Hi,
In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets converted to X when it gets passed to the tool executable.
Is there a way to work around this or should I be doing something else to pass environment variables via Galaxy tool UI.
Thanks, Ketan
On Fri, Jan 31, 2014 at 5:13 PM, Ketan Maheshwari ketancmaheshwari@gmail.com wrote:
Hi,
In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets converted to X when it gets passed to the tool executable.
Is there a way to work around this or should I be doing something else to pass environment variables via Galaxy tool UI.
Thanks, Ketan
This is a security feature I think - or it may just need escaping as $
Since you are writing the script, why not pass in the environment variable name without the dollar?
Peter
Thanks!
Just wanted to report that $ does not work; \ adds one more X.
On Fri, Jan 31, 2014 at 11:29 AM, Peter Cock p.j.a.cock@googlemail.comwrote:
On Fri, Jan 31, 2014 at 5:13 PM, Ketan Maheshwari ketancmaheshwari@gmail.com wrote:
Hi,
In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying
running
script. However, it seems that the $ sign gets converted to X when it
gets
passed to the tool executable.
Is there a way to work around this or should I be doing something else to pass environment variables via Galaxy tool UI.
Thanks, Ketan
This is a security feature I think - or it may just need escaping as $
Since you are writing the script, why not pass in the environment variable name without the dollar?
Peter
Hi Ketan!
it sounds like your input is sanitized. You can disable it for your whole wrapper or you can write a special sanitizer for your input field:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E...
Cheers, Bjoern
Hi,
In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets converted to X when it gets passed to the tool executable.
Is there a way to work around this or should I be doing something else to pass environment variables via Galaxy tool UI.
Thanks, Ketan
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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Thank you. It worked and the sanitizer tag sounds very useful.
On Sat, Feb 1, 2014 at 4:14 AM, Björn Grüning bjoern.gruening@gmail.comwrote:
Hi Ketan!
it sounds like your input is sanitized. You can disable it for your whole wrapper or you can write a special sanitizer for your input field:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E...
Cheers, Bjoern
Hi,
In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets converted to X when it gets passed to the tool executable.
Is there a way to work around this or should I be doing something else to pass environment variables via Galaxy tool UI.
Thanks, Ketan
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
galaxy-user@lists.galaxyproject.org
-
Björn Grüning -
Ketan Maheshwari -
Peter Cock