On Apr 3, 2012, at 6:07 AM, Peter Cock wrote:

> On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster <g...@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.

>> Care must be taken when following instructions in README files since some of
>> the information may be outdated.  For example, the Galaxy functional test
>> framework was recently enhanced to support testing tools included in
>> installed repositories, but I've seen some README files currently in
>> repositories that instruct installers to move test data to the Galaxy
>> installation environment, which is no longer necessary.
> Some of my tools' README files will need a little clarification following
> those changes to Galaxy.

My next big feature will be supporting installation of tool dependencies 
automatically with the repository contents, so keep that in mind if you're 
making changes to install instructions.  This enhancement will take a bit of 

> Thanks,
> Peter

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