[galaxy-user] March 12, 2012 Galaxy Development News Brief

Dear Galaxy Community, The latest Galaxy distributionhas been released: March 12, 2012 Galaxy Development News Brief *Mercurial pull:* new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 40f1816

Re: [galaxy-user] [galaxy-dev] Welcome.html page

Thanks everybody's help. It is not a problem anymore if I "empty cache" first then reload the page. But I got a more big problem here. Actually I am struggling with this problem for a long time. I am trying to deploy the galaxy production server. Originally I set up the galaxy using root use

[galaxy-user] March 12, 2012 Galaxy Development News Brief

Dear Galaxy Community, The latest *Galaxy distribution* has been released: March 12, 2012 Galaxy Development News Brief . *Mercurial pull:* new: % hg clone http://www.bx.psu.edu/hg/galaxygalaxy-dist upgrade: % hg pull -u -r 40f

Re: [galaxy-user] Advice on disabling SGE queue on galaxy-cloudman

Hi John, I'm glad you found an alternative solution. Late last night, I realized I had forgotten to email you yesterday as I completed implementing the feature for disabling the master from running jobs within CloudMan ( https://bitbucket.org/galaxy/cloudman/changeset/b21e967d30f9). I have not yet

Re: [galaxy-user] Metagenomics

Dear GALAXY and Jennifer Although the windshield analysis papers were good starters, They do not address conversed sequence purging or how to get at this information. If anyone has an automated approach I'd be interested . [Discard sequences from blast that have more then 4 hit >99%] Scott

Re: [galaxy-user] Metagenomics

On Mon, Mar 12, 2012 at 6:28 PM, John Major wrote: > A small warning re-the current cloud-Blast+ config. > > To properly use the metagenomic tools, if you use the blast+ galaxy tool, > make sure to export in blast.XML, then you'll need a script to parse out the > readID and the Hit_def (as the hit

Re: [galaxy-user] Metagenomics

A small warning re-the current cloud-Blast+ config. To properly use the metagenomic tools, if you use the blast+ galaxy tool, make sure to export in blast.XML, then you'll need a script to parse out the readID and the Hit_def (as the hit ID). It appears that the 'Hit_def' field contains the corre

[galaxy-user] Extracting number of reads from Bowtie analysis

Hello, I am new here! I am aligning Solexa files to genome using tool: NGS: Mapping: Map with Bowtie for Illumina. My question: What is the most easy way to check the number of aligned reads in the output from above? I couldn't find this number directly. I found a way, but it looks circula

Re: [galaxy-user] Problems starting Galaxy Cloudman

Also Greg Starting a new cloudman instance with a different cluster name than previously used will always give you a clean environment and setup so you can continue to always use the us-east region. Cheers, Enis On 10/03/2012 2:08 PM, "Ross" wrote: > Since Dannon is likely asleep, maybe this wil

Re: [galaxy-user] [galaxy-dev] Welcome.html page

If you right click (no idea what you do on a mac) inside the galaxy center panel and choose "reload frame", that might do the trick. On Mon, Mar 12, 2012 at 9:17 PM, Greg Edwards wrote: > Hi, > I've found that I need to be really aggressive with forcing a purge & > refresh of the browser when ch

Re: [galaxy-user] [galaxy-dev] Welcome.html page

Hi, I've found that I need to be really aggressive with forcing a purge & refresh of the browser when changing things like static/welcome.html and static/images/whatever.png. It might be a function of the nginx light-weight HTML renderer within Galaxy caching things on top of the normal caching. Yo