[galaxy-dev] Can I contribute my Chinese locale files to the galaxy?

2011-11-01 Thread Hanfei Sun
Hi, all I'm from China and was interested in the i18n of galaxy. I wrote 4 locale files such as ginga.po/mo and tools.po/mo ,tried them on my server and it worked well. I want to contribute it to the galaxy repository but don't know how to do that because I don't have the permission to push

Re: [galaxy-dev] Running galaxy on external hard drive

2011-11-01 Thread Hotz, Hans-Rudolf
Hi Alessia Well, I am not a linux system expert, but I don't see a reason, why you can't run Galaxy from an external drive as long as it is mounted correctly and you have all the read and write permissions. The basic installation of Galaxy does not need any modification. The configuration files a

Re: [galaxy-dev] Can I contribute my Chinese locale files to the galaxy?

2011-11-01 Thread Dannon Baker
The easiest way is for you to issue a bitbucket pull request. http://confluence.atlassian.com/display/BITBUCKET/Forking+a+Bitbucket+Repository#ForkingaBitbucketRepository-Step-by-StepExampleNowthePullRequest Thanks for the contribution! -Dannon On Nov 1, 2011, at 5:16 AM, Hanfei Sun wrote: >

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-11-01 Thread Jesse Erdmann
Sorry, I think I went a little too deep into the weeds and lost my way there last night. I think the answer is to just leave the BED/WIG files visible in the first place and hide and link to the other items generated that aren't as likely to be reused is subsequent tasks. The metadata, like which

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-11-01 Thread Ross
On Tue, Nov 1, 2011 at 9:51 AM, Jesse Erdmann wrote: > files visible in the first place and hide and link to the other items > generated that aren't as likely to be reused is subsequent tasks.  The That sounds like a good way to use Html outputs - use the html history item to hide all the 'inform

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-11-01 Thread Jesse Erdmann
On Tue, Nov 1, 2011 at 9:07 AM, Ross wrote: > On Tue, Nov 1, 2011 at 9:51 AM, Jesse Erdmann wrote: >> files visible in the first place and hide and link to the other items >> generated that aren't as likely to be reused is subsequent tasks.  The > > That sounds like a good way to use Html outputs

Re: [galaxy-dev] Running galaxy on external hard drive

2011-11-01 Thread James Taylor
Excerpts from Hotz, Hans-Rudolf's message of 2011-11-01 09:42:38 +: > Well, I am not a linux system expert, but I don't see a reason, why you > can't run Galaxy from an external drive as long as it is mounted correctly > and you have all the read and write permissions. Also, if you want galaxy

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

2011-11-01 Thread Ross
Hi, Jesse. >Yep, that's what I meant. Meaning that if I set that on my HTML file, >the extra_files would hopefully pick up the metadata from the >metadata_source. AFAIK, not possible. No metadata is stored anywhere in the Galaxy database tables for any of the files *inside* an html object files_

Re: [galaxy-dev] Re Acutal user code

2011-11-01 Thread Chorny, Ilya
So it looks like for some reason galaxy is not picking up the information in the .e file. Not sure why. I even switched it back to writing the files to the pbs directory and it still did not pick up the .e files. BWA was core dumping but I was not given the error message in galaxy. BTW, I find

Re: [galaxy-dev] Clusters, Runners, and user credentials

2011-11-01 Thread Fields, Christopher J
I recall at the Galaxy conf there were questions on how secure this is (having the 'galaxy' user submit jobs as someone else). This would involve switching users on the cluster or would require user login information, correct? The way we planned on working around this was to just specify a user