Re: [galaxy-dev] Galaxy tool creation help

Hi Guys Regarding my earlier question about history names. I found my answer on the wiki. ${input1.name} was what I was looking for. Cheers James. ___ Please keep all replies on the list by using "reply all" in your mail client. To man

[galaxy-dev] Galaxy Tool Creation Help

Hi All, Just a quick question regarding galaxy tool creation. In the tags Is it possible to get a datasets history number for the history the user initiated the job from? Seems unlikely, the reason I ask is that I have a tool that creates and output file for every input file and the program c

[galaxy-dev] Is the galaxy main toolshed compatible with local installs of galaxy-dist?

I was wondering whether the general policy is to keep the toolshed at toolshed.g2.bx.psu.edu compatible with galaxy-dist or galaxy-central. The reason I ask is that I went to install a tool from a production server I'm trying to setup based on galaxy-dist ... but got an error; The resource co

Re: [galaxy-dev] Tophat and bowtie jobs failed!

Hello Avazeh, Your jobs were effected by two issues: 1 - This specific error was due to a problem on our side with the data processing around the time that you submitted this email. Next time, submitting a bug report (green bug icon) for failed jobs that are clearly processing related will en

Re: [galaxy-dev] Job doesn't runnig

Hello Amandin, The job queue for NGS jobs on the public main Galaxy instance has been very busy since last Friday. We have been tracking the queue carefully all week and this afternoon took additional action to ensure fair access to the public resource. I didn't find any of your jobs in the

Re: [galaxy-dev] Tool migration errors

Hi John, On Jul 11, 2012, at 4:53 PM, John Chilton wrote: > On Wed, Jul 11, 2012 at 3:25 PM, Greg Von Kuster wrote: >> >> The way the tool shed components are architected do not result in this >> "syncing issues". You do not have to use the tool shed at all. Based on >> your statements that y

Re: [galaxy-dev] Where are the datatype associations stored?

Yeah, I had messed around with the database already, but removing the repository worked...Not sure why it was still loading it, but its all cool now...Thanks!ThonOn Jul 11, 2012, at 04:20 PM, Greg Von Kuster wrote:How did you try to remove the tool?  Do you mean that you used the Galaxy Admin UI t

Re: [galaxy-dev] Where are the datatype associations stored?

How did you try to remove the tool? Do you mean that you used the Galaxy Admin UI to Uninstall the repository? The datatypes are defined in a file named datatypes_conf.xml in the installed gmap repository. Assuming you can uninstall this repository, doing so will eliminate this problem. I

[galaxy-dev] Where are the datatype associations stored?

Hi,I had some more bad luck trying to install the GMAP stuff from the TOOLSHEd but revision 10 is broken since it does not allow you to select a section and just stores the programs in the main tree...But when I tried to remove the tool I got the following error for every run, since the sniffers wh

Re: [galaxy-dev] Tool migration errors

On Wed, Jul 11, 2012 at 3:25 PM, Greg Von Kuster wrote: > Hi Thon, > > > On Jul 11, 2012, at 3:38 PM, Anthonius deBoer wrote: > > My Galaxy version is the most recent, but I had cloned this from an earlier > version and have made lots of changes over the months... > > > This could pose problems un

Re: [galaxy-dev] Tool migration errors

I would not advise doing this. Based on your environment, I recommend that you do not attempt to install tools from the tool shed as doing so may pose problems for the same tools that you have altered in your environment and that you do not want to get "out of sync". On Jul 11, 2012, at 4:09

Re: [galaxy-dev] Tool migration errors

Hi Thon, On Jul 11, 2012, at 3:38 PM, Anthonius deBoer wrote: > My Galaxy version is the most recent, but I had cloned this from an earlier > version and have made lots of changes over the months... This could pose problems unless you are sure that your code is in a functional state after you

Re: [galaxy-dev] Tool migration errors

If I drop the following two tables, would those be reconstructed again correctly if I had the XML files in order?tool_version_associationand tool_versionThanksThonOn Jul 11, 2012, at 12:29 PM, Greg Von Kuster wrote:Hi Thon, What revision of Galaxy are you running? Have you made multiple attempts

Re: [galaxy-dev] Tool migration errors

My Galaxy version is the most recent, but I had cloned this from an earlier version and have made lots of changes over the months...I'm a little confused by the fact that the tool_shed tools seem to be defined BOTH by the various XML files AND the databaseI have on occasions manually edited the

Re: [galaxy-dev] Tool migration errors

Hi Thon, What revision of Galaxy are you running? Have you made multiple attempts at the migration? Are you running a postgres database? How many records do you have in your tool_dependency table in your database, and what is the status of each record? Have you made any changes to the Gala

[galaxy-dev] Tool migration errors

I'm getting this error when I try to run the tool migration:sh ./scripts/migrate_tools/0003_tools.sh install_dependenciesNo handlers could be found for logger "docutils"Repositories will be installed into configured tool_path location  ../shed_toolsAdding new row (or updating an existing row) for r

Re: [galaxy-dev] is there a way too automatically select references based on the genome of the dataset?

(1) There are quite a few tools that use the input's dbkey in some way, such as to retrieve sequence/index data. You'll see this quite a bit in tool command lines: --dbkey=${input.metadata.dbkey} With this approach, you won't need to provide a reference list parameter at all. Tools such as

Re: [galaxy-dev] Output file permissions different pbs:/// VS local:/// job runners

On Jul 5, 2012, at 9:21 PM, Rob Syme wrote: > Hi all. > > When I run the FastQC tool using the default local job runner, it produces a > folder of files with permission 664: > > -rw-rw-r-- 1 galaxy galaxy 17K Jul 5 17:29 duplication_levels.png > -rw-rw-r-- 1 galaxy galaxy 1.6K Jul 5 17:29 er

Re: [galaxy-dev] Galaxy cleaning up after it self after jobs fail

On Jul 5, 2012, at 8:02 PM, Anthonius deBoer wrote: > I am running galaxy on a system that normally runs all jobs on the cluster, > but some jobs need to be run locally... > But when I restart galaxy when these jobs are running, those jobs fail (and I > am fine with that)... > > But then when I

[galaxy-dev] is there a way too automatically select references based on the genome of the dataset?

I would like the reference list to be automatically selected based on the dbkey of the selected input... I think I've seen this, but I can'f seem to find an example. Anybody know? Should be some easy jquery i guess. Brad -- Brad Langhorst langho...@neb.com 978-380-756

Re: [galaxy-dev] Byte-range support for IGV ?

HI Nate ! Thanks for your response. However, I have a little problem concerning the launch of IGV application from my local galaxy tool main. In fact to run IGV I have always to connect to my server machine where IGV is installed. So it is embarrassing, since that other users cannot display IGV i

Re: [galaxy-dev] Byte-range support for IGV ?

On Jul 4, 2012, at 7:57 AM, Chebbi Mohamed Amine wrote: > HI Geert ! > I did well : > > > XSendFile on > XSendFilePath / > > > and > > > # Compress all uncompressed content. > SetOutputFilter DEFLATE > SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary >

Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever

Hi Greg, I will be at the galaxy conference and am experiencing the same problem. I would love to meet with you to look at this together. Emily From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Wednesday, July 11, 2012 7:55 AM To: Luobin Yang Cc: TerAvest, Emily; galaxy-...@bx.psu.edu Subje

Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever

Hello Luobin, I'm on my way to ISMB for a week, and then will be at the Galaxy Community Conference the following week, so I won't have time to help you track this problem down until some time in August unless you will be at either of these 2 conferences. Sorry for the inconvenience on this, b

Re: [galaxy-dev] pbs_python issues

I was successful in getting the bps_python egg to load finally. However, there is an issue that remains. When I submit a job it is sent to the local runner and not to pbs. Where should I start looking to change this work? Thanks, Iry On 7/10/12 12:00 PM, "galaxy-dev-requ...@lists.bx.psu.edu"

[galaxy-dev] DRMAA.NoActiveSessionError

Dear Galaxy-Dev-Team, I just restarted our local Galaxy instance at the University of Tuebingen, Germany, and obtained a DRMAA.NoActiveSessionError. You can find an excerpt from my shell below. The error can be avoided by disabling the SGE support in the universe.wsgi.ini. However, as our gal

Re: [galaxy-dev] javascript

> I just now tried visiting Galaxy main with my browser's javascript > turned off. Formerly the left Tools panel would appear with all > of the sections expanded, however now it is empty except for > "Workflows". Also, some of the top menu bar items work without > scripting, but others (including

[galaxy-dev] Job doesn't runnig

Dear Galaxy Dev Team- I try to run a job with Tophat for Illumina (version 1.5.0) but in my history job always stay at "Job is waiting to run". I use the following parameters : RNA-Seq FASTQ file: FASTQ Groomer on upload dataset Reference Genome : build-in index : Chicken (Gallus gallus): galGal

[galaxy-dev] javascript

Hi all, I just now tried visiting Galaxy main with my browser's javascript turned off. Formerly the left Tools panel would appear with all of the sections expanded, however now it is empty except for "Workflows". Also, some of the top menu bar items work without scripting, but others (including