Re: [galaxy-user] genome-wide Bisulfite analyses ... was Re: Infinite TopHat run

Hi Kanwar, > I interested in trying Bismark under Galaxy. Could you please point me > where I can use it. please have a look at the pull request ... https://bitbucket.org/galaxy/galaxy-central/pull-request/73/bismark-wrapper-issue-626 Cheers, bjoern > > Thanks > Kanwar > > On Mon, Oct 8, 201

Re: [galaxy-user] genome-wide Bisulfite analyses ... was Re: Infinite TopHat run

Bjoern, I interested in trying Bismark under Galaxy. Could you please point me where I can use it. Thanks Kanwar On Mon, Oct 8, 2012 at 8:08 AM, Björn Grüning < bjoern.gruen...@pharmazie.uni-freiburg.de> wrote: > Hi David, > > please do not hijack a different thread :) > If you are analysing B

Re: [galaxy-user] RNA-seq analysis withtout reference genome

Hello Alicia, There are two tools in the main Galaxy Tool Shed (http://toolshed.g2.bx.psu.edu/) that would likely be helpful. Read the input requirements for each to decide which is a better fit. Search for 'deseq' to find them: deseq_and_sam2counts deseq_hts To use these tools, a local

Re: [galaxy-user] Infinite TopHat run

Hi Philip, I'll reply to your bug report, but just for general information to others, the most common cause for delays is that the Galaxy main server is busy and/or the job itself large. Jobs can be queued ('grey') for up to a day when we are at peak usage. It is important to not stop/restar

Re: [galaxy-user] Data Limit

Hi Mark, The suggestions Kathy has given are all exactly on target. In addition, after purging, it may take up to a few hours (but usually less) for the database to fully update. If you need help, this wiki has help, including a screencast that walks through how to check for deleted/purged h

Re: [galaxy-user] data expiration policy

Hi Hiram, Thanks for contacting us about the issue, I hope I can help to clarify. Datasets in Galaxy histories exist until a user deletes them. On 10/5/12 9:57 AM, Hiram Clawson wrote: Good Morning Galaxy Universe: What is the data expiration policy at Galaxy for user created big* files that

Re: [galaxy-user] 答复: How to do an GO enrichment analysis in Galaxy?

Hi Yan, If you already have the GO terms, then the summary, counting, and statistics tools for tab delimited are probably what you are looking for. Tool groups to look in are: Text Manipulation -> Cut, Compute Join, Subtract and Group -> Group Statistics There is also the tool "Phenotype Ass

Re: [galaxy-user] galaxyTools volume not given enough time to attach

Thanks, I'll probably wait until that commit makes its way downstream. Joel From: eaf...@emory.edu Date: Mon, 8 Oct 2012 17:17:02 +1100 Subject: Re: [galaxy-user] galaxyTools volume not given enough time to attach To: thisisj...@hotmail.com CC: galaxy-user@lists.bx.psu.edu Hi Joel, This has been

[galaxy-user] please restore my account

Dear Sir or Madam, I had onpened multiple accounts at Galaxy Main, I did not know that it is against policy. I noticed this policy when I found that all the accounts are blocked. Would you please restore the account with email address jia...@iupui.edu? If you are not r

Re: [galaxy-user] Cannot install ncbi_blast_plus or other tools from Tool Shed: HTTP 500 error

Ah, I'll check with them. Thanks for the user list clarification. > Date: Mon, 8 Oct 2012 09:55:18 +0100 > Subject: Re: [galaxy-user] Cannot install ncbi_blast_plus or other tools from > Tool Shed: HTTP 500 error > From: p.j.a.c...@googlemail.com > To: thisisj...@hotmail.com > CC: galaxy-u...@bx

Re: [galaxy-user] Data Limit

Hi Mark, Did you have deleted data on multiple histories? The purging should have permanently deleted data on your currently active history. Maybe try going through your other histories and purging? You can navigate to them by clicking on the gear icon and selecting "Saved Histories." Kathy

Re: [galaxy-user] Data Limit

Hi Kathy I have just tried the "Purge Deleted Datasets' and refreshed + logged in/out but still have the 'You are over your disk quota". Don't suppose you have any other suggestions? BW Mark On 8 Oct 2012, at 16:02, So, Kathy GZ/US wrote: > Hi Mark, > > Galaxy still lets you reinstate dele

[galaxy-user] genome-wide Bisulfite analyses ... was Re: Infinite TopHat run

Hi David, please do not hijack a different thread :) If you are analysing Bisulfite data i would recommend to have a look at http://www.bioinformatics.babraham.ac.uk/projects/ ... especially at bismark. We have written a wrapper for bismark, its still in testing phase but if you like to try it ou

Re: [galaxy-user] Are tools must be installed in local machine?

Hi Sachit, Björn answer is correct. The issue is what is a "tool". There are what Galaxy calls "tools". Some of which are installed by default and some of which you can install from the toolshed. There are in many cases just wrappers to third-party tools that need to be installed and available in

Re: [galaxy-user] Data Limit

Hi Mark, Galaxy still lets you reinstate deleted files unless you permanently delete them. You can do this by hitting "Purge Deleted Datasets," which pops up in the list when you click on the gear icon in your history. Hope this helps! Kathy -Original Message- From: galaxy-user-boun...@

Re: [galaxy-user] Infinite TopHat run

Hi, there, I just got two genome-wide Bisulfite sequences from BGI and start to analyze the data. I am trying to use Galaxy; but I find there is no such platform available. Does anybody know where I can find this kind platform at Galaxy or other places. Thanks David On Fri, Oct 5, 2012 at 3:53

[galaxy-user] Data Limit

Despite clearly all my files and histories, the history is red (using 100%) and stating 'You are over your disk quota'. Is there a way to remedy this situation? Mark ___ The Galaxy User list should be used for the discussion of Galaxy anal

[galaxy-user] Infinite TopHat run

I am running Galaxy online, excuting TopHat on a fastq file, something which I previously have done without problems. This time, my data file is maybe double the size and does not seem to ever get done (I'm on the fourth day or so). Previously I have never experienced that this has taken more th

Re: [galaxy-user] Are tools must be installed in local machine?

I don't think you understood my question very well. Tophat and Bowtie are available by default in Galaxy. Tophat and Bowtie however is not installed in my operating system. Will it still work in Galaxy? On Mon, Oct 8, 2012 at 3:22 PM, Björn Grüning < bjoern.gruen...@pharmazie.uni-freiburg.de> wrot

Re: [galaxy-user] Are tools must be installed in local machine?

Hi Sachit, you need to install such tools by yourself, unless you are using some new tools from the toolshed. For example the ncbi-tools or BWA from the toolshed are capable of installing all dependency automatically. In the future the plan is to move all heavy tools to the toolshed with automatic

[galaxy-user] Are tools must be installed in local machine?

Hello. The tools like Tophat, Bowtie etc are pre-installed in Galaxy. Are those tools must be installed in order to work in Galaxy. For example: I am using Debian machine(Don't have tophat and bowtie installed). Will tophat and bowtie work in my local galaxy? Thanks

Re: [galaxy-user] Cannot install ncbi_blast_plus or other tools from Tool Shed: HTTP 500 error

On Mon, Oct 8, 2012 at 8:26 AM, Joel Rosenberg wrote: > So I'm trying to install the recently migrated ncbi_blast_plus tool from the > Tool Shed to my local galaxy instance running in EC2 and am getting errors at > the installation step. > > After clicking "Install to local Galaxy" I immediately

[galaxy-user] Cannot install ncbi_blast_plus or other tools from Tool Shed: HTTP 500 error

So I'm trying to install the recently migrated ncbi_blast_plus tool from the Tool Shed to my local galaxy instance running in EC2 and am getting errors at the installation step. After clicking "Install to local Galaxy" I immediately get: "Server Error An error occurred. See the error logs for m