Hi Peter, I've added the package to the test toolshed now as well, but there the revision is not seen in the metadata (see screenshot). What is needed to get this repository "active"? Is this still the "reset metadata" (is this a bug or by design)? Thanks for your help! [cid:image001.jpg@01CED0D8.90AAA960] Regards, Pieter. -----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: donderdag 24 oktober 2013 13:27 To: Lukasse, Pieter Cc: Greg Von Kuster (greg@bx.psu.edu); galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents On Thu, Oct 24, 2013 at 12:09 PM, Lukasse, Pieter <pieter.lukasse@wur.nl<mailto:pieter.lukasse@wur.nl>> wrote:

Hi ,

I have a toolshed repository where I expect 5 tools to appear in the

"Contents of this repository" section but one of them fails to appear

in the list (see screenshot). Where can I find out what is going

wrong?

Thanks,

Pieter.

Hi Pieter, The first thing to confirm is if the missing tool a valid XML file? Next, does it work in your Galaxy instance (if installed manually). Now if this problem is only in the Tool Shed, which toolshed is it in? Your own local tool shed, the main Penn State public Tool Shed, the Penn State Test Tool Shed, or somewhere else? If it is your own tool shed, you should be able to look at its logging for clues. If it is a public tool shed, please share the URL for the repository. Regards, Peter

I'm taking a look - will have comments shortly - thanks! On Oct 24, 2013, at 10:51 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

On Thu, Oct 24, 2013 at 3:46 PM, Lukasse, Pieter <pieter.lukasse@wur.nl> wrote: Hi Peter,

I've added the package to the test toolshed now as well, but there the revision is not seen in the metadata (see screenshot). What is needed to get this repository "active"? Is this still the “reset metadata” (is this a bug or by design)? Thanks for your help!

The shareable link is: http://testtoolshed.g2.bx.psu.edu/view/pieterlukasse/prims_masscomb

There does seem to be something amiss - probably a question for Greg.

Peter

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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Hi Greg, Thanks for the tips. A validator would indeed be great as I made the changes you suggested but still it did not solve the issue (the tool still does not appear - so probably yet another mistake is there...). Regards, Pieter. From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: donderdag 24 oktober 2013 17:29 To: Lukasse, Pieter Cc: 'Peter Cock'; galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents Hello Pieter, There are 2 different issues in 2 of your xml files that make them invalid XML. 1. In your tool_dependencies.xml file, you need to close the version string attribute in the <package> tag. So the following line with the problem: <package name="xtandem" version="12.10011> is fixed when it looks like this: <package name="xtandem" version="12.10011"> 2. In your mass comb_dbsearch_xtandem.xml file, the comment outside of the </tool> tag on the last line problematic. </tool> <!-- NB: edit /etc/profile and add the xtandem bin folder to PATH --> The above XML results in the XML document being parsed such that the XML root is the comment itself. If you move the comment line insideo of the <tool> tag set, all is well: <!-- NB: edit /etc/profile and add the xtandem bin folder to PATH --> </tool> Unfortunartely, it is difficult to render meaningful messages for invalid XML like this as the XMNL parser does not provide much of anything meaningful that can be passed on in the UI. At some point I may find the chance to incorporate a validator, but just don't currently have the time. Greg Von Kuster On Oct 24, 2013, at 10:46 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl<mailto:pieter.lukasse@wur.nl>> wrote: Hi Peter, I've added the package to the test toolshed now as well, but there the revision is not seen in the metadata (see screenshot). What is needed to get this repository "active"? Is this still the "reset metadata" (is this a bug or by design)? Thanks for your help! <image001.jpg> Regards, Pieter. -----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com<http://googlemail.com>] Sent: donderdag 24 oktober 2013 13:27 To: Lukasse, Pieter Cc: Greg Von Kuster (greg@bx.psu.edu<mailto:greg@bx.psu.edu>); galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu> Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents On Thu, Oct 24, 2013 at 12:09 PM, Lukasse, Pieter <pieter.lukasse@wur.nl<mailto:pieter.lukasse@wur.nl>> wrote:

Hi ,

I have a toolshed repository where I expect 5 tools to appear in the "Contents of this repository" section but one of them fails to appear in the list (see screenshot). Where can I find out what is going wrong?

Thanks,

Pieter.

Hi Pieter, The first thing to confirm is if the missing tool a valid XML file? Next, does it work in your Galaxy instance (if installed manually). Now if this problem is only in the Tool Shed, which toolshed is it in? Your own local tool shed, the main Penn State public Tool Shed, the Penn State Test Tool Shed, or somewhere else? If it is your own tool shed, you should be able to look at its logging for clues. If it is a public tool shed, please share the URL for the repository. Regards, Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Kind of assuming Greg did this yesterday when he replied with only two problems....but you are right, I can check the XML correctness locally (although this does not solve the fundamental problem). Regards, Pieter. -----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: vrijdag 25 oktober 2013 15:49 To: Lukasse, Pieter Cc: Greg Von Kuster; galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents On Fri, Oct 25, 2013 at 2:26 PM, Lukasse, Pieter <pieter.lukasse@wur.nl> wrote:

Hi Greg,

Thanks for the tips. A validator would indeed be great as I made the changes you suggested but still it did not solve the issue (the tool still does not appear - so probably yet another mistake is there...).

Try any generic XML validator - it won't know about the special Galaxy tags etc, but will still catch the majority of stupid mistakes. Peter

Hi Greg, what I mean is that I don't expect any other errors in my files since I corrected the errors you reported. When using my XML editor I also don't get any errors, so the files seem OK. However, the problem remains: one of the tools and also the dependencies definitions don't appear in the toolshed package. Are there .xsd files I can check these files against? Thanks and regards, Pieter. ________________________________________ From: Greg Von Kuster [greg@bx.psu.edu] Sent: Friday, October 25, 2013 3:57 PM To: Lukasse, Pieter Cc: 'Peter Cock'; galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents Hi Pieter, Perhaps I'm misunderstanding this issue. Can you clarify the problem? Thanks, Greg Von kuster On Oct 25, 2013, at 9:53 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl> wrote:

Kind of assuming Greg did this yesterday when he replied with only two problems....but you are right, I can check the XML correctness locally (although this does not solve the fundamental problem).

Regards,

Pieter.

-----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: vrijdag 25 oktober 2013 15:49 To: Lukasse, Pieter Cc: Greg Von Kuster; galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents

On Fri, Oct 25, 2013 at 2:26 PM, Lukasse, Pieter <pieter.lukasse@wur.nl> wrote:

...

Hi Greg,

Thanks for the tips. A validator would indeed be great as I made the changes you suggested but still it did not solve the issue (the tool still does not appear - so probably yet another mistake is there...).

Try any generic XML validator - it won't know about the special Galaxy tags etc, but will still catch the majority of stupid mistakes.

Peter

Hi Pieter, The tool shed is undoubtedly not the problem here. The tool is simply not identified as a Galaxy tool for some reason. When it had xml validation errors, it was not loaded as a Galaxy tool due to the errors. I'm not sure what new issue is causing the xml to not load properly as a Galaxy tool. But Peter's direction is correct - discover why the xml file is not properly loading into Galaxy as a Galaxy tool. The Tool Shed uses virtually the same loading process as Galaxy. I'm travelling currently, but I'll try to get some time ove rhte next couple of days to look at this again if you haven't been able to discover the cause of the problem. Thanks, Greg Von Kuster On Oct 29, 2013, at 7:00 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

On Tue, Oct 29, 2013 at 6:23 AM, Lukasse, Pieter <pieter.lukasse@wur.nl> wrote:

...

Hi Greg,

what I mean is that I don't expect any other errors in my files since I corrected the errors you reported. When using my XML editor I also don't get any errors, so the files seem OK. However, the problem remains: one of the tools and also the dependencies definitions don't appear in the toolshed package. Are there .xsd files I can check these files against?

As far as I know there are no XML schema definitions for the Galaxy tool definition format (e.g. DTD files), so this cannot be fully validated by an XML validator.

As your problem, according to the Tool Shed you have four valid tools: http://testtoolshed.g2.bx.psu.edu/view/pieterlukasse/prims_masscomb

* MsPicture * FASTA validator * DB Search Converter * Mascot

The missing (invalid) tool is masscomb_dbsearch_xtandem.xml - X Tandem. Does the tool work on your local Galaxy instance? If so then it seems the Tool Shed is being too strict, or failing to parse this tool for some reason.

Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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