If you are running galaxy on a cluster, you can do one of two things: 1. install python on every node in your cluster and ensure they are identical. <-- I've had problems with this method 2. use pyenv to create a python environment that gets sourced before you start galaxy and before any galaxy jobs are run. I usually activate it by putting it in .bashrc
Iyad Kandalaft Bioinformatics Programmer Microbial Biodiversity Bioinformatics Science & Technology Branch Agriculture & Agri-Food Canada [email protected] | (613) 759-1228 ________________________________ From: [email protected] [[email protected]] on behalf of INKozin [[email protected]] Sent: June 14, 2014 6:18 PM To: Kandalaft, Iyad Cc: [email protected] Subject: Re: [galaxy-dev] troubleshooting Galaxy with LSF I'm not sure what you mean. I'm not using python virtual env, anaconda etc But I do set all variables which are required to run Galaxy such as DRMAA path, PYTHONPATH. In addition to the default Python 2.6, I also tried Python 2.7 built from source. On 13 June 2014 17:34, Kandalaft, Iyad <[email protected]<mailto:[email protected]>> wrote: Just for my curiosity, are you running a python environment isolated for galaxy or just using a system wide python environment? Regards, Iyad Kandalaft Microbial Biodiversity Bioinformatics Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada 960 Carling Ave.| 960 Ave. Carling Ottawa, ON| Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel [email protected]<mailto:[email protected]> Telephone | Téléphone 613-759-1228<tel:613-759-1228> Facsimile | Télécopieur 613-759-1701<tel:613-759-1701> Teletypewriter | Téléimprimeur 613-773-2600<tel:613-773-2600> Government of Canada | Gouvernement du Canada From: [email protected]<mailto:[email protected]> [mailto:[email protected]<mailto:[email protected]>] On Behalf Of INKozin Sent: Thursday, June 12, 2014 11:35 AM To: [email protected]<mailto:[email protected]> Subject: Re: [galaxy-dev] troubleshooting Galaxy with LSF The problem seems to be with DRMAA for Python. While it works fine on the OpenSuse 12.1 box, I'm getting a segfault on RH 6.4. Surprisingly, the job however gets submitted and run successfully. ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
