Re: [galaxy-dev] Multi File upload api

2013-05-31 Thread Alex.Khassapov
Thanks John, We do have pretty old code, so I applied your patches. One minor problem, in multi_upload tool Dataset Name is ignored, just picks the first file name. Do we need to update upoald.py or multi_upload.xml? -Alex -Original Message- From: jmchil...@gmail.com

[galaxy-dev] [GSoC 2013] Introduction

2013-05-31 Thread Saket Choudhary
Hi Everyone! I have been selected to work on the eQTL pipeline and visualisation for the Galaxy Project as part of the Google Summer of Code 2013 ( http://www.google-melange.com/gsoc/homepage/google/gsoc2013) I am pursuing my fourth year of undergraduate studies at Indian Institute of Technology

Re: [galaxy-dev] [GSoC 2013] Introduction

2013-05-31 Thread Björn Grüning
Welcome Saket! Interesting topic ... wish you all the best and don't hesitate to ask. There is also a galaxyproject channel on freenode. Cheers, Björn Hi Everyone! I have been selected to work on the eQTL pipeline and visualisation for the Galaxy Project as part of the Google Summer of

Re: [galaxy-dev] [GSoC 2013] Introduction

2013-05-31 Thread Björn Grüning
Welcome Saket! Interesting topic ... wish you all the best and don't hesitate to ask. There is also a #galaxyproject channel on freenode. Cheers, Björn Hi Everyone! I have been selected to work on the eQTL pipeline and visualisation for the Galaxy Project as part of the Google Summer of

Re: [galaxy-dev] [GSoC 2013] Introduction

2013-05-31 Thread Ross
Hi, Saket. Welcome aboard - help is always available here or irc if you're in the right timezone. https://chgr.mc.vanderbilt.edu/plato/https://chgr.mc.vanderbilt.edu/plato/steps/3 is a brand new eQTL option from Marylyn Ritchie's group I stumbled across at

Re: [galaxy-dev] Internal Server Error during installation of ncbi_blast_plus

2013-05-31 Thread Keilwagen, Jens
Hi Greg, thanks for your comment. Some days ago, I updated Galaxy following: http://wiki.galaxyproject.org/News/2013_04_08_Galaxy_Security_Release Here is what hg sum said parent: 9292:2cc8d10988e0 security_2013.04.08 controllers/history: use get_history in switch_to_history Zweig: stable

[galaxy-dev] Status of Galaxy Cloud Instance dev

2013-05-31 Thread Joachim Jacob | VIB |
Hi all, I am planning to launch a Galaxy Cloud Instance, to run for about one month. But I believe I've read somewhere a new image of Galaxy on AWS is being prepared right now. Can somebody update me on the status? Perhaps it is smart to wait a few days with launching through CloudLaunch

Re: [galaxy-dev] Status of Galaxy Cloud Instance dev

2013-05-31 Thread Dannon Baker
No firm release set for the new cloudman yet, but you can always follow development here: https://trello.com/board/galaxy-cloudman/5136209e9beefacb77004e6d There are a few final issues we're wrapping up before we can release, but we're hoping it'll be soon. On Fri, May 31, 2013 at 7:31 AM,

Re: [galaxy-dev] Status of Galaxy Cloud Instance dev

2013-05-31 Thread John Chilton
Hey Dannon, Thanks for the link, I saw that you had moved some cards to a CloudMan board but I was never able to find it. Could you enable comments for non-board members like the Galaxy Development Trello allows? You know I have a compulsion to comment on everything Galaxy related anywhere on

Re: [galaxy-dev] [GSoC 2013] Introduction

2013-05-31 Thread Samuel Lampa
Cool! :) Feel free to join the Google+ group as well, and link your blog posts there, to notify users (and make it easy for us to share further): http://gplus.to/galaxyportal Cheers // Samuel On 05/31/2013 08:35 AM, Saket Choudhary wrote: Hi Everyone! I have been selected to work on the

Re: [galaxy-dev] Status of Galaxy Cloud Instance dev

2013-05-31 Thread Dannon Baker
On Fri, May 31, 2013 at 9:51 AM, John Chilton chil...@msi.umn.edu wrote: Could you enable comments for non-board members like the Galaxy Development Trello allows? Of course, actually thought I'd already done that. Fixed! ___ Please

Re: [galaxy-dev] Multi File upload api

2013-05-31 Thread Hakeem Almabrazi
Hi guys, I am sure I will be looking into this shortly but now I want to get the one file case working first :). Do you guys have any idea why the example_watch_folder.pl will copy the file but not its contents? The file it copies into the library folder is empty. How can I go about

[galaxy-dev] June 2013 Galaxy Update

2013-05-31 Thread Dave Clements
Hello all, The June 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_06 . *Highlights:* - *Register http://wiki.galaxyproject.org/Events/GCC2013/Register for GCC2013 http://wiki.galaxyproject.org/GalaxyUpdates/2013_06#GCC2013 by 7 June to avoid

Re: [galaxy-dev] Multi File upload api

2013-05-31 Thread John Chilton
This changeset is where I implemented collecting and assigning names for multiple file datasets: https://bitbucket.org/msiappdev/galaxy-extras/commits/bfb07a8c8b7b4c404339cd1efe50f9b2becb3b62 -John On Fri, May 31, 2013 at 1:21 AM, alex.khassa...@csiro.au wrote: Thanks John, We do have

[galaxy-dev] login to ftp server failed or Problem with ftp connexion to Galaxy

2013-05-31 Thread Danni Yu
To whom this may concern, This is Danni Yu, a Galaxy user starting to use Galaxy since 2011. I was able to upload large files through ftp in 2011 and 2012. Now, I am facing the same problem as the other users (such as Barbara Sixt on May 27, 2013 and Fabrice Besnard on May 22, 2013). The

Re: [galaxy-dev] login to ftp server failed or Problem with ftp connexion to Galaxy

2013-05-31 Thread Björn Grüning
Hi Danni, the following is copied from a Mail from Jennifer Jackson 2 days ago. For some reason this mail is not indexed from google, yet. Hope that helps, Björn Dear Galaxy Main Community, We apologize for recent FTP login issues, but are glad to report that a solution is now in

Re: [galaxy-dev] Getting example_watch_folder.py to work...

2013-05-31 Thread Hakeem Almabrazi
In case someone has the same issue, This is resolved by extending the sleep time found here http://gmod.827538.n3.nabble.com/Trouble-Shooting-example-watch-folder-py-td4030355.html From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Hakeem

[galaxy-dev] uploading large datasets into a new instance of Galaxy on a Mac Pro

2013-05-31 Thread Elwood Linney
Hello, I installed Galaxy on a new Mac Pro with 64gb of ram and a solid state first drive and 3 , 2tb normal drives. I can upload from my desktop a smaller file like a reference list or a cuffdiff file but when I try to load a 16gb fastq file it just does not load. Given that I have my files on

Re: [galaxy-dev] Storage question for Galaxy-Admins

2013-05-31 Thread Adam Brenner
Raj, I agree with the points Alex made. It would be much easier to start small and then work your way up. I recently setup galaxy for our HPC cluster for the entire school of medicine. Its only a few ~month into our setup but we are currently using ~300GB of storage. This is part of our larger

Re: [galaxy-dev] uploading large datasets into a new instance of Galaxy on a Mac Pro

2013-05-31 Thread Adam Brenner
How are you trying to upload the data to Galaxy? Are you using the web interface? Or...? -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/