Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml
Hi Dave,
> 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.
Great, thanks!
> --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
> >> wrote:
> >>
> >>> Hi Greg,
> >>>
> Hello Björn,
>
> This would be great! I'm not sure about the type attribute - type="cheetah_command" may be ok, but maybe a more generic type like
> I'm not quite sure, so go with what you feel is best.
> >>> I come up with the following:
> >>>
> >>>
> >>> #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
> >>>
> >>>
> >>> $env is the global access point to the env variables and its working
> >>> fine for the few repositories I tested it.
> >>> I had hoped to get it a little bit prettier but fabric and cheetah
> >>> doesn't work well together.
> >>>
> >>> If that is still satisfying I would clean up my code and crea
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Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml
Björn,
I've uploaded the modified tool_dependencies.xml to devteam's
package_emboss_5_0_0 repository on the test tool shed, and verified that
it works. Again, thank you for your contributions.
--Dave B.
On 7/7/13 18:59:57.000, Björn Grüning wrote:
Hi Greg,
bitbucket has a downtime so I have attached a patch. I will create
tomorrow a pull request if I find time.
It will work as described and we have now a new variable (__is64bit__)
that we can use to determine if python is running under 64bit (assuming
that the rest is also 64bit-ish).
Attached is a ported version of emboss as test case (Dave B wrapper).
Have a nice evening!
Bjoern
Hi Björn,
This is great. A pull request or a patch is fine. Whatever one is
most convenient for you. The code doesn't have to be pretty, just
functional. We can always pretty it up later.
Thanks very much for doing this!
Greg
On Jul 7, 2013, at 1:19 PM, Björn Grüning
wrote:
Hi Greg,
Hello Björn,
This would be great! I'm not sure about the type attribute -
I come up with the following:
#if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR',
False):
./configure --prefix=$env.INSTALL_DIR --x-includes=
$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR
#else:
./configure --prefix=$env.INSTALL_DIR
#end if
$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
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 $REPOSITORY_DIR can also be a cheetah
variable and we do not need to replace it later manually.
What do you think any comments?
If no one has any objections I can try to implement an .
Thanks,
Björn
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Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml
Hello Björn,
Thanks very much for the patch - I've committed alsightly alterered verson of
it in changetset 10204:afec613d77fa which is currently running on the test tool
shed.
Greg Von Kuster
On Jul 7, 2013, at 6:59 PM, Björn Grüning
wrote:
> Hi Greg,
>
> bitbucket has a downtime so I have attached a patch. I will create
> tomorrow a pull request if I find time.
>
> It will work as described and we have now a new variable (__is64bit__)
> that we can use to determine if python is running under 64bit (assuming
> that the rest is also 64bit-ish).
>
> Attached is a ported version of emboss as test case (Dave B wrapper).
>
> Have a nice evening!
> Bjoern
>
>
>> Hi Björn,
>>
>>
>> This is great. A pull request or a patch is fine. Whatever one is
>> most convenient for you. The code doesn't have to be pretty, just
>> functional. We can always pretty it up later.
>>
>>
>> Thanks very much for doing this!
>>
>>
>> Greg
>>
>> On Jul 7, 2013, at 1:19 PM, Björn Grüning
>> wrote:
>>
>>> Hi Greg,
>>>
Hello Björn,
This would be great! I'm not sure about the type attribute - >>> type="cheetah_command" may be ok, but maybe a more generic type like
>>> I'm not quite sure, so go with what you feel is best.
>>> I come up with the following:
>>>
>>>
>>>#if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR',
>>> False):
>>> ./configure --prefix=$env.INSTALL_DIR --x-includes=
>>> $env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR
>>> #else:
>>> ./configure --prefix=$env.INSTALL_DIR
>>> #end if
>>>
>>>
>>> $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
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 $REPOSITORY_DIR can also be a cheetah
> variable and we do not need to replace it later manually.
>
> What do you think any comments?
> If no one has any objections I can try to implement an type="cheetah_command">.
>
> Thanks,
> Björn
>
>>>
>>>
>>>
>>> ___
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>>> in your mail client. To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> http://lists.bx.psu.edu/
>>>
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>>> http://galaxyproject.org/search/mailinglists/
>>
>>
>
>
> ___
> Please keep all replies on the list by using "reply all"
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> and other Galaxy lists, please use the interface at:
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>
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Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml
I'll soon be committing a slightly altered version of your patch which includes
a language attribute for the template_command action type.
On Jul 8, 2013, at 10:02 AM, Björn Grüning
wrote:
> Hi James,
>
>> It probably makes sense to specify the template type in this case.
>> Maybe an additional attribute, language='cheetah' ?
>
> My first suggestion was to reflect the
> template engine. I'm fine with both.
>
>> On Sun, Jul 7, 2013 at 1:19 PM, Björn Grüning
>> wrote:
>>>
>>>#if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR', False):
>>> ./configure --prefix=$env.INSTALL_DIR
>>> --x-includes=$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR
>>> #else:
>>> ./configure --prefix=$env.INSTALL_DIR
>>> #end if
>>>
>>
>>
>>
>>
>> --
>> James Taylor, Assistant Professor, Biology/CS, Emory University
>
>
>
> ___
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> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
> To search Galaxy mailing lists use the unified search at:
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>
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Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml
Hi James,
> It probably makes sense to specify the template type in this case.
> Maybe an additional attribute, language='cheetah' ?
My first suggestion was to reflect the
template engine. I'm fine with both.
> On Sun, Jul 7, 2013 at 1:19 PM, Björn Grüning
> wrote:
> >
> > #if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR', False):
> >./configure --prefix=$env.INSTALL_DIR
> > --x-includes=$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR
> >#else:
> > ./configure --prefix=$env.INSTALL_DIR
> >#end if
> >
>
>
>
>
> --
> James Taylor, Assistant Professor, Biology/CS, Emory University
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Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml
It probably makes sense to specify the template type in this case.
Maybe an additional attribute, language='cheetah' ?
On Sun, Jul 7, 2013 at 1:19 PM, Björn Grüning
wrote:
>
> #if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR', False):
>./configure --prefix=$env.INSTALL_DIR
> --x-includes=$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR
>#else:
> ./configure --prefix=$env.INSTALL_DIR
>#end if
>
--
James Taylor, Assistant Professor, Biology/CS, Emory University
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Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml
Hi Greg,
bitbucket has a downtime so I have attached a patch. I will create
tomorrow a pull request if I find time.
It will work as described and we have now a new variable (__is64bit__)
that we can use to determine if python is running under 64bit (assuming
that the rest is also 64bit-ish).
Attached is a ported version of emboss as test case (Dave B wrapper).
Have a nice evening!
Bjoern
> Hi Björn,
>
>
> This is great. A pull request or a patch is fine. Whatever one is
> most convenient for you. The code doesn't have to be pretty, just
> functional. We can always pretty it up later.
>
>
> Thanks very much for doing this!
>
>
> Greg
>
> On Jul 7, 2013, at 1:19 PM, Björn Grüning
> wrote:
>
> > Hi Greg,
> >
> > > Hello Björn,
> > >
> > > This would be great! I'm not sure about the type attribute - > > type="cheetah_command" may be ok, but maybe a more generic type like
> > > > > I'm not quite sure, so go with what you feel is best.
> > I come up with the following:
> >
> >
> > #if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR',
> > False):
> >./configure --prefix=$env.INSTALL_DIR --x-includes=
> > $env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR
> >#else:
> > ./configure --prefix=$env.INSTALL_DIR
> >#end if
> >
> >
> > $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
> > > 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 > > > 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/
>
>
tool_dependencies.xml
Description: XML document
diff -r 434335f80161 lib/galaxy/util/template.py
--- a/lib/galaxy/util/template.py Fri Jun 21 04:37:07 2013 -0400
+++ b/lib/galaxy/util/template.py Mon Jul 08 00:55:36 2013 +0200
@@ -6,4 +6,4 @@
def fill_template( template_text, context=None, **kwargs ):
if not context:
context = kwargs
-return str( Template( source=template_text, searchList=[context] ) )
\ No newline at end of file
+return str( Template( source=template_text, searchList=[context] ) )
diff -r 434335f80161 lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py Fri Jun 21 04:37:07 2013 -0400
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py Mon Jul 08 00:55:36 2013 +0200
@@ -11,6 +11,15 @@
log = logging.getLogger( __name__ )
+def get_env_substitutions( install_dir ):
+# # Added for compatibility with CloudBioLinux.
+# TODO: Add tool_version substitution for compat with CloudBioLinux.
+return { "INSTALL_DIR" : install_dir,
+"system_install" : install_dir,
+#"REPOSITORY_INSTALL_DIR": get_tool_shed_repository_install_dir( app, tool_shed_repository ),
+"__is64bit__": sys.maxsize > 2**32, #checks if the python interpreter is 64bit, we assume that the underlying system is also 64bit
+}
+
def create_env_var_dict( elem, tool_dependency_install_dir=None, t
Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml
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
wrote:
> Hi Greg,
>
>> Hello Björn,
>>
>> This would be great! I'm not sure about the type attribute - > type="cheetah_command" may be ok, but maybe a more generic type like > 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:
>
>
> #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
>
>
> $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
>> 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 $REPOSITORY_DIR can also be a cheetah
>> > variable and we do not need to replace it later manually.
>> >
>> > What do you think any comments?
>> > If no one has any objections I can try to implement an > > type="cheetah_command">.
>> >
>> > Thanks,
>> > Björn
>> >
>>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml
Hi Greg,
> Hello Björn,
>
> This would be great! I'm not sure about the type attribute - type="cheetah_command" may be ok, but maybe a more generic type like type="template_command" would be better.
> I'm not quite sure, so go with what you feel is best.
I come up with the following:
#if env.get('X11_LIB_DIR', False) and env.get('X11_INCLUDE_DIR',
False):
./configure --prefix=$env.INSTALL_DIR --x-includes=
$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR
#else:
./configure --prefix=$env.INSTALL_DIR
#end if
$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
> 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 > type="cheetah_command">.
> >
> > Thanks,
> > Björn
> >
>
___
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Re: [galaxy-dev] RFC: Cheetah template in tool_dependencies.xml
Hello Björn,
This would be great! I'm not sure about the type attribute - 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 type="cheetah_command">.
>
> Thanks,
> Björn
>
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[galaxy-dev] RFC: Cheetah template in tool_dependencies.xml
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 .
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/
