Hi Galaxy team, I am experiencing a problem with visualizing my BAM files through Trackster at my Galaxy instance. Please find the attached image along with this mail.
From the log file I am not seeing any clues about the error message which is
displayed on my browser page (A dependency (bai) was in an error state.) I updated my instance recently, It will be great if you can help me on the same. Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Tuebingen
Vipin, Are you able to visualize any BAM files in Trackster or do all files fail with the same error? Were you able to visualize BAM files before you updated your instance? Do you have SAMTools--which is required by Trackster--installed and available via your path? J. On Jul 6, 2011, at 2:19 PM, Vipin TS wrote:
Hi Galaxy team,
I am experiencing a problem with visualizing my BAM files through Trackster at my Galaxy instance. Please find the attached image along with this mail. From the log file I am not seeing any clues about the error message which is displayed on my browser page (A dependency (bai) was in an error state.)
I updated my instance recently, It will be great if you can help me on the same.
Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Tuebingen
<trackster_image_vipin.png>___________________________________________________________ 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 Jeremy,
Are you able to visualize any BAM files in Trackster or do all files fail with the same error? Were you able to visualize BAM files before you updated your instance? Do you have SAMTools--which is required by Trackster--installed and available via your path?
Yes, all BAM fails are failing with the same error message. Before updating my instance I did not try to visualize through Trackster. Samtools path are available to Galaxy. I am not seeing any error/warning message in my log file. Thanks for your consideration --Vipin
Yes, all BAM fails are failing with the same error message. Before updating my instance I did not try to visualize through Trackster. Samtools path are available to Galaxy. I am not seeing any error/warning message in my log file.
Try this in the main interface: (1) click the pencil on a BAM dataset; (2) try converting from BAM to BAI; If the conversion failed, you should receive an informative error message about why it's failing. Once you get this conversion to pass, you should be able to visualize your BAM dataset in Trackster. Let us know if you're still having trouble. Best, J.
Hi Jeremy, Sorry for the delayed response from my side. (1) click the pencil on a BAM dataset;
(2) try converting from BAM to BAI;
If the conversion failed, you should receive an informative error message about why it's failing. Once you get this conversion to pass, you should be able to visualize your BAM dataset in Trackster.
Thanks for your suggestions and they helped me to debug the issue. The conversion from BAM to BAI was working fine at my end. After few hours of debugging I had found that the error was caused by a mistake from my side, the BAM file which I tried to display on trackster was corrupted. Many thanks for your quick replies, Also I have a request about a search option in Trackster (We discussed at GCC) It will be great if you would enable a search option such that biologist/user can look for a particular feature based on feature ID or Name, (for example: read coverage for a candidate gene) Right now user need to go through all regions over the chromosomes. In my point most of users are more familiar with names than location in the genome. Thanks for considering, --Vipin
Let us know if you're still having trouble.
Best, J.
Hello Vipin, I opened a ticket at bitbucket for this type of search in Trackster. Please feel free to add detail to the enhancement request. http://bitbucket.org/galaxy/galaxy-central/issue/611/search-in-trackster-by-... Thanks! Jen Galaxy team On 7/11/11 9:11 AM, Vipin TS wrote:
feature ID or Name, (for example: read coverage for a candidate gene)
-- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/
Is this from a recent changeset that you pulled? On Wed, Jul 6, 2011 at 2:19 PM, Vipin TS <vipin.ts@gmail.com> wrote:
Hi Galaxy team,
I am experiencing a problem with visualizing my BAM files through Trackster at my Galaxy instance. Please find the attached image along with this mail. From the log file I am not seeing any clues about the error message which is displayed on my browser page (A dependency (bai) was in an error state.)
I updated my instance recently, It will be great if you can help me on the same.
Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Tuebingen
___________________________________________________________ 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 (4)
-
Jennifer Jackson -
Jeremy Goecks -
Kanwei Li -
Vipin TS