Re: [galaxy-dev] database migration error 79->80 (NameError: name 'BigInteger' is not defined)

2011-08-31 Thread Edward Kirton
please disregard my previous message, it was the developer's error; he accidentally had deleted or reverted something in the libs folder. On Wed, Aug 31, 2011 at 3:36 PM, Edward Kirton wrote: > hi, we are getting the following error migrating from 79 to 80. > curiously, my own galaxy didn't have

[galaxy-dev] database migration error 79->80 (NameError: name 'BigInteger' is not defined)

2011-08-31 Thread Edward Kirton
hi, we are getting the following error migrating from 79 to 80. curiously, my own galaxy didn't have this problem, but another developer here was getting this error. i moved him from sqlite to postgres but that didn't help. thanks for any assistance, ed Migrating 79 -> 80... galaxy.model.migrate.

[galaxy-dev] Question about data size

2011-08-31 Thread Jennifer Jackson
Hi Doug, I am going to forward your question to the galaxy-dev mailing list so that the development community can offer feedback based on their experience. Best, Jen Galaxy team On 8/15/11 9:47 AM, Douglas Hinerfeld wrote: HI There, I am trying to get my head around how much data is generat

Re: [galaxy-dev] [API] managing histories

2011-08-31 Thread Louise-Amélie Schmitt
Le 31/08/2011 19:34, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hello everyone, I'm currently trying to automate data loading and pre-processing through Galaxy's API, and I will need to delete and share histories at some point. I know the API is still very new but is there a way to do t

Re: [galaxy-dev] contribute tools to galaxy?

2011-08-31 Thread Greg Von Kuster
Hello Dongjun, see my answers to your question inline. On Aug 28, 2011, at 10:12 AM, Dongjun Chung wrote: > Hi All, > > I'm a newbie to galaxy and enjoying it a lot these days. Thanks for the great > work. > > I have a question regarding contribution of software to galaxy. We developed > a Ch

Re: [galaxy-dev] [galaxy-user] install tools on cluster

2011-08-31 Thread Nate Coraor
Wei,Xintao wrote: > Hi, > > I am learning how to install and configure Galaxy on our computer cluster. > Many third party tools, for example, bowtie, samtools, R and so on, have to > be installed and configured in order to install galaxy. Do I have to convert > the third party tools to MPI ver

[galaxy-dev] Backup strategy

2011-08-31 Thread Oleksandr Moskalenko
Hello, Considering the fact that a galaxy instance can grow to be quite large I wonder what Galaxy backup strategies and implementations other people actually have in use and are happy with. Thanks, Alex ___ Please keep all replies on the

Re: [galaxy-dev] [API] managing histories

2011-08-31 Thread Nate Coraor
Louise-Amélie Schmitt wrote: > Hello everyone, > > I'm currently trying to automate data loading and pre-processing > through Galaxy's API, and I will need to delete and share histories > at some point. I know the API is still very new but is there a way > to do that by any chance? Hi L-A, As of

Re: [galaxy-dev] bug or feature :)

2011-08-31 Thread Nate Coraor
Sarah Diehl wrote: > I just also found out about this bug (or feature). It is exactly the > same for me and I'm running an older Galaxy version (galaxy-dist > from April 8, 2011). Hi Sarah, Alex, Dannon fixed this bug back in July, in changeset 5814:ebb1014b237d, which is now available in galaxy-

[galaxy-dev] Wrapper generator (2).

2011-08-31 Thread J. F. J. Laros
Dear, A few months ago we proposed a wrapper generator, we are now at a point where we can present our idea as a working prototype. The wrapper generator is not specific for Galaxy, in principle any target can be used, but since Galaxy is our most prominent use case at the moment, we already impl

[galaxy-dev] Tophat non Sanger input

2011-08-31 Thread Stephen Taylor
Hi, Is there any plans to enhance the tophat wrapper to accept non Sanger fastqs, as for bowtie? https://bitbucket.org/galaxy/galaxy-central/changeset/7a9476924daf ? Kind regards and thanks, Steve ___ Please keep all replies on the list