Re: [galaxy-dev] API keys and id encryption (silly questions)

2011-08-30 Thread Louise-Amélie Schmitt
Le 29/08/2011 18:54, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Le 29/08/2011 15:52, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hello everyone, These questions are a bit silly but I'm really ignorant when it comes to security. Sorry about that. Why use API keys instead of

[galaxy-dev] set metadata step

2011-08-30 Thread Shantanu Pavgi
Hi, There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What is involved in this step? Is it run for every dataset/output being generated in the galaxy? -- Thanks, Shantanu. ___ Please keep all replies on the list

Re: [galaxy-dev] set metadata step

2011-08-30 Thread Nate Coraor
Shantanu Pavgi wrote: Hi, There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What is involved in this step? Is it run for every dataset/output being generated in the galaxy? Hi Shantanu, Metadata is always detected/set on all job outputs. This setting simply

Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

2011-08-30 Thread Louise-Amélie Schmitt
I just changed it and ran into an error, so I modified the line and it now works fine: $__app__.security.encode_id( '%s' % $input1.id ) What was the 'file.' originally for? Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit : Thanks a lot! I found another way to do it but it is awfully more

Re: [galaxy-dev] set metadata step

2011-08-30 Thread Shantanu Pavgi
On Aug 30, 2011, at 9:16 AM, Nate Coraor wrote: Shantanu Pavgi wrote: Hi, There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What is involved in this step? Is it run for every dataset/output being generated in the galaxy? Hi Shantanu, Metadata is always

Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

2011-08-30 Thread Nate Coraor
Louise-Amélie Schmitt wrote: I just changed it and ran into an error, so I modified the line and it now works fine: $__app__.security.encode_id( '%s' % $input1.id ) What was the 'file.' originally for? On the API side, a library or history's contents are all identified by ID, so:

Re: [galaxy-dev] set metadata step

2011-08-30 Thread Nate Coraor
Shantanu Pavgi wrote: On Aug 30, 2011, at 9:16 AM, Nate Coraor wrote: Shantanu Pavgi wrote: Hi, There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What is involved in this step? Is it run for every dataset/output being generated in the galaxy? Hi

Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

2011-08-30 Thread Louise-Amélie Schmitt
Le 30/08/2011 16:51, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: I just changed it and ran into an error, so I modified the line and it now works fine: $__app__.security.encode_id( '%s' % $input1.id ) What was the 'file.' originally for? On the API side, a library or history's contents

Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

2011-08-30 Thread Nate Coraor
Louise-Amélie Schmitt wrote: Le 30/08/2011 16:51, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: I just changed it and ran into an error, so I modified the line and it now works fine: $__app__.security.encode_id( '%s' % $input1.id ) What was the 'file.' originally for? On the API side,

[galaxy-dev] Tools requiring java can't find java

2011-08-30 Thread Chorny, Ilya
This is probably a question for our sys admin but when I run tools such as GATK I get an error java command not found. I can execute java from the command line and it works. Further I can grab the drmaa submission script (ie galaxy_job_id.sh) and qsub it from the command line and it finds

Re: [galaxy-dev] Tools requiring java can't find java

2011-08-30 Thread George Marselis
Yes, your java path is not set, because you are using an non-login shell. Indeed, you should be talking to your sysadmins. George Marselis, systems administrator Building #2, Level 4, room 4327 Computational Bioscience Research Center, KAUST Land: +966-2-808-2944, Mobile: +966-56-321-7713,

Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

2011-08-30 Thread Louise-Amélie Schmitt
Le 30/08/2011 18:00, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Le 30/08/2011 16:51, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: I just changed it and ran into an error, so I modified the line and it now works fine: $__app__.security.encode_id( '%s' % $input1.id ) What was the

Re: [galaxy-dev] Tools requiring java can't find java

2011-08-30 Thread Chorny, Ilya
How do I set my path in a non login shell? From: George Marselis [mailto:george.marse...@kaust.edu.sa] Sent: Tuesday, August 30, 2011 9:40 AM To: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tools requiring java can't find java Yes, your java path is not set, because you

Re: [galaxy-dev] Tools requiring java can't find java

2011-08-30 Thread Chris Fields
The following has a bit of advice on that: http://www.admon.org/difference-between-login-shell-and-non-login-shell/ chris On Aug 30, 2011, at 1:03 PM, Chorny, Ilya wrote: How do I set my path in a non login shell? From: George Marselis [mailto:george.marse...@kaust.edu.sa] Sent:

Re: [galaxy-dev] Tools requiring java can't find java

2011-08-30 Thread Chris Fields
Gah, wrong link, apologies (the other one is okay, if a bit wonky): http://www.linuxfromscratch.org/blfs/view/cvs/postlfs/profile.html chrus On Aug 30, 2011, at 1:12 PM, Chris Fields wrote: The following has a bit of advice on that:

[galaxy-dev] August 30, 2011 Galaxy Development News Brief

2011-08-30 Thread Jennifer Jackson
August 30, 2011 Galaxy Development News Brief http://galaxyproject.org/wiki/News%20Briefs/2011_08_30 Source: http://getgalaxy.org new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 949e4f5fa03a What's New ISMB/ECCB, BOSC, and 3DSIG 2011 Slides