[galaxy-dev] Adding a Tool for PANAMA

As part of a warmup, I added a tool for perming eQTL analysis using PANAMA( http://ml.sheffield.ac.uk/qtl/panama/). By default PANAMA writes to stderr and creates a PANAM_results.csv file in the same directory as the input files. I wrote a python wrapper https://bitbucket.org/saketkc/galaxy-cen

Re: [galaxy-dev] Adding a Tool for PANAMA

On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary wrote: > As part of a warmup, I added a tool for perming eQTL analysis using > PANAMA(http://ml.sheffield.ac.uk/qtl/panama/). > > > By default PANAMA writes to stderr and creates a PANAM_results.csv file in > the same directory as the input files. >

Re: [galaxy-dev] Adding a Tool for PANAMA

Hi Saket If you want to redirect the executable's stdout to a new Galaxy dataset you've defined as $output, something like: > '$output' is a workable idiom for a command line AFAIK - you need to escape the redirection '>' character or you'll confuse the xml parser. It's often possible to hack a com

[galaxy-dev] FW: order of menu items

Dear all, We have 2 different instances of Galaxy within our institute (a test and a production instance). The thing is that the two tool menus are not in the same order and we don't understand why because we've got the same configuration files on both instance. Test instance [cid:1A999B49-4E2D

Re: [galaxy-dev] FW: order of menu items

Hi Stephanie Try removing "integrated_tool_panel.xml" before you restart your galaxy server. There used to be a bug, where "integrated_tool_panel.xml" was not properly re-written after a restart. Regards, Hans-Rudolf On 06/03/2013 02:17 PM, Stephanie LE GRAS wrote: Dear all, We have 2 d

Re: [galaxy-dev] FW: order of menu items

Thank you very much for your very fast answer!! It's worked! Stephanie Le 03/06/13 14:36, « Hans-Rudolf Hotz » a écrit : >Hi Stephanie > > >Try removing "integrated_tool_panel.xml" before you restart your galaxy >server. There used to be a bug, where "integrated_tool_panel.xml" was >not prope

[galaxy-dev] Problem with tool in R

I have a problem with a tool in R. I can't load the RPostgreSQL library that I get the following error: ERROR: carregando pacotes exigidos: dbi My xml is this: r_wrapper.sh $script_file library(RPostgreSQL) ... I have this library installed at my system, what can I do?

[galaxy-dev] Tool Visibility

Suppose a tool didn't have any kind of configuration and therefore didn't need to be displayed in the "Analyze Data" part of Galaxy. Is there a way to modify tool_conf.xml so that a particular tool is only displayed in the Workflow editor? Thanks! Sincerely, Michael E. Cotterell Ph.D. Stude

Re: [galaxy-dev] Run galaxy on a specific SGE queue

Thanks Nate, In fact, our ~/.sge_request set workq by default. So, we have changed this parameter in ~/.sge_request file in order to change the working queue. Thanks again for your help, Sarah Nate Coraor a écrit : On May 22, 2013, at 11:36 AM, Sarah Maman wrote: Hi everyone, Gala

Re: [galaxy-dev] "login to ftp server failed" or "Problem with ftp connexion to Galaxy"

Dear Björn, Yes, this helps so much! Thanks a lot! Sincerely, Danni On May 31, 2013, at 3:34 PM, Björn Grüning wrote: > Hi Danni, > > the following is copied from a Mail from Jennifer Jackson 2 days ago. > For some reason this mail is not indexed from google, yet. > > Hope that helps, > B

Re: [galaxy-dev] [galaxy-user] List of genomes

Hi All, Can some one tell me the parameters used in the Galaxy "Mapping Illumina with Bowtie" defined as the "common settings"? I was trying to replicate the results from Galaxy using my own desktop installation of Bowtie but they differ by a rather big margin. Thanks much, Yongde On Mon, Apr

[galaxy-dev] storage utilisation on the main galaxy instance

Hi, I had storage utilisation of +60% and two days ago I decided to remove a large chunk of my data. I did this by clicking on the "delete" links for each of these datasets. Today I've logged in and see that my storage utilisation hasn't changed. Is there anything else that I need to do to free up

[galaxy-dev] Stable usegalaxy.org links for main Tool Shed repositories?

Hello all, Having asked this before, I knew the friendly and memorable alias http://usegalaxy.org/toolshed/ existed for the main Galaxy Tool Shed, http://toolshed.g2.bx.psu.edu Currently tools there have a unique stable shareable URL like this: http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blas

Re: [galaxy-dev] Information for Galaxy Event Horizon

Hi Sarah, We'd be happy to put this on the Galaxy Event Horizon page on the wiki. Since the event is over, we would list it in the past events section. Is there a web page for the workshop or slides that we can link to? And, for future reference, wiki update requests can be sent directly to Gal

Re: [galaxy-dev] Problem with tool in R

On Jun 3, 2013, at 10:13 AM, Ramon Tiburski wrote: > I have a problem with a tool in R. I can't load the RPostgreSQL library that > I get the following error: > > ERROR: carregando pacotes exigidos: dbi > > My xml is this: > > r_wrapper.sh $script_file > > > > library(RPostgreSQL) > ... >

[galaxy-dev] June 3, 2013 Galaxy Distribution

June 3, 2013 Galaxy Distribution *Complete News Brief * *Highlights:* * Visualization tool updates to Scatterplot

[galaxy-dev] mapping Summary from Bowtie

Dear Developers, I am running Bowtie2 through galaxy interface, previously it gives the the mapping summary and convert the format to sam.. but now it directly convert the fastq file to bam and doesnt give the mapping summary. how to get the mapping summary from bowtie2 using galaxy interface..