Re: [galaxy-dev] Making symlinks in "command" section of tool XML

[Peter Briggs]

Hello John

Thanks for the prompt reply, and the heads-up re the deprecation of the 
"interpreter" attribute. It looks removing this attribute from the 
"command" tag fixes the linking problem, as you say.


I'll try the new idiom referencing $__tool_directory__ and let you know 
if I have any issues.


Thanks for your help!

Best wishes

Peter

On 19/01/17 15:38, John Chilton wrote:

At first glace I think the problem is that when you use the
``interpreter`` tag Galaxy has really broken logic for modifying the
command line to use that. ln works just like cp and mv. Those too
would be broken for this tool because of the interpreter attribute I
think. For this reason ``interpreter`` has been deprecated
(https://docs.galaxyproject.org/en/latest/dev/schema.html#id3) and
should not be used.

I would drop the interpreter="bash" stuff and just where ever your
script (lets say script_name.bash) appears in the command replace the
reference to script_name.bash with:

bash $__tool_directory__/script_name.bash

I think this will work a lot better for you. Let me know if it does not.

-John


On Thu, Jan 19, 2017 at 10:05 AM, Peter Briggs
 wrote:

Dear Developers

I'm currently looking at develop a tool for a local pipeline, and want to
make symlinks as part of the script in the "command" section of the tool XML
- something like e.g.

  

Re: [galaxy-dev] Making symlinks in "command" section of tool XML

[John Chilton]

At first glace I think the problem is that when you use the
``interpreter`` tag Galaxy has really broken logic for modifying the
command line to use that. ln works just like cp and mv. Those too
would be broken for this tool because of the interpreter attribute I
think. For this reason ``interpreter`` has been deprecated
(https://docs.galaxyproject.org/en/latest/dev/schema.html#id3) and
should not be used.

I would drop the interpreter="bash" stuff and just where ever your
script (lets say script_name.bash) appears in the command replace the
reference to script_name.bash with:

bash $__tool_directory__/script_name.bash

I think this will work a lot better for you. Let me know if it does not.

-John


On Thu, Jan 19, 2017 at 10:05 AM, Peter Briggs
 wrote:
> Dear Developers
>
> I'm currently looking at develop a tool for a local pipeline, and want to
> make symlinks as part of the script in the "command" section of the tool XML
> - something like e.g.
>
>   

[galaxy-dev] Making symlinks in "command" section of tool XML

[Peter Briggs]

Dear Developers

I'm currently looking at develop a tool for a local pipeline, and want 
to make symlinks as part of the script in the "command" section of the 
tool XML - something like e.g.


  

Re: [galaxy-dev] Blast db permission

[Peter Cock]

Hello Mohamed,

Right now this is not possible, and I can't think of any way to
restrict access to system level BLAST databases listed in
the blast*.loc files by user. However, since other Galaxy
tools use *.loc files, someone else may have some ideas.

You might be able to try using a BLAST database in a
shared data library (Galaxy has a role based permissions
system you could use), but the user would first have to
import the database into their current history.

I hope that helps,

Peter

On Thu, Jan 19, 2017 at 1:45 PM, Mohamed Kassam  wrote:
> Dear all,
>
> I would like to know if it is possible to put permission on the macro.xml
> for ncbi-blast + database.
> For example if I want to show the db to one user and not to all.
>
> Best reagards,
>
> Mohamed
>
> ___
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[galaxy-dev] Blast db permission

[Mohamed Kassam]

Dear all,

I would like to know if it is possible to put permission on the macro.xml
for ncbi-blast + database.
For example if I want to show the db to one user and not to all.

Best reagards,

Mohamed
___
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/