Re: [galaxy-dev] Bug report: within

I have applied your patch here (https://bitbucket.org/galaxy/galaxy-central/commits/19309418c86450b7f39691460eb430e100883cb4) and one correction to James' previous comment - multi-page tools actually do work through the API - this was required for multi-page tool testing via the API. -John On Tue

Re: [galaxy-dev] Bug report: within

Hey James thanks for the feedback! But on the other hand I know of no alternative to creating an input form with several steps/pages/subforms, or is there? Our group really wants something like this to enhance the user friendliness for some tools with rather complicated input stages... actually

Re: [galaxy-dev] Bug report: within

Philipp, Pages are seriously deprecated -- do not use them. Many things will not work, they are not supported in workflows, the API, et cetera. They only still exist for backward compatibility with ANCIENT tools. Thanks, James -- jt On Tue, Aug 12, 2014 at 4:59 AM, Hans-Philipp Brachvogel wr

[galaxy-dev] Bug report: within

Hello, I found that it is possible for tool-xmls defined with tags to also have multipage helps, but this feature is not really documented and also does not work because of a tiny bug. You can have multipage helps by writing something like this (if your tool has two s): Helpt

Re: [galaxy-dev] Bug report

What format are the files you are trying to process with MACS in? -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jul 23, 2013 at 3:05 PM, Jianxin Wang wrote: > Hi Galaxy dev team, > > I'm trying to the you galaxy server to do NGS peak calling: Tools -> NGS: > Peak Ca

[galaxy-dev] Bug report

Hi Galaxy dev team, I'm trying to the you galaxy server to do NGS peak calling: Tools -> NGS: Peak Calling -> MACS Model-based Analysis of ChIP-Seq. However, the page won't allow me enter the input files: the drop-down selection b

Re: [galaxy-dev] Bug report and patch for whitespace

On Wed, Apr 17, 2013 at 3:56 PM, Dannon Baker wrote: > Thanks Peter, you're correct -- I've added this in 9460:da5a5077ef1e. > Great, thanks. https://bitbucket.org/galaxy/galaxy-central/commits/da5a5077ef1ebffa9e0ad9039ca4463298815de1 Peter (Reading my email I can see at least two grammar typos

Re: [galaxy-dev] Bug report and patch for whitespace

Thanks Peter, you're correct -- I've added this in 9460:da5a5077ef1e. On Wed, Apr 17, 2013 at 10:49 AM, Peter Cock wrote: > Hello all, > > I recently tried adding a tag as follows, > > > blastxml_to_top_descr.py --version > > > This kind of white space is tolerated in the tag,

[galaxy-dev] Bug report and patch for whitespace

Hello all, I recently tried adding a tag as follows, blastxml_to_top_descr.py --version This kind of white space is tolerated in the tag, so should work here too I think. However, it resulting the Galaxy attempting to run 'python' (which stalled as there was no user input), and

Re: [galaxy-dev] Bug report : JSONDecodeError

l original - > De: "Greg Von Kuster" > À: "Mathieu Bahin" > Cc: "Galaxy Dev" > Envoyé: Mardi 13 Novembre 2012 14:29:39 > Objet: Re: [galaxy-dev] Bug report : JSONDecodeError > Hi Mathieu, > As I mentioned in my previous email,

Re: [galaxy-dev] Bug report : JSONDecodeError

quot;Mathieu Bahin" > Cc: "Galaxy Dev" > Envoyé: Lundi 12 Novembre 2012 22:18:05 > Objet: Re: [galaxy-dev] Bug report : JSONDecodeError > Hi Mathieu, > It's pretty difficult to tell you where to start looking within your > environment for the cause of the prob

Re: [galaxy-dev] Bug report : JSONDecodeError

still existing. > > Cheers, > Mathieu Bahin > > > > De: "Greg Von Kuster" > À: "Mathieu Bahin" > Cc: "Galaxy Dev" > Envoyé: Lundi 12 Novembre 2012 22:18:05 > Objet: Re: [galaxy-dev] Bug report : JSONDecodeError > > Hi M

Re: [galaxy-dev] Bug report : JSONDecodeError

'/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', > line 1620 in _get_col > return processor(row[index]) > File > '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/types.py', > line 284 in process >

Re: [galaxy-dev] Bug report : JSONDecodeError

8 in raw_decode JSONDecodeError: Unterminated string starting at: line 1 column 65522 (char 65522) -- I hope this can help you find the problem ! Thanks, Mathieu - Mail original - > De: "Greg Von Ku

Re: [galaxy-dev] Bug report : JSONDecodeError

Mathieu Bahin - Mail original - De: "Greg Von Kuster" À: "Mathieu Bahin" Cc: galaxy-...@bx.psu.edu Envoyé: Vendredi 9 Novembre 2012 19:28:09 Objet: Re: [galaxy-dev] Bug report : JSONDecodeError Hello Mathieu, What version of Galaxy are you running? Also, I can

Re: [galaxy-dev] Bug report : JSONDecodeError

> À: "Greg Von Kuster" > Cc: galaxy-...@bx.psu.edu > Envoyé: Lundi 12 Novembre 2012 10:54:21 > Objet: Re: [galaxy-dev] Bug report : JSONDecodeError > > Hi Greg ! > > Thanks for the quick answer. > > I am using the 7720 parent version but I keep it up-to

Re: [galaxy-dev] Bug report : JSONDecodeError

Hello Mathieu, What version of Galaxy are you running? Also, I cannot read the stack trace from your pasted image, so can you send a text version of the complete stack trace from your paster log? Thanks, Greg Von Kuster On Nov 9, 2012, at 11:26 AM, Mathieu Bahin wrote: > Hi, > > I am usi

[galaxy-dev] Bug report - when trying to use Bam and Bai files

Hello all, I have a problem with Galaxy, and until now I haven't found a solution for it. We have a tool that has two inputs: one BAM file and one BAI file. The BAI file is the index of this BAM file. I noticed that when there is a needed for BAI file of some BAM file, Galaxy first generate a B

Re: [galaxy-dev] bug report

On Sep 29, 2011, at 11:02 PM, KOH Jia Yu Jayce wrote: > Hi > > I’d like to enquire about the bug report. Apparently when someone sends a bug > report, everyone in the mailing list and the sender himself are supposed to > receive the bug report (as can be seen in the to field in the email sent

Re: [galaxy-dev] bug report submission bug

Got another problem with the bug reporting tool: "POST /dataset/report_error HTTP/1.1" 500 - "http://galaxy.hpc.ufl.edu/dataset/errors?id=775"; "Mozilla/5.0 (compatible; MSIE 9.0; Windows NT 6.1; Trident/5.0)"Error - : local variable 'dataset_id' referenced before assignmentURL: http://galaxy.h

[galaxy-dev] bug report submission bug

Someone shared a history with me for the purpose of debugging their Galaxy problem in our local Galaxy instance. I set the "error_email_to" to our bug reporting email address, but I can't submit a bug report using the "bug" icon in the history for datasets in an error state. The traceback is bel

[galaxy-dev] bug report

Hi I'd like to enquire about the bug report. Apparently when someone sends a bug report, everyone in the mailing list and the sender himself are supposed to receive the bug report (as can be seen in the to field in the email sent out). However in our case the sender never receives the bug repor