[galaxy-user] Concatenate fasta tool problem

Hi, I'm trying to use the concatenate fasta tool at http://main.g2.bx.psu.edu/root?tool_id=fasta_concatenate0 to concatenate an xmfa file output from mauve (headers formatted to following standard: >1:517-24215(+)|0402981.fa but am receiving the following error. Traceback (most recent call last):

Re: [galaxy-user] biomart error

Hello Christophe, I am unable to duplicate - BioMart appears to be functioning as expected this morning. Would you have time to run your query again? If the problem persists, if you could share your history with me (Options -> Share or Publish -> email back link) and list out the exact steps

Re: [galaxy-user] keeping aditional data in the aaChanges tool

Hello Ximena, Thank you for bring this to our attention, we are able to duplicate these same results. A "name" attribute (such as an rs number) is an important data tag and we would like to be able to have the tool retain this data if possible. Our development team is currently investigating

Re: [galaxy-user] Concatenate fasta tool problem

Hello Paul, As a double check that this was not a transient server problem (due to usage), please try a quick re-run. If the problem persists, would you have time to share your history containing the error? Please use "Options -> Share or Publish" and email the link back to me directly. We w

Re: [galaxy-user] error occurred when converting the SOLID output to fastq

Hello Jia-Xing, It might be a good idea to double check the file format and FTP transfer by reloading the data and running the tool again. Then, if the problem is persistent, please share a link to your history containing the original and new loaded data tool errors and we would be glad to exa

Re: [galaxy-user] biomart error

I am also getting the same error with my local biomart and local galaxy installations. Thanks, Liisa From: Jennifer Jackson To: Christophe Klopp Cc: galaxy-user@lists.bx.psu.edu Date: 2011-05-31 09:32 Subject: Re: [galaxy-user] biomart error Sent by: galaxy-user-boun...@lists.bx.psu.edu

Re: [galaxy-user] Mycoplasma pneumoniae M129 and FH reference genome

Hello David, The genome for Mycoplasma pneumonia M129 is available as a reference genome (see "attributes" assignment too via the pencil icon), however it is not yet available in all NGS tools. We add both M129 and Mycoplasma pneumonia FH to our list of new genomes to process through all too

Re: [galaxy-user] biomart error

This is the exact error I am getting... Traceback (most recent call last): File "galaxy_dist/lib/galaxy/jobs/runners/local.py", line 58, in run_job job_wrapper.prepare() File "galaxy_dist/lib/galaxy/jobs/__init__.py", line 361, in prepare self.tool.exec_before_job( self.queue.app, inp

Re: [galaxy-user] Mycoplasma pneumoniae M129 and FH reference genome

Jen, Thanks for the useful tips! Yes, the NCBI bioproject link is the correct source for the FH strain. Thanks, David -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Tuesday, May 31, 2011 10:07 AM To: David K Crossman Cc: galaxy-user@lists.bx.psu.ed

Re: [galaxy-user] biomart error

Hello Lisa, I noticed your stack trace in another message you sent - pasted below. If this is the problem you are seeing, then upgrading your Galaxy instance to the latest version will fix the problem. This issue was fixed in change set 5589. This is the exact error I am getting... Tracebac

Re: [galaxy-user] biomart error

Hi Greg, I thought I was up to date. When I run the following command I get 'no changes found' hg incoming real URL is https://bitbucket.org/galaxy/galaxy-dist comparing with http://www.bx.psu.edu/hg/galaxy searching for changes no changes found [galaxy@galaxy_dist]$ Thanks, Liisa From: Greg

Re: [galaxy-user] biomart error

Hi Lisa, Very sorry for the confusion - you are correct! The tip of the galaxy-dist repo at https://bitbucket.org/galaxy/galaxy-dist is change set 5585, so the fix is not available in the dist repo yet, and probably won't be there for another few weeks. If you don't want to wait, you can pu

Re: [galaxy-user] biomart error

Hello Christophe, Very sorry, the Biomart issue was known and addressed in the galaxy-central code repository, but we have determined that is has not yet been applied to the Galaxy main server. We will be doing this shortly. Once it is done, I will write again. If you would be able to re-test

Re: [galaxy-user] biomart error

Hello - Galaxy main has been updated and I was able to send the D.rerio data from BioMart back to into my test history without any problems. Please give this a try as well and if you continue to have issues, sharing your history with us would be very helpful. Thank you for your patience and

Re: [galaxy-user] biomart error

You can also only pull the 5589 changeset - this one *just* missed the stable release (stable is at 5588): % hg pull -r 316f79f7bc1a https://bitbucket.org/galaxy/galaxy-central/ % hg update --nate Greg Von Kuster wrote: > Hi Lisa, > > Very sorry for the confusion - you are correct! The tip

Re: [galaxy-user] biomart error

Thanks! Working now :) Liisa From: Nate Coraor To: Greg Von Kuster Cc: Liisa Koski , galaxy-user@lists.bx.psu.edu Date: 2011-05-31 14:02 Subject: Re: [galaxy-user] biomart error You can also only pull the 5589 changeset - this one *just* missed the stable release (stable is at 5588):