problems with 'Profile Annotations' tool UI
Hi we are looking into different methods to display dynamic contents in the tool user interface. To start, we looked at the 'Operate on Genomic Intervals:Profile Annotations' tool. We turned it on in a local installation (May 20, "8c11dd28a3cf" release), but we struggled to get the interface to work. On 'http://main.g2.bx.psu.edu/', the tables to choose from are only displayed if there is a history item with: "format: bed, database: hg18". But in our local test installation, we don't get the list of tables, no matter whether we have a ('hg18') bed file in our history or not. It looks like as if the 'from_file="annotation_profiler_options.xml"' statement in the "annotation_profiler.xml" is ignored. I know, the file 'annotation_profiler_options.xml' is read, since I get an error during restart, if I provide invalid xml. Is there anything else, I have to enable, in order to get this interface to work? Currently, I don't care about the tools functionality, I just want the (cool) interface to work. Thank you very much for your help. Regards, Hans PS: this question is connected to Tim's question yesterday - I just should have sent mine first - sorry.
Hi Hans, Very sorry for the delay in response. The sample file that was included was incorrect, but has been updated in changeset 5775:4220f8a5c571 and should now display an interface. If you would like to use or run the tool, you may find $GALAXY_ROOT/scripts/tools/annotation_profiler/README.txt helpful. Please let us know if you encounter further difficulties. Thanks for using Galaxy, Dan On Jun 8, 2011, at 8:10 AM, Hans-Rudolf Hotz wrote:
Hi
we are looking into different methods to display dynamic contents in the tool user interface.
To start, we looked at the 'Operate on Genomic Intervals:Profile Annotations' tool. We turned it on in a local installation (May 20, "8c11dd28a3cf" release), but we struggled to get the interface to work.
On 'http://main.g2.bx.psu.edu/', the tables to choose from are only displayed if there is a history item with: "format: bed, database: hg18".
But in our local test installation, we don't get the list of tables, no matter whether we have a ('hg18') bed file in our history or not. It looks like as if the 'from_file="annotation_profiler_options.xml"' statement in the "annotation_profiler.xml" is ignored.
I know, the file 'annotation_profiler_options.xml' is read, since I get an error during restart, if I provide invalid xml.
Is there anything else, I have to enable, in order to get this interface to work? Currently, I don't care about the tools functionality, I just want the (cool) interface to work.
Thank you very much for your help.
Regards, Hans
PS: this question is connected to Tim's question yesterday - I just should have sent mine first - sorry. ___________________________________________________________ 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:
Hi Dan Thank you very much. The display works nicely, now. Thanks, Hans On 07/07/2011 06:14 PM, Daniel Blankenberg wrote:
Hi Hans,
Very sorry for the delay in response. The sample file that was included was incorrect, but has been updated in changeset 5775:4220f8a5c571 and should now display an interface.
If you would like to use or run the tool, you may find $GALAXY_ROOT/scripts/tools/annotation_profiler/README.txt helpful. Please let us know if you encounter further difficulties.
Thanks for using Galaxy,
Dan
On Jun 8, 2011, at 8:10 AM, Hans-Rudolf Hotz wrote:
Hi
we are looking into different methods to display dynamic contents in the tool user interface.
To start, we looked at the 'Operate on Genomic Intervals:Profile Annotations' tool. We turned it on in a local installation (May 20, "8c11dd28a3cf" release), but we struggled to get the interface to work.
On 'http://main.g2.bx.psu.edu/', the tables to choose from are only displayed if there is a history item with: "format: bed, database: hg18".
But in our local test installation, we don't get the list of tables, no matter whether we have a ('hg18') bed file in our history or not. It looks like as if the 'from_file="annotation_profiler_options.xml"' statement in the "annotation_profiler.xml" is ignored.
I know, the file 'annotation_profiler_options.xml' is read, since I get an error during restart, if I provide invalid xml.
Is there anything else, I have to enable, in order to get this interface to work? Currently, I don't care about the tools functionality, I just want the (cool) interface to work.
Thank you very much for your help.
Regards, Hans
PS: this question is connected to Tim's question yesterday - I just should have sent mine first - sorry. ___________________________________________________________ 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:
participants (2)
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Daniel Blankenberg -
Hans-Rudolf Hotz