[galaxy-dev] Disable cheetah filtering
Hi all, A Cheetah question: when I enter ; as a value in a text box of a tool (stored in $exp), Cheetah prints this as X, and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team ___ 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/
Re: [galaxy-dev] Disable cheetah filtering
Hi Joachim, try that one: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set Cheers, Bjoern Hi all, A Cheetah question: when I enter ; as a value in a text box of a tool (stored in $exp), Cheetah prints this as X, and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim ___ 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/
Re: [galaxy-dev] Disable cheetah filtering
On Wed, Jul 24, 2013 at 9:40 AM, Joachim Jacob | VIB | joachim.ja...@vib.be wrote: Hi all, A Cheetah question: when I enter ; as a value in a text box of a tool (stored in $exp), Cheetah prints this as X, and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim That sounds like the Galaxy character sanitation making the change, things like pipes etc can have unexpected results in command lines. Have a look at the sanitizer tag for use in the tool's XML file. Peter ___ 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/
Re: [galaxy-dev] Disable cheetah filtering
Thanks both of you! Okay, so I was looking in the wrong direction. This solved the issue. Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/24/2013 11:13 AM, Björn Grüning wrote: Hi Joachim, try that one: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set Cheers, Bjoern Hi all, A Cheetah question: when I enter ; as a value in a text box of a tool (stored in $exp), Cheetah prints this as X, and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim ___ 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/
Re: [galaxy-dev] Disable cheetah filtering
Okay, normally I would have forked the galaxy-dist and do a pull request with my change. But the change I want to commit is in the tool 'add_value', which is in the toolshed. Seems like a safer approach to me to contribute to the toolshed. How can I commit my changes to that tool? Can somebody of the devteam grant me acces? Do I send the diff by email :-) ? Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/24/2013 11:17 AM, Peter Cock wrote: On Wed, Jul 24, 2013 at 9:40 AM, Joachim Jacob | VIB | joachim.ja...@vib.be wrote: Hi all, A Cheetah question: when I enter ; as a value in a text box of a tool (stored in $exp), Cheetah prints this as X, and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim That sounds like the Galaxy character sanitation making the change, things like pipes etc can have unexpected results in command lines. Have a look at the sanitizer tag for use in the tool's XML file. Peter ___ 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/
Re: [galaxy-dev] Disable cheetah filtering
Hi, Okay, normally I would have forked the galaxy-dist and do a pull request with my change. But the change I want to commit is in the tool 'add_value', which is in the toolshed. Seems like a safer approach to me to contribute to the toolshed. How can I commit my changes to that tool? Can somebody of the devteam grant me acces? Do I send the diff by email :-) ? Yes, please send the patch to the mailing list and/or the devteam (toolshed should have a contact button). Also try to fill a trello card :) Thanks! Bjoern Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/24/2013 11:17 AM, Peter Cock wrote: On Wed, Jul 24, 2013 at 9:40 AM, Joachim Jacob | VIB | joachim.ja...@vib.be wrote: Hi all, A Cheetah question: when I enter ; as a value in a text box of a tool (stored in $exp), Cheetah prints this as X, and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim That sounds like the Galaxy character sanitation making the change, things like pipes etc can have unexpected results in command lines. Have a look at the sanitizer tag for use in the tool's XML file. Peter ___ 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/
Re: [galaxy-dev] Disable cheetah filtering
On Wed, Jul 24, 2013 at 11:25 AM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi, Okay, normally I would have forked the galaxy-dist and do a pull request with my change. But the change I want to commit is in the tool 'add_value', which is in the toolshed. Seems like a safer approach to me to contribute to the toolshed. How can I commit my changes to that tool? Can somebody of the devteam grant me acces? Do I send the diff by email :-) ? Yes, please send the patch to the mailing list and/or the devteam (toolshed should have a contact button). Also try to fill a trello card :) Thanks! Bjoern In general the upstream repository for a given tool will depend on the tool author's preferences. They may not even use a separate repository and work directly with the ToolShed in some cases. In other cases you might be able to contribute directly via a github pull request (planned for the NCBI BLAST+ tools), or a bitbucket pull request (the Galaxy team like bitbucket). The 'add_value' tool is under 'devteam' and it was original in the main Galaxy repository under BitBucket - I don't know where it lives now outside the tool shed: http://toolshed.g2.bx.psu.edu/view/devteam/add_value Regards, Peter ___ 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/
Re: [galaxy-dev] Disable cheetah filtering
Hmm, seems that collaborating on tools is kind of a burden... Three places to notify this small change you say? (trello, galaxy-dev and direct emailing to the authors.) I have opted for Trello, card #1013 Cheers, J Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/24/2013 12:45 PM, Peter Cock wrote: On Wed, Jul 24, 2013 at 11:25 AM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi, Okay, normally I would have forked the galaxy-dist and do a pull request with my change. But the change I want to commit is in the tool 'add_value', which is in the toolshed. Seems like a safer approach to me to contribute to the toolshed. How can I commit my changes to that tool? Can somebody of the devteam grant me acces? Do I send the diff by email :-) ? Yes, please send the patch to the mailing list and/or the devteam (toolshed should have a contact button). Also try to fill a trello card :) Thanks! Bjoern In general the upstream repository for a given tool will depend on the tool author's preferences. They may not even use a separate repository and work directly with the ToolShed in some cases. In other cases you might be able to contribute directly via a github pull request (planned for the NCBI BLAST+ tools), or a bitbucket pull request (the Galaxy team like bitbucket). The 'add_value' tool is under 'devteam' and it was original in the main Galaxy repository under BitBucket - I don't know where it lives now outside the tool shed: http://toolshed.g2.bx.psu.edu/view/devteam/add_value Regards, Peter ___ 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/
Re: [galaxy-dev] Disable cheetah filtering
On Wed, Jul 24, 2013 at 1:56 PM, Joachim Jacob | VIB | joachim.ja...@vib.be wrote: Hmm, seems that collaborating on tools is kind of a burden... Three places to notify this small change you say? (trello, galaxy-dev and direct emailing to the authors.) I have opted for Trello, card #1013 Cheers, https://trello.com/c/GVq8Vpsi/1013-bug-some-characters-not-permitted-in-add-column-tool Well in this case the tool authors are the Galaxy Developers, so you can email them directly, via the galaxy-dev list, or their issue tracker which is Trello. Ideally every tool's README file would include contact details... Peter ___ 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/
