[galaxy-dev] Galaxy Workshops @ USC June 23-24
Hello all, There will be two Galaxy workshops at the University of Southern California (USC) next week. Both are presented by Jeremy Goecks of Emory University and the Galaxy team. *Both workshops are open to the public:* *Galaxy: A web‐based workbench for interactive and reproducible analysis of high‐throughput sequencing data, Thursday, June 23, 2011* At Aresty Auditorium, Harylene J Norris Cancer Research Tower, USC Health Science Campus, 1450 Biggy Street Registration is free, but required. Register at https://uschsl.qualtrics.com/SE/?SID=SV_bDaxnZwEfrfk1BG 9:15am-Noon Introduction to Galaxy including 30 min. QA Session 2:00pm-5:00pm High‐throughput sequencing data analysis including 45 min. QA Session *Progress and Challenges in Developing a Web-based Platform for Computational Biomedical Research, Friday, June 24, 2011 * See USC ISI AI Seminar Page ( http://ai.isi.edu/index.php?module=seminars/index) for details on time and location. The recent reliance on computation in biology has created an informatics crisis for biomedical researchers: computational resources are often difficult to use, communicating techniques and experiments is challenging, and reproducibility is very limited. Galaxy is one approach for addressing these problems. Galaxy is a popular Web-based platform for performing accessible, reproducible, and transparent genomics research. Galaxy provides a collaborative environment for performing complex analyses with automatic and unobtrusive provenance tracking; these features allow transparent sharing of both the precise computational details underlying an analysis and also intent, context, and narrative. Based on experiences with Galaxy, Jeremy will discuss some open problems that might be addressed using artificial intelligence methods and techniques. Thanks, Dave C. -- http://getgalaxy.org http://usegalaxy.org/ ___ 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] LDAP and API issue?
Ok, again sorry for being an idiot. I just had to modify the Apache .conf file related to Galaxy. For the time being I allowed everyone on the API (since it's not accessible via the Internet it's allright) so the all will eventually be changed but here is what I added in the file: Location /galaxy-dev AuthName Galaxy (development) AuthType Basic AuthBasicProvider ldap AuthLDAPURL ldap://ocs.embl.org/cn=Users,dc=embl,dc=org?uid; AuthzLDAPAuthoritative off Require valid-user /Location Location /galaxy-dev/api AuthName Galaxy (API) AuthType Basic AuthBasicProvider ldap AuthLDAPURL ldap://ocs.embl.org/cn=Users,dc=embl,dc=org?uid; AuthzLDAPAuthoritative off Satisfy any Allow from all /Location L-A Le 17/06/2011 14:14, Louise-Amélie Schmitt a écrit : Hi everyone I'm currently trying to use the API, but I think that our LDAP logging doesn't really help. When I call the script specifying the port in the url, here's what I get: urlopen error [Errno 111] Connection refused Then when I don't specify it Here's what I get: HTTP Error 401: Authorization Required !DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN htmlhead title401 Authorization Required/title /headbody h1Authorization Required/h1 pThis server could not verify that you are authorized to access the document requested. Either you supplied the wrong credentials (e.g., bad password), or your browser doesn't understand how to supply the credentials required./p hr addressApache/2.2.3 (CentOS) Server at localhost Port 80/address /body/html Did I miss anything? Is there a way to avoid that? Thanks LA ___ 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] LDAP and API issue?
Louise-Amélie Schmitt wrote: Ok, again sorry for being an idiot. I just had to modify the Apache .conf file related to Galaxy. For the time being I allowed everyone on the API (since it's not accessible via the Internet it's allright) so the all will eventually be changed but here is what I added in the file: Location /galaxy-dev AuthName Galaxy (development) AuthType Basic AuthBasicProvider ldap AuthLDAPURL ldap://ocs.embl.org/cn=Users,dc=embl,dc=org?uid; AuthzLDAPAuthoritative off Require valid-user /Location Location /galaxy-dev/api AuthName Galaxy (API) AuthType Basic AuthBasicProvider ldap AuthLDAPURL ldap://ocs.embl.org/cn=Users,dc=embl,dc=org?uid; AuthzLDAPAuthoritative off Satisfy any Allow from all /Location Hi L-A, I was about to reply, but you figured it out just in time. This is not inherently unsafe since everything behind the /api route requires an API key. --nate L-A Le 17/06/2011 14:14, Louise-Amélie Schmitt a écrit : Hi everyone I'm currently trying to use the API, but I think that our LDAP logging doesn't really help. When I call the script specifying the port in the url, here's what I get: urlopen error [Errno 111] Connection refused Then when I don't specify it Here's what I get: HTTP Error 401: Authorization Required !DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN htmlhead title401 Authorization Required/title /headbody h1Authorization Required/h1 pThis server could not verify that you are authorized to access the document requested. Either you supplied the wrong credentials (e.g., bad password), or your browser doesn't understand how to supply the credentials required./p hr addressApache/2.2.3 (CentOS) Server at localhost Port 80/address /body/html Did I miss anything? Is there a way to avoid that? Thanks LA ___ 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/ ___ 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] galaxy with SGE cluster
yes, your web server needs to be configured as an sge submit host to work seamlessly with galaxy. alternatives include submitting the jobs to the cluster outside of galaxy using another script that will either ssh or use expect. these alternatives are messy and to be avoided unless necessary. conditions which would require these solutions include if you wish to submit to multiple clusters or queues (e.g. user-specific queues, application-specific clusters) or require cluster jobs to be submitted as individual users rather than as the galaxy user (eg. for accounting). On Mon, May 16, 2011 at 10:44 AM, Shantanu Pavgi pa...@uab.edu wrote: Just want to confirm SGE configuration again. As mentioned earlier we started with a separate galaxy VM without any SGE installation. The SGE master node is installed on a separate system altogether. As I understand from your reply, we will need to install SGE on the galaxy VM first and configure it as a submit host with the main SGE master node. Is that correct? Are their any alternative approaches? ___ 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] galaxy with SGE cluster
On Jun 17, 2011, at 2:12 PM, Edward Kirton wrote: yes, your web server needs to be configured as an sge submit host to work seamlessly with galaxy. alternatives include submitting the jobs to the cluster outside of galaxy using another script that will either ssh or use expect. these alternatives are messy and to be avoided unless necessary. conditions which would require these solutions include if you wish to submit to multiple clusters or queues (e.g. user-specific queues, application-specific clusters) or require cluster jobs to be submitted as individual users rather than as the galaxy user (eg. for accounting). Thanks for the reply Edward and Nate. We got it working by configuring galaxy system as a submit host to master sge node, but I forgot to follow-up on the thread later on. Thanks again for your inputs.. -- Shantanu. On Mon, May 16, 2011 at 10:44 AM, Shantanu Pavgi pa...@uab.edu wrote: Just want to confirm SGE configuration again. As mentioned earlier we started with a separate galaxy VM without any SGE installation. The SGE master node is installed on a separate system altogether. As I understand from your reply, we will need to install SGE on the galaxy VM first and configure it as a submit host with the main SGE master node. Is that correct? Are their any alternative approaches? ___ 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/
