon2.7/site-packages/pbs/_pbs.so)
>>>
>>>
>>>
>>> I'm told by an administrator of the cluster that updating to glibc
>>> version 2.14 or higher would require a major overhaul of all the software
>>> on the cluster. Does anybody have a workaround for this problem? Could a
>>> newer version of glibc be used next to version 2.12 just for installation
>>> purposes?
>>>
>>>
>>> Thanks for your help, David
>>>
>>> ___
>>> 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/
>>>
>>
>>
>
___
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Re: [galaxy-dev] Using pbs-python with glibc version 2.12

2016-11-18 Thread David Lee 
Hi Nate,

Thanks for your help. I now get the following error message:


(.venv)[galaxy@newblue3 ~]$ python
Python 2.7.5 (default, Oct 16 2013, 10:52:17)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-3)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pbs
Traceback (most recent call last):
  File "", line 1, in 
  File "/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/
lib/python2.7/site-packages/pbs/pbs.py", line 26, in 
_pbs = swig_import_helper()
  File "/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/
lib/python2.7/site-packages/pbs/pbs.py", line 22, in swig_import_helper
_mod = imp.load_module('_pbs', fp, pathname, description)
ImportError: /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/
lib/python2.7/site-packages/pbs/_pbs.so: undefined symbol:
_Z13log_availablei
>>>


David

On 17 November 2016 at 17:13, Nate Coraor  wrote:

> Hi David,
>
> It sounds like you may have installed the version of pbs-python currently
> in PyPI, which includes a copy of the Torque C library that is not
> "manylinux"-safe (it is not backwards compatible to older systems). The
> solution here is to install pbs-python from its source distribution:
>
> 1. Activate Galaxy's virtualenv: `. /panfs/panasas01/dedicated-
> galaxy/galaxy/galaxy/.venv/bin/activate`
> 2. `pip uninstall pbs-python`
> 3. Download/unpack the source tarball from ftp://ftp.surfsara.nl/
> pub/outgoing/pbs_python.tar.gz
> 4. In the pbs_python source: `./configure --prefix=/panfs/panasas01/
> dedicated-galaxy/galaxy/galaxy/.venv`
> 5. `make install`
>
> --nate
>
> On Thu, Nov 17, 2016 at 11:08 AM, David Lee 
> wrote:
>
>> Hi,
>>
>>
>> I'm trying to install Galaxy version 16.07 on a cluster with the PBS job
>> scheduler that is using glibc version 2.12. The following error message
>> suggests that pbs-python needs at least glibc version 2.14 -
>>
>>
>>
>> assert pbs is not None, PBS_IMPORT_MESSAGE
>>
>> AssertionError: The Python pbs-python package is required to use this
>> feature, please install it or correct the following error:
>>
>> ImportError /lib64/libc.so.6: version `GLIBC_2.14' not found (required by
>> /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/
>> python2.7/site-packages/pbs/_pbs.so)
>>
>>
>>
>> I'm told by an administrator of the cluster that updating to glibc
>> version 2.14 or higher would require a major overhaul of all the software
>> on the cluster. Does anybody have a workaround for this problem? Could a
>> newer version of glibc be used next to version 2.12 just for installation
>> purposes?
>>
>>
>> Thanks for your help, David
>>
>> ___
>> 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/
>>
>
>
___
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/