[galaxy-dev] External/custom display applications
Hi,
Is there more documentation on the topic of custom display applications?
I only found
http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20Tutorial
which has a few examples, but these are incomplete. For example, they use some
variables like ${BASE_URL} and ${DATASET_HASH} but I cannot find extra
information on these and if there are more variables which I could use.
Basically I want to build a tool which also its own display application next to
the normal textual output file.
Thanks and regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
http://www.pri.wur.nlhttp://www.pri.wur.nl/
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Re: [galaxy-dev] Toolshed not accessible
Hello Sajoscha, If you're pulling from central to get this fix, this is the change set that should be used - it includes some additional fixes: 255f4bde822b Again, sorry for the inconvenience. On Nov 22, 2011, at 5:18 PM, Greg Von Kuster wrote: Hello Sajoscha, I've committed a fix for this (I believe) in change set 6326:af8f5887b977, which is available in our central repository at https://bitbucket.org/galaxy/galaxy-central. This fix will not be available in the Galaxy distribution for a while - very sorry for any inconvenience. If you want it now you can pull from the central repo to get it. Thanks for letting me know about this issue. Greg Von Kuster On Nov 22, 2011, at 10:22 AM, Sajoscha Sauer wrote: Hi all, We are just about to enable the Toolshed on our development installation of Galaxy. We run the latest build (rev. b258de1e6cea) of Galaxy. The toolshed that we try to access is 'http://toolshed.g2.bx.psu.edu/' Our workflow is the following: - On the admin panel, click 'Search and browse tool sheds' - 'Browse valid repositories' on 'Galaxy main tool shed' - Select any tool and 'Preview and install' - 'Install to local Galaxy' What we see on the website is: Screen Shot 2011-11-22 at 4.13.56 PM.png The apache error log says: Screen Shot 2011-11-22 at 4.06.34 PM.png Any ideas and/or hints? Thanks a lot for your help! Sajoscha ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/
Re: [galaxy-dev] Toolshed not accessible
Hi Sajoscha, What were you attempting to do when you saw this error? Are you still seeing this when you attempt to install a tool from the tool shed? By the way,m I just sent you an email - there are a few more fixes in the latest change set. On Nov 23, 2011, at 11:26 AM, Sajoscha Sauer wrote: Hi Greg, Thanks for the quick response! We updated to the newest version from the Galaxy central repository, but still get the same error. But now there is a different error (or better, a different referer) in the apache log, see below. Screen Shot 2011-11-23 at 5.11.19 PM.png Thanks again for your help! Sajoscha On Nov 22, 2011, at 4:22 PM, Sajoscha Sauer wrote: Hi all, We are just about to enable the Toolshed on our development installation of Galaxy. We run the latest build (rev. b258de1e6cea) of Galaxy. The toolshed that we try to access is 'http://toolshed.g2.bx.psu.edu/' Our workflow is the following: - On the admin panel, click 'Search and browse tool sheds' - 'Browse valid repositories' on 'Galaxy main tool shed' - Select any tool and 'Preview and install' - 'Install to local Galaxy' What we see on the website is: Screen Shot 2011-11-22 at 4.13.56 PM.png The apache error log says: Screen Shot 2011-11-22 at 4.06.34 PM.png Any ideas and/or hints? Thanks a lot for your help! Sajoscha ___ 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/ ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/
[galaxy-dev] workflow suggestions
Some questions/suggestions about workflows. How do you remove a workflow that was shared with you by others from the list? You can view workflows shared with you, but can't view your own workflows, why? The annotations show up nice in the view format and especially for older workflows it would be good to see the annotations you made easily. Also good to see them as others will before publishing the workflow. I know this can be done through edit and clicking on each step, but not a nice as the view. Belinda ___ 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/
