Re: [galaxy-dev] Galaxy server configuration question

Dear Nate, I have a follow up question for you. If I move galaxy out of my DocumentRoot "/var/www/html" to "/home/galaxy/galaxy-dist" , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else

[galaxy-dev] 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

[galaxy-dev] 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-dev] [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-dev] Error while uploading

You can change the default location of tmp files by modifying the environment; we ran into this with samtools directly dumping temp sort files to a local node, causing the job to shut down. Setting TMPDIR worked for me. chris On Mar 11, 2012, at 5:10 PM, Dorset, Daniel C wrote: > Hi Luciano,

Re: [galaxy-dev] Error when installing toolshed tool

Hello Thon, This issue has been corrected in change set revision 6817:b199460443af, which is available in our central repository. The problem was due to the following tool contained in the repository not properly loading in the tool shed due to the required file named tool_data_table_conf.xml.

Re: [galaxy-dev] bacterial genomes missing?

Hi Alex, This particular issue didn't involve a correction to any code, just to the processing (our mistake). However, we do frequently make changes to code, mostly as general improvements but also in response to bugs found. These are available in the galaxy-central repository immediately, go

[galaxy-dev] Bug in "Export to File"

Hello, I am new here. I am running Galaxy at http://main.g2.bx.psu.edu/ using Mozilla Firefox 10.0.1 I try using "Export to File" tool on different files and workflows, and every time the report is: "Server Error An error occurred. See the error logs for more information. (Turn debug on to

Re: [galaxy-dev] NFS, Cluster and working directories questions

Hi Nate, and thanks for the reply - We saw the outputs_to_working_directory option in the .ini file, but it only concerns output files, is there a way to make a local copy of all the input files in the job working directory? (including indices) Hi L-A, Unfortunately no. This option was only

Re: [galaxy-dev] Bugs in FASTQ Quality Trimmer (version 1.0.0) on-line window

I have a guess: In the history (right hand column) entry for your FASTQ file, click on the pencil icon to edit the attributes. Try explicitly setting the type of FASTQ, e.g. for Sanger FASTQ Galaxy uses the filetype 'fastqsanger'. This controls how the quality string is interpreted (which is impor