If you have a form with an input like this:
<param name="input1" type="select" dynamic_options="get_options()" />
And the options dynamically generated have integers as values, e.g.
options tuples like this:
[ "One", 1, 1 ],
[ "Two", 2, 0 ],
[ "Three", 3, 0 ]
When you try to submit the galaxy form you always get the validation
error "An invalid option was selected, please verify".
On Mon, Mar 12, 2012 at 6:28 PM, John Major <john.e.major.jr(a)gmail.com> wrote:
> A small warning re-the current cloud-Blast+ config.
> To properly use the metagenomic tools, if you use the blast+ galaxy tool,
> make sure to export in blast.XML, then you'll need a script to parse out the
> readID and the Hit_def (as the hit ID). It appears that the 'Hit_def' field
> contains the correct key to the taxonomy database. Specifically, the
> Hit_def field is in the format #_#, where the 'gi' id is the first #. The
> tabular (normal and extended) data does not contain this info.
> I noticed this after attempting to use the tabular data, and using a trimmed
> col (supposed to be hit seqID), but my results always came back as a
> ranked list of the most sequenced genomes in nt.... basically keying in
Can you expand on that with a specific example (ideally on the galaxy-dev
list, CC'd, since BLAST+ isn't event available on the public galaxy)?
Also which version of BLAST+ are you using since I recall some changes
to the tabular output IDs prior to 2.2.25 (which is what the wrappers were
tested on, I've not tried 2.2.26 yet).
I'm getting this error when I try to install the NGS Java toolkit toolshed...
Version information for the tools included in the java_genomics_toolkit repository is missing. Reset all of this repository's metadata in the tool shed, then set the installed tool versions from the installed repository's Repository Actions menu. Installed 1 repository and all tools were loaded into tool panel section NGS: Toolkit:
Installed repositories: java_genomics_toolkit.
Any idea why the version number stuff is not correctly inserted in the database?
This particular issue didn't involve a correction to any code, just to
the processing (our mistake). However, we do frequently make changes to
code, mostly as general improvements but also in response to bugs found.
These are available in the galaxy-central repository immediately, go to
the public server at the next update (timing can vary), and can be
tracked in the changelog at bitbucket here:
Hopefully this helps!
On 3/12/12 9:50 AM, Oleksandr Moskalenko wrote:
> On Mar 10, 2012, at 12:14 AM, Jennifer Jackson wrote:
>> Yes, this was noticed but it took a few days to track down and correct the problem. As of this afternoon, the genome builds list was restored to the original content plus a few new additions.
>> If you notice any genome missing that was previously present, we would definitely like to know.
>> Very sorry for the inconvenience!
>> Galaxy team
> Hi Jen,
> I keep wondering from time to time how wonderful it would be to have the Public Galaxy changelog somewhere people like myself who are running local Galaxy instances could reach to avoid re-inventing the bicycle and spending time figuring out the same problems the illustrious Galaxy team already successfully solved. Has anything like that been ever discussed?
Hello, I am new here.
I am running Galaxy at http://main.g2.bx.psu.edu/ using Mozilla Firefox
I try using "Export to File" tool on different files and workflows, and
every time the report is:
An error occurred. See the error logs for more information. (Turn debug
on to display exception reports here) "
I don't know what to do, and I cannot find the option "turn debug on".
best regards, :)
1. Where you are using Galaxy (Main, local or cloud instance, etc.).
Site http://main.g2.bx.psu.edu/, on-line.
# The date/time the bug was detected
# Exact steps to reproduce the issue
FASTQ Quality Trimmer (version 1.0.0). No posiibility to upload fastq file
for treat. Pulldone for uploading does not work.
Used browsers -Mozilla Firefox 3.6.6 and IE. OS - Linux Mandiva.
# What troubleshooting steps (if any) you have tested out
Using of Windows and Debian browsers. Uploading fastq file to Galaxy witn
another application and using FASTQ Groomer on uploading file.
# Request for private communication/discussion (as needed)
If problem on my side.
s.r. CIT BAS RAS,
It seems that the bacterial genomes that used to come from ucsc via update_ucsc.sh are now gone...
Has anybody else observed this? Fixed it?