[galaxy-dev] 8-bit bytestrings

Hi, I am new to Galaxy and have not found a solution on dev-list to this 8-bit bytestrings error. That occurs on my local installation but not on Galaxy main server. Cheers Dataset generation errors *Dataset 22: Neighbor Joining Tree on data 20* The Galaxy framework encountered the follo

[galaxy-dev] Filter options for type=select based on former selection

Hi all!   I am facing a simple problem but can?t find a solution to solve it.   Before I start describing my problem here is the code from my tool:   mm9_64 hg19 custom (from history, fasta)

[galaxy-dev] Toolsheds and job runners

I've "inherited" a galaxy setup from someone (details: a contractor set it up but left it unfinished so I'm completing the job while discovering and documenting what was done). The catch: it's setup as a twin galaxy instance with one as a front-end web-server and the other as the job runner. Admit

Re: [galaxy-dev] Tool shed empty

Ahh.. Just realized that the installation to local galaxy is done from the web runner interface...under "search and browse toolsheds"...forgotten about that one! :) On Tue, Sep 4, 2012 at 2:13 PM, Ivan Lovric wrote: > Hi there, > > I've been having some trouble with the Tool Shed recently. This

Re: [galaxy-dev] Filter options for type=select based on former selection

Hi Sascha I don't quite understand your question... $sReference.ref is the variable you are looking for, isn't-it? Regards, Hans On 09/04/2012 11:40 AM, Sascha Kastens wrote: Hi all! I am facing a simple problem but can’t find a solution to solve it. Before I start describing my problem he

Re: [galaxy-dev] Filter options for type=select based on former selection

Hi Hans! I try to clarify my problem: The user selects a reference genome from . So in my scenario the value for $sReference.reference will be either "mm9_64" or "hg19". This value is needed to filter the supported reference annotations in case the user wants cuffcompare to be run. That?s why

Re: [galaxy-dev] Toolsheds and job runners

Hi Paul, In case you are not aware of it, the Galaxy tool shed wiki explains the tool shed: http://wiki.g2.bx.psu.edu/Tool%20Shed On Sep 4, 2012, at 6:25 AM, Paul-Michael Agapow wrote: > I've "inherited" a galaxy setup from someone (details: a contractor set it up > but left it unfinished so

[galaxy-dev] Programmatically deleting data sets from data libraries?

Hi, Galaxy Developers, I apologize for resurrecting another old thread (http://dev.list.galaxyproject.org/delete-data-library-via-API-td4553000.html), and for this long-winded email... First things first, I am trying to confirm what is suggested in the thread cited above (that data sets cannot

[galaxy-dev] password param type

Hi, Kind of feature request: parameter of type 'password' so that an entered password is not shown in the html form nor in the logs. Or is there already a way to achieve this that I missed out ? Cheers, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE

Re: [galaxy-dev] using data_ref to refer to column names?

So, sounds like maybe this feature does not existI'd like to request it (given a dataset, I'd like to be able to show the column headers of that dataset in a select box). Thanks, Dan On Wed, Aug 29, 2012 at 11:09 AM, Dan Tenenbaum wrote: > Hi, > I have some code that makes a plot and creates

Re: [galaxy-dev] Getting syntax error on Join + environment_setup_file not read

On Jul 28, 2012, at 8:09 PM, Peter Schmitt wrote: > New galaxy install. Running the tutorial Galaxy 101 and trying to do the > join. Get the following error in the stderr of the job: > Traceback (most recent call last): > File "/opt/galaxy/galaxy-dist/tools/new_operations/gops_join.py", line

[galaxy-dev] Would like to Post to Galaxy List

I would like to be able to post questions to the galaxy-dev and/or galaxy-user lists. I am using Galaxy with Amazon Cloud EC2. Could I have my name added to the list? Gloria I tried registering myself under my university's email: gkreitin...@wisc.edu _

[galaxy-dev] Automatic installation of third party dependancies

I've put together a tool wrapper for the htseq-count script that is part of the HTSeq python package and uploaded that to the tool shed. However, I have discovered that the tool dependancies do not install properly. There are a couple of issues that I've run into. 1) The biggest issue is the

[galaxy-dev] Migrate Galaxy database from MySQL to Postgres

Dear list members, Did anyone migrate the Galaxy database from MySQL to Postgres lately? Any verified script available? Simple solution by adding a postgres flag in mysqldump (http://dev.list.galaxyproject.org/MySQL-2-Postgres-td4139570.html) didn't work for me. It throws lots of syntax errors on

Re: [galaxy-dev] Automatic installation of third party dependancies

Hi Lance, Thanks for reporting these issues - the tool dependencies component is fairly new, so you may have uncovered some problems that need correction. I'll take a look at these. make corrections if necessary, and get back to you when all is functional. Thanks! Greg Von Kuster On Sep 4,

Re: [galaxy-dev] using data_ref to refer to column names?

On Tue, Sep 4, 2012 at 4:54 PM, Dan Tenenbaum wrote: > So, sounds like maybe this feature does not existI'd like to > request it (given a dataset, I'd like to be able to show the column > headers of that dataset in a select box). > Thanks, > Dan No, it doesn't, but I'd like it too: https://bi

Re: [galaxy-dev] using data_ref to refer to column names?

On Tue, Sep 4, 2012 at 4:57 PM, Peter Cock wrote: > On Tue, Sep 4, 2012 at 4:54 PM, Dan Tenenbaum wrote: >> So, sounds like maybe this feature does not existI'd like to >> request it (given a dataset, I'd like to be able to show the column >> headers of that dataset in a select box). >> Thank