[galaxy-dev] Fastq quality score format

Hi, I have installed the local galaxy. In galaxy, I noticed that the quality score of fastq datasets have to be converted to sanger format before mapping with bowtie etc. But I did not find that the mapping tools (e.g. bowtie) require the quality score of fastq datasets must be sanger format.

[galaxy-dev] Fastq Groomer

Hi, I have installed our local galaxy. I have a question for Fastq Groomer: Is it an interior tool within Galaxy ? I mean you already incorporate it into Galaxy? Or, you incorporate an external tool into Galaxy ? Do you know some programs that can be used to do the quality score conversion ?

Re: [galaxy-dev] Local display application questions

As an alternative you can return "hidden" history items. Not exactly what you want perhaps... Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] namens Peter Cock [p.j.a.c...@googlemail.com] Verzonden: maandag 2 april 2012 15:38

Re: [galaxy-dev] [galaxy-user] Blast2GO local instance Re: Table with gene count reads

On Mar 24, 2012, at 7:30 AM, Peter Cock wrote: > > Have you seen the README file that comes with the > Blast2GO wrapper? Perhaps the 'install from toolshed' > could be tweaked to make this kind of documentation > more visible... > If you are installing a single repository that contains a file

[galaxy-dev] April 2012 Galaxy Update

Hello all, The April 2012 Galaxy Updateis now available. *Galaxy Update * is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy Updates * complements the *Galaxy Development News

[galaxy-dev] JSONDecodeERROR thrown, job left in "running" state.

Hi all - In running a samtools sort, we experienced the following exception from Galaxy: galaxy.jobs.runners.drmaa ERROR 2012-04-01 12:01:27,200 Job wrapper finish method failed Traceback (most recent call last): File "/Groups/Galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 286

Re: [galaxy-dev] Toolshed error when browsing own repo's

Try completely dropping and recreating your tool shed database. Also, what version of Galaxy are you running and what version of Python are you running? What database / version are you using? On Apr 2, 2012, at 11:13 AM, Joachim Jacob wrote: > Thanks for the suggestions, but no joy. > > 1.

Re: [galaxy-dev] Toolshed error when browsing own repo's

Thanks for the suggestions, but no joy. 1. I have created hgweb.config like this in the main install dir [galaxy@galaxy galaxy-dist]$ pwd /home/galaxy/galaxy-dist [galaxy@galaxy galaxy-dist]$ cat hgweb.config [paths] 2. I have removed all repo directories from the toolshed database [galaxy@galax

Re: [galaxy-dev] Toolshed error when browsing own repo's

This is the problem - it's unclear how your local tool shed environment is missing this file as it must have been generated the first time your started your tool shed application ( via sh run_community.sh ). Since this file does not exist, you must not yet have created any repositories, so manu

[galaxy-dev] Tool's xml: conditionals

Is it possible to have not-strictly-hierarchical conditionals in a tool's xml file? I would like to have a parameter being available depending on the state of another (previously defined) condition: ... ... According to the current documentation this doesn't seem to be suppor

Re: [galaxy-dev] Toolshed error when browsing own repo's

I am sorry, but I do not have a hgweb.config file in the install dir. My organisation: /home/galaxy/toolshed --> toolshed database for local repositories /home/galaxy/galaxy-dist --> main installation directory /home/galaxy/shed_tools --> dir for shed tools installed in galaxy Note:

Re: [galaxy-dev] Toolshed error when browsing own repo's

It should be in your Galaxy installation directory, and your on-disk repositories will be in a directory under the setting you've defined for the "file_path" configuration in your community_wsgi.ini file. On Apr 2, 2012, at 10:17 AM, Joachim Jacob wrote: > Hi Greg, > > > If it is most likely

Re: [galaxy-dev] Toolshed error when browsing own repo's

Hi Greg, If it is most likely a configuration error, I will check my settings, and let you know my progress. But one note: I do not have a hgweb.config file. Where is it supposed to reside? I cannot find this info on the toolshed wiki. Joachim On 04/02/2012 03:30 PM, Greg Von Kuster wro

Re: [galaxy-dev] Local display application questions

On Mon, Apr 2, 2012 at 2:00 PM, Lukasse, Pieter wrote: > Hi Greg, > > I made a tool for Galaxy which produces a normal XML output file and next to > that it also produces a HTML report with some quick summarized details for > the user. > > I could solve this by using 2 output files, but ... That

Re: [galaxy-dev] Toolshed error when browsing own repo's

Hi Joachim, I've not seen this in any of my tool shed development environments, nor using the test or main Galaxy tool sheds, so it is unlikely that this is a bug. It looks more likely to be a configuration problem in your local tool shed environment. Do the repositories defined in your hgweb

[galaxy-dev] Local display application questions

Hi Greg, I made a tool for Galaxy which produces a normal XML output file and next to that it also produces a HTML report with some quick summarized details for the user. I could solve this by using 2 output files, but I don't want to keep the history as concise as possible. To I found the opt

[galaxy-dev] Toolshed error when browsing own repo's

Hi all, On a local Toolshed freshly installed, I got these errors when browsing my repository. Perhaps a bug? Cheers, Joachim Server Error URL: http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories

Re: [galaxy-dev] R scripts for DESeq

Hello Vipin, Good to see this. just a quick question, does your interface has the functionality to define groups (say normal or control) for replicates/samples, as the way we define in edgeR/DESeq R script. Carlos, I think BAM input would be okay as it can be connected with tophat in the work

[galaxy-dev] Action in the Input tag

Dear Sir, Is it possible to include a localy stored HTML page in the action attribute of the inputs tag when defining a tool ? Best regards, Mohammed J. Chbeib __ Mohammed J. Chbeib +49-172-2044731 ___ Please