Re: [galaxy-user] [galaxy-dev] Peep view for history elements broken on IE?
On Fri, Feb 18, 2011 at 3:13 PM, Kanwei Li kan...@gmail.com wrote:
All:
I retested under IE7 and found the bugs you were mentioning. This has all
been fixed on trunk by using a newer local storage library. The only IE7
issue that I am now aware of is when the tool pane is empty when using
workflows. Please let me know if you see any other issues.
Thanks,
K
On Fri, Feb 18, 2011 at 10:50 PM, Kanwei Li kan...@gmail.com wrote:
The empty tool pane issue for IE is now fixed on tip as well.
Thanks,
-K
Hi Kanwei,
I presume this was the fix for the peep view not working on IE7,
https://bitbucket.org/galaxy/galaxy-central/changeset/1dfad17e81a8
That doesn't seem to have been included in the latest galaxy-dist
release.
I've tried both main.g2.bx.psu.edu and test.g2.bx.psu.edu with
IE7 and the peep view is still unchanged. Should the test machine
be working? Perhaps there is a caching problem...
Also, when using either main.g2.bx.psu.edu or test.g2.bx.psu.edu
with IE7 I am now getting a JavaScript error when I click on any tool:
Line: 52
Error: Object doesn't support this property or method
Offending line:
var section_title =
$(this).parents(div.toolSectionWrapper).find(div.toolSectionTitle).text().trim();
Context:
// Log clicks on tools.
$(div.toolTitle a).click( function()
{
var tool_title = $(this).attr('id').split(-)[1];
var section_title =
$(this).parents(div.toolSectionWrapper).find(div.toolSectionTitle).text().trim();
var search_active =
$(this).parents(div.toolTitle).hasClass(search_match);
// Log action.
galaxy_async.log_user_action(tool_menu_click. + tool_title,
section_title,
JSON.stringify({search_active : search_active}));
});
This may be unrelated, but you said you'd been working on the tool
pane too, so I'm mentioning it here rather than starting a new thread
or filing a bug..
Peter
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Re: [galaxy-user] [galaxy-dev] Peep view for history elements broken on IE?
On Mon, Feb 21, 2011 at 9:48 AM, Peter pe...@maubp.freeserve.co.uk wrote:
On Fri, Feb 18, 2011 at 3:13 PM, Kanwei Li kan...@gmail.com wrote:
All:
I retested under IE7 and found the bugs you were mentioning. This has all
been fixed on trunk by using a newer local storage library. The only IE7
issue that I am now aware of is when the tool pane is empty when using
workflows. Please let me know if you see any other issues.
Thanks,
K
On Fri, Feb 18, 2011 at 10:50 PM, Kanwei Li kan...@gmail.com wrote:
The empty tool pane issue for IE is now fixed on tip as well.
Thanks,
-K
Hi Kanwei,
I presume this was the fix for the peep view not working on IE7,
https://bitbucket.org/galaxy/galaxy-central/changeset/1dfad17e81a8
That doesn't seem to have been included in the latest galaxy-dist
release.
I've tried both main.g2.bx.psu.edu and test.g2.bx.psu.edu with
IE7 and the peep view is still unchanged. Should the test machine
be working? Perhaps there is a caching problem...
Also, when using either main.g2.bx.psu.edu or test.g2.bx.psu.edu
with IE7 I am now getting a JavaScript error when I click on any tool:
Line: 52
Error: Object doesn't support this property or method
Offending line:
var section_title =
$(this).parents(div.toolSectionWrapper).find(div.toolSectionTitle).text().trim();
Context:
// Log clicks on tools.
$(div.toolTitle a).click( function()
{
var tool_title = $(this).attr('id').split(-)[1];
var section_title =
$(this).parents(div.toolSectionWrapper).find(div.toolSectionTitle).text().trim();
var search_active =
$(this).parents(div.toolTitle).hasClass(search_match);
// Log action.
galaxy_async.log_user_action(tool_menu_click. + tool_title,
section_title,
JSON.stringify({search_active : search_active}));
});
This may be unrelated, but you said you'd been working on the tool
pane too, so I'm mentioning it here rather than starting a new thread
or filing a bug..
And another JScript error, possibly related, but which
I am unable to reproduce reliably:
1. Goto main.g2.bx.psu.edu or test using IE7
2. From the right hand pane, select delete history
(I often find I need to refresh the history pane here
otherwise it shows the old deleted history, and also
sometimes it still leaves the current dataset shown)
3. Click on Get Data, Upload File
4. Ignore this error (don't debug):
Line: 52
Error: Object doesn't support this property or method
5. Select a FASTA file, click execute
6. Middle pane shows green Job added to queue message
7. Long wait with no feedback other than occasional increase in IE
progress bar...
(Again sometimes the history pane has gone back to
showing the deleted history)
8. Click on the blue history refresh button
9. Sometimes get error:
Line: 17
Error: 'E.activeEngine()' is null or not an object
Debugging says this is a JScript anonymous function:
(function(aP,E){var ae=aP.document;var a=(function(){var
bf=function(bA,bB){return new ...
/*
* Sizzle CSS Selector Engine
* Copyright 2011, The Dojo Foundation
* Released under the MIT, BSD, and GPL Licenses.
* More information: http://sizzlejs.com/
*/
(function(){var bj=...
Hopefully that is enough to reproduce or guess what the
problem could be.
Peter
___
The Galaxy User list should be used for the discussion
of Galaxy analysis and other features on the public
server at usegalaxy.org. 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:
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[galaxy-user] Problem Adding a Custom Build in Trackster
Hello, I am trying to 'Add a Custom Build' to my local instance of Galaxy/Trackster. There seems to be a problem when I enter the chromosome length info, both when I paste directly on the screen and when I use the upload button (for the .len file). After I press Submit I can see the Name and Key info that I specified but it always says that the 'Number of Chroms' is 0. Is there a bug or I am doing something wrong? Thanks for you help, Liisa ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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: http://lists.bx.psu.edu/
Re: [galaxy-user] get wig file after tophat
Hi, You can get an equivalent visualisation from the IGV viewer by the Broad Institute - its under IGV tools and generates a tdf file from bam or sam files. This also gives a quick and easy way of looking at depth at any particular site and is very accessible. Cheers David On 21 Feb 2011, at 21:44, Jeremy Goecks wrote: Hi all, Ann is correct - Tophat does not produce .wig files when run anymore. However, it's fairly easy to use Galaxy to make a wiggle-like coverage file from a BAM file: (a) run the pileup tool on your BAM to create a pileup file; (b) cut columns 1 and 4 to get your coverage file. A final note: it's often difficult to visualize coverage files because they're so large. You might be better off visualizing the BAM file and using the coverage file for statistics. Best, J. Hello, I think I know the answer (sort of) to this question. This may be because newer versions of tophat stopped running the wiggles program, which is still part of the tophat distribution and is the program that makes the coverage.wig file. A later version of tophat might bring this back, however - there's a note to this effect in the tophat python code. So if you can run wiggles, you can make the coverage.wig file on your own. A student here at UNC Charlotte (Adam Baxter) made a few changes to the wiggles source code that would allow you to use it with samtools to make a coverage.wig file from the accepted_hits.bam file that TopHat creates. If you (or anyone else) would like a copy, please email Adam, who is cc'ed on this email. We would be happy to help add it to Galaxy if this would be of interest to you or other Galaxy users. If there is any way we can be of assistance, please let us know! Very best wishes, Ann Loraine On 2/21/11 3:39 PM, Ying Zhang ying.zhang.yz...@yale.edu wrote: Hi: I am using tophat in galaxy to analyze my paired-end RNA-seq data and find out that after the tophat analysis, we can not get the wig file from it anymore which is used to be able to. Do you have any idea of how to still be able to get the wig file after tophat analysis? Thanks a lot! Best Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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: http://lists.bx.psu.edu/ -- Ann Loraine Associate Professor Dept. of Bioinformatics and Genomics, UNCC North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 www.transvar.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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: http://lists.bx.psu.edu/
Re: [galaxy-user] get wig file after tophat
FYI: samtools + bam file + a bit of perl == to wiggle conversion: https://lists.soe.ucsc.edu/pipermail/genome/2010-December/024318.html - Original Message - From: Ying Zhang ying.zhang.yz...@yale.edu To: galaxy-u...@bx.psu.edu Sent: Monday, February 21, 2011 12:39:47 PM Subject: [galaxy-user] get wig file after tophat Hi: I am using tophat in galaxy to analyze my paired-end RNA-seq data and find out that after the tophat analysis, we can not get the wig file from it anymore which is used to be able to. Do you have any idea of how to still be able to get the wig file after tophat analysis? Thanks a lot! Best Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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: http://lists.bx.psu.edu/
Re: [galaxy-user] Installing Galaxy locally
Hi David, Yes, it is free and easy to set up, and we have instructions here: https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy Thanks! Kanwei On Mon, Feb 21, 2011 at 5:42 PM, David Matthews d.a.matth...@bristol.ac.ukwrote: Hi, I am not a computer person and very much like using Galaxy because its nice and easy for non-bioinformaticians. Tomorrow I am going to have a meeting with the computer science department here at Bristol and I am hoping to persuade them to install Galaxy within the High Performance Computing Centre for University of Bristol users. As I understand it this is relatively straight forward - that is to say the project was designed for them to install the whole thing locally and reproduce the set up here so I and others can use it here instead of clogging up your machines with our data and requests (!). Is this right? There are no fees or anything and this is something most computer centres should be able to do? I know this may seem a silly question but it seems prudent to ask! Cheers David ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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: http://lists.bx.psu.edu/
Re: [galaxy-user] [galaxy-dev] Peep view for history elements broken on IE?
Hi Peter, The changes are on tip, which aren't in galaxy-dist or on main yet. I will look into the other issues when I get access to my IE7 VM tomorrow. Thanks! K ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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: http://lists.bx.psu.edu/
