Re: [galaxy-dev] a problem with python version
On Aug 2, 2012, at 1:59 PM, Rui Wang wrote: Hi All, we are installing a local galaxy instance but we met something puzzling. we are running galaxy on cent os 5.x and python 2.6.1. when we tried to upload data, it failed with the message * Dataset generation errors Dataset 5: brain.fa Tool execution generated the following error message: /usr/usc/python/2.6.1/lib/python2.6/site-packages/pytz/tzinfo.py:5: DeprecationWarning: the sets module is deprecated from sets import Set * However, when we tried to use the galaxy version tied to the OS, which is 2.4.3, we were able to upload successfully. Did anyone have the same experience? Any advice will be greatly appreciated. Hi Rui, I'd suggest upgrading your version of pytz with `easy_install --upgrade pytz`. Newer versions should correctly handle importing sets. --nate Thanks, Rui ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] a problem with python version
Hi Nate, Thanks for the suggestion. Our cluster does not belong to us so we had to request that to be added by their sysadmin. Before that we modified the code in a few scripts to ignore the deprecation warning, that also fixed the problem, should we remove these mods now since the new pytz is installed? A separate question, do you happen to know where I could find the instructions for setting up job submission for PBS/torque? There are pieces and bits information here and there but I didn't see any comprehensive one... Best Regards, Rui On Wed, Aug 8, 2012 at 7:54 AM, Nate Coraor n...@bx.psu.edu wrote: On Aug 2, 2012, at 1:59 PM, Rui Wang wrote: Hi All, we are installing a local galaxy instance but we met something puzzling. we are running galaxy on cent os 5.x and python 2.6.1. when we tried to upload data, it failed with the message * Dataset generation errors Dataset 5: brain.fa Tool execution generated the following error message: /usr/usc/python/2.6.1/lib/python2.6/site-packages/pytz/tzinfo.py:5: DeprecationWarning: the sets module is deprecated from sets import Set * However, when we tried to use the galaxy version tied to the OS, which is 2.4.3, we were able to upload successfully. Did anyone have the same experience? Any advice will be greatly appreciated. Hi Rui, I'd suggest upgrading your version of pytz with `easy_install --upgrade pytz`. Newer versions should correctly handle importing sets. --nate Thanks, Rui ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] a problem with python version
On Aug 8, 2012, at 12:06 PM, Rui Wang wrote: Hi Nate, Thanks for the suggestion. Our cluster does not belong to us so we had to request that to be added by their sysadmin. Before that we modified the code in a few scripts to ignore the deprecation warning, that also fixed the problem, should we remove these mods now since the new pytz is installed? If you upgrade pytz, the DeprecationWarnings should go away, and then you would not need to handle them. A separate question, do you happen to know where I could find the instructions for setting up job submission for PBS/torque? There are pieces and bits information here and there but I didn't see any comprehensive one... Our documentation is at: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster If there's something missing from this, please let us know. Thanks, --nate Best Regards, Rui On Wed, Aug 8, 2012 at 7:54 AM, Nate Coraor n...@bx.psu.edu wrote: On Aug 2, 2012, at 1:59 PM, Rui Wang wrote: Hi All, we are installing a local galaxy instance but we met something puzzling. we are running galaxy on cent os 5.x and python 2.6.1. when we tried to upload data, it failed with the message * Dataset generation errors Dataset 5: brain.fa Tool execution generated the following error message: /usr/usc/python/2.6.1/lib/python2.6/site-packages/pytz/tzinfo.py:5: DeprecationWarning: the sets module is deprecated from sets import Set * However, when we tried to use the galaxy version tied to the OS, which is 2.4.3, we were able to upload successfully. Did anyone have the same experience? Any advice will be greatly appreciated. Hi Rui, I'd suggest upgrading your version of pytz with `easy_install --upgrade pytz`. Newer versions should correctly handle importing sets. --nate Thanks, Rui ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
