ToolShed README files, was: Blast2GO local instance
On Tue, Apr 3, 2012 at 12:16 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
On Apr 3, 2012, at 6:07 AM, Peter Cock wrote:
On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:
Have you seen the README file that comes with the Blast2GO wrapper? Perhaps the 'install from toolshed' could be tweaked to make this kind of documentation more visible...
If you are installing a single repository that contains a file named one of (case is ignored) readme, readme.txt, read_me, read_me.txt, the contents of the file will be displayed on the "tool panel section selection page". An example using the antismash repository on the main tool shed is below. This new feature is available in change set revision 6945:5ea04ccb61e8, which is currently running on the Galaxy tool shed and our central development repository. It will be available in the next Galaxy distribution.
Great. In this case I've actually called the file blast2go.txt (to match the use of blast2go.xml and blast2go.py). I didn't want to use a generic name like README since there could be other tools installed in the same folder (this predates the auto-install system). Is this naming pattern common used enough to justify including in the Galaxy Tool Shed code for spotting a README file?
Since the "read me" file contains instructions for installing the tools in the repository, would it be better to assume only 1 installation file that includes different instructions per contained tool if necessary? If multiple "read me" files are allowed per repository, they would all have to be merged together with the entire content displayed on the tool panel section selection screen anyway, so allowing only a single file would be better. The "read me" in your blast2go repository is named blast2go.txt, so I suppose we could expand the read me file name list to include <repository name>.txt. I'll do this.
Hi Greg, Could you include <repository name>.txt on the list of README filenames looked for by the ToolShed as you said please? I've just checked and it isn't working at the moment. e.g. blast2go, seq_rename, clinod, venn_list, ... - in fact most of my tools :( Thanks, Peter
HI Peter, On Aug 23, 2012, at 9:52 AM, Peter Cock wrote:
Hi Greg,
Could you include <repository name>.txt on the list of README filenames looked for by the ToolShed as you said please?
I've just checked and it isn't working at the moment. e.g. blast2go, seq_rename, clinod, venn_list, ... - in fact most of my tools :(
Thanks,
Peter
I've checked each of your listed repositories and the information in each of your <repository name>.txt files is in fact displayed when installing into a local Galaxy instance. This works only if using the tool shed installation process, so for example, if installing the venn_list repository, clicking "Install to local Galaxy" in this screenshot: Will produce the following information in the README section when choosing the tool panel section:
On Tue, Aug 28, 2012 at 2:30 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
HI Peter,
On Aug 23, 2012, at 9:52 AM, Peter Cock wrote:
Hi Greg,
Could you include <repository name>.txt on the list of README filenames looked for by the ToolShed as you said please?
I've just checked and it isn't working at the moment. e.g. blast2go, seq_rename, clinod, venn_list, ... - in fact most of my tools :(
Thanks,
Peter
I've checked each of your listed repositories and the information in each of your <repository name>.txt files is in fact displayed when installing into a local Galaxy instance.
That's good - so the wiki needs updating: http://wiki.g2.bx.psu.edu/Tool%20Shed
This works only if using the tool shed installation process, so for example, if installing the venn_list repository, clicking "Install to local Galaxy" in this screenshot:
Ah. I see now it just isn't doing what I expected - apologies for any misdirection. I had assumed if a README file was present, it would be shown prominent while browsing on the ToolShed. On closer examination of an example repository where there is a file named exactly 'README' (e.g. fubar's clustalw tool) that isn't shown either. Is there any reason not to show the contents of the README file (using the discussed name variations) on the main ToolShed repository view, e.g. under a new yellow section header? Thanks, Peter P.S. It would be nice to automatically line wrap the "Detailed description", as in many cases the raw text doesn't do this. For example, fubar's clustalw tool.
Hello Peter, My recent change set 7753:c28c5f906c6b added the ability to view a tool shed repository's README file from the pop-up menu on pages in the tool shed repository as well as in the Galaxy Admin UUI for installed repositories. Since many of these README files are rather large, I needed to display them on a separate page, hence the need for the new Repository Actions popup menu "View README" item. On Aug 28, 2012, at 9:48 AM, Peter Cock wrote:
This works only if using the tool shed installation process, so for example, if installing the venn_list repository, clicking "Install to local Galaxy" in this screenshot:
Ah. I see now it just isn't doing what I expected - apologies for any misdirection.
I had assumed if a README file was present, it would be shown prominent while browsing on the ToolShed. On closer examination of an example repository where there is a file named exactly 'README' (e.g. fubar's clustalw tool) that isn't shown either.
Is there any reason not to show the contents of the README file (using the discussed name variations) on the main ToolShed repository view, e.g. under a new yellow section header?
On Thursday, September 27, 2012, Greg Von Kuster wrote:
Hello Peter,
My recent change set 7753:c28c5f906c6b added the ability to view a tool shed repository's README file from the pop-up menu on pages in the tool shed repository as well as in the Galaxy Admin UUI for installed repositories. Since many of these README files are rather large, I needed to display them on a separate page, hence the need for the new Repository Actions popup menu "View README" item.
Great - and thank you for the line wrapping change too - I look forward to seeing these refinements in action :) Peter
Hi Peter, I've handled this request in change set revision 7761:9972ac6ee91d, which will be included in the next Galaxy release scheduled for about 10 days from now. Thanks! Greg Von Kuster On Aug 28, 2012, at 9:48 AM, Peter Cock wrote:
P.S. It would be nice to automatically line wrap the "Detailed description", as in many cases the raw text doesn't do this. For example, fubar's clustalw tool.
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Greg Von Kuster -
Peter Cock