Re: [galaxy-dev] Missing tool previews in tool shed, e.g. hmmer.xml
On Tue, Apr 3, 2012 at 7:25 PM, Greg Von Kuster g...@bx.psu.edu wrote: Invalid tools are now displayed in the Preview tools and inspect metadata by tool version section - here is the list for the hmmer repository. Lovely - that will help with the existing tools which are not all fully compliant with these new requirements :) 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/
[galaxy-dev] Missing tool previews in tool shed, e.g. hmmer.xml
Hello all, I was looking at Edward's updated HMMER wrapper on the toolshed, http://toolshed.g2.bx.psu.edu/ There is a preview offered for the (simple) hmmpress.xml only, giving the impression that Edward's repository isn't very useful. Why isn't anything shown for the more complex hmmer.xml? If there is a problem rendering the preview, it would still be useful to list the tool in the table with its description, version and requirements. Edward - I have a query (which might be what the Tool Shed preview is unhappy about), where is the hmmer file format referenced in hmmer.xml defined? In hmmpress.xml you use hmm (as an input) and hmmpressed (as an output) which are both defined in hmmer.py, so is this an accidental inconsistency? Thanks, Peter P.S. Edward, hmmpress.xml is missing hmmpress as a requirement. ___ 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/
Re: [galaxy-dev] Missing tool previews in tool shed, e.g. hmmer.xml
Hi Peter, Here is the error produced by attempting to load the hmmr.xml tool config into the tool shed. With regard to tool validity, the definition of a valid tool in the tool shed has always been restricted to the tool properly loading in a Galaxy instance. If a tool is not valid, it will not be returned in a search and it cannot be automatically installed (unless it belongs to a repository containing other valid tools). I'll consider ways to list invalid tools contained in repositories in the tool shed, but the preference is for tool developers to share only valid tools, or the value of the tool shed will be significantly diminished over time. Filtering out files that actually are not tools from a list of invalid tools could become a bit messy. Thanks, Greg Von Kuster Repository Actions Metadata was defined for some items in revision '66f8262e1686'. Correct the following problems if necessary and reset metadata. hmmer.xml - This file refers to a file named hmmdb.loc. Upload a file named hmmdb.loc.sample to the repository to correct this error. On Mar 19, 2012, at 6:15 AM, Peter Cock wrote: Hello all, I was looking at Edward's updated HMMER wrapper on the toolshed, http://toolshed.g2.bx.psu.edu/ There is a preview offered for the (simple) hmmpress.xml only, giving the impression that Edward's repository isn't very useful. Why isn't anything shown for the more complex hmmer.xml? If there is a problem rendering the preview, it would still be useful to list the tool in the table with its description, version and requirements. Edward - I have a query (which might be what the Tool Shed preview is unhappy about), where is the hmmer file format referenced in hmmer.xml defined? In hmmpress.xml you use hmm (as an input) and hmmpressed (as an output) which are both defined in hmmer.py, so is this an accidental inconsistency? Thanks, Peter P.S. Edward, hmmpress.xml is missing hmmpress as a requirement. ___ 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/ ___ 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/
Re: [galaxy-dev] Missing tool previews in tool shed, e.g. hmmer.xml
On Mon, Mar 19, 2012 at 1:28 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, Here is the error produced by attempting to load the hmmr.xml tool config into the tool shed. With regard to tool validity, the definition of a valid tool in the tool shed has always been restricted to the tool properly loading in a Galaxy instance. If a tool is not valid, it will not be returned in a search and it cannot be automatically installed (unless it belongs to a repository containing other valid tools). I'll consider ways to list invalid tools contained in repositories in the tool shed, but the preference is for tool developers to share only valid tools, or the value of the tool shed will be significantly diminished over time. Filtering out files that actually are not tools from a list of invalid tools could become a bit messy. I see - I hope you can make some improvements for browsing the tool shed for this kind of situation. Thanks for confirming there was something the Tool Shed didn't like in hmmer.xml (missing a hmmdb.loc.sample file). For the tool uploader (in this case Edward) that kind of error is very helpful. 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/
