Björn,

I've uploaded the modified tool_dependencies.xml to devteam's package_emboss_5_0_0 repository on the test tool shed, and verified that it works. Again, thank you for your contributions.


   --Dave B.

On 7/7/13 18:59:57.000, Björn Grüning wrote:
Hi Greg,

bitbucket has a downtime so I have attached a patch. I will create
tomorrow a pull request if I find time.

It will work as described and we have now a new variable (__is64bit__)
that we can use to determine if python is running under 64bit (assuming
that the rest is also 64bit-ish).

Attached is a ported version of emboss as test case (Dave B wrapper).

Have a nice evening!
Bjoern


Hi Björn,


This is great.  A pull request or a patch is fine.  Whatever one is
most convenient for you.  The code doesn't have to be pretty, just
functional.  We can always pretty it up later.


Thanks very much for doing this!


Greg

On Jul 7, 2013, at 1:19 PM, Björn Grüning
<bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:

Hi Greg,

Hello Björn,

This would be great!  I'm not sure about the type attribute - <action type="cheetah_command" 
may be ok, but maybe a more generic type like <action type="template_command" would be 
better.
I'm not quite sure, so go with what you feel is best.
I come up with the following:

<action type="template_command">
     #if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR',
False):
            ./configure --prefix=$env.INSTALL_DIR --x-includes=
$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR
    #else:
           ./configure --prefix=$env.INSTALL_DIR
    #end if
</action>

$env is the global access point to the env variables and its working
fine for the few repositories I tested it.
I had hoped to get it a little bit prettier but fabric and cheetah
doesn't work well together.

If that is still satisfying I would clean up my code and create a
pull request [1].
What do you think?

Cheers,
Bjoern

[1] or patch, I heard rumours that you do not like pull
requests ;)?

Thanks for looking into this!

Greg Von Kuster


On Jul 7, 2013, at 5:50 AM, Björn Grüning 
<bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:

Hi,

I was thinking how to tackle the build failures like the atlas library
on OS-X or the ones from xlib and ease the writing of the shell_command
a little bit.

Dave B did some fancy shell scripting in 'package_emboss_5_0_0' and I
was also sometimes forced to use some bash tricks.

What about to make that more easy and powerful, and as a plus more
consistent with the tool-command tag, and use cheetah for that kind of
work.

Something like that could work easily:

#if ${os.environ}.getVar('X11_LIB_DIR', None):
        ./configure ... --x-includes=....
#else:
        ./configure
#end if

Also we could define some reserved variables like $__is64__ and cheetah
evaluate that. $INSTALL_DIR and $REPOSITORY_DIR can also be a cheetah
variable and we do not need to replace it later manually.

What do you think any comments?
If no one has any objections I can try to implement an <action
type="cheetah_command">.

Thanks,
Björn





___________________________________________________________
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/






___________________________________________________________
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/

___________________________________________________________
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/

Reply via email to