Base Recalibration tool on usegalaxy
Dear all, I can't find either of Table Recalibration or Base Recalibrator on usegalaxy public server. I am defident this is right place to ask, but seqanswers is clouded with many other pipelines. Is there an update of base recalibration tool on usegalaxy? Best, Kaz
Hi Kaz, you are searching for GATK tools, right? Please have a look at the GATK suites in the Tool Shed. Cheers, Bjoern Am 12.04.2014 00:16, schrieb KS:
Dear all,
I can't find either of Table Recalibration or Base Recalibrator on usegalaxy public server. I am defident this is right place to ask, but seqanswers is clouded with many other pipelines.
Is there an update of base recalibration tool on usegalaxy?
Best, Kaz ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
Hi Bjoern, Thank you for the reply. I found Table Recalibration, probably from GATK, on Tool Shed as you informed. http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&advanced_search=false&operation=view_or_manage_repository&page=1&async=false&show_item_checkboxes=false&f-free-text-search=recalibration&id=797c55906a13241a But I am only a user of usegalaxy public server, so I am afraid I think I can't install tool from tool shed. What I am doing is here: https://usegalaxy.org/u/ksfk/h/illumina-exome I think I need Table Recalibration in "NGS: GATK Tools (beta)" tool group of left pane of usegalaxy, but I cannot find it. I am wondering whether there is any way to directly call Table Recalibration without web-application wrapper. Regards, Kaz 2014-04-12 7:26 GMT+09:00 Björn Grüning <bjoern.gruening@gmail.com>:
Hi Kaz,
you are searching for GATK tools, right? Please have a look at the GATK suites in the Tool Shed.
Cheers, Bjoern
Am 12.04.2014 00:16, schrieb KS:
Dear all,
I can't find either of Table Recalibration or Base Recalibrator on usegalaxy public server. I am defident this is right place to ask, but seqanswers is clouded with many other pipelines.
Is there an update of base recalibration tool on usegalaxy?
Best, Kaz ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
Hi Kaz, We do have a problem with the Table Recalibration tool on Main right now. We’ll let you know when we have a fix. Thanks for using Galaxy, Dan On Apr 11, 2014, at 10:24 PM, KS <ksf@kyudai.jp> wrote:
Hi Bjoern,
Thank you for the reply.
I found Table Recalibration, probably from GATK, on Tool Shed as you informed. http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&advanced_search=false&operation=view_or_manage_repository&page=1&async=false&show_item_checkboxes=false&f-free-text-search=recalibration&id=797c55906a13241a But I am only a user of usegalaxy public server, so I am afraid I think I can't install tool from tool shed.
What I am doing is here: https://usegalaxy.org/u/ksfk/h/illumina-exome
I think I need Table Recalibration in "NGS: GATK Tools (beta)" tool group of left pane of usegalaxy, but I cannot find it.
I am wondering whether there is any way to directly call Table Recalibration without web-application wrapper.
Regards, Kaz
2014-04-12 7:26 GMT+09:00 Björn Grüning <bjoern.gruening@gmail.com>:
Hi Kaz,
you are searching for GATK tools, right? Please have a look at the GATK suites in the Tool Shed.
Cheers, Bjoern
Am 12.04.2014 00:16, schrieb KS:
Dear all,
I can't find either of Table Recalibration or Base Recalibrator on usegalaxy public server. I am defident this is right place to ask, but seqanswers is clouded with many other pipelines.
Is there an update of base recalibration tool on usegalaxy?
Best, Kaz ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
Hi Dan, Thank you for informing. I know I should install my own local galaxy server for repetitive analyses, but this is the first time for me to analyse exome. Thank you for giving me opportunity to use galaxy in public. Hoping recovery of Table Recalibration tool. Regards, Kaz 2014-04-12 13:08 GMT+09:00 Daniel Blankenberg <dan@bx.psu.edu>:
Hi Kaz,
We do have a problem with the Table Recalibration tool on Main right now. We'll let you know when we have a fix.
Thanks for using Galaxy,
Dan
On Apr 11, 2014, at 10:24 PM, KS <ksf@kyudai.jp> wrote:
Hi Bjoern,
Thank you for the reply.
I found Table Recalibration, probably from GATK, on Tool Shed as you informed. http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&advanced_search=false&operation=view_or_manage_repository&page=1&async=false&show_item_checkboxes=false&f-free-text-search=recalibration&id=797c55906a13241a But I am only a user of usegalaxy public server, so I am afraid I think I can't install tool from tool shed.
What I am doing is here: https://usegalaxy.org/u/ksfk/h/illumina-exome
I think I need Table Recalibration in "NGS: GATK Tools (beta)" tool group of left pane of usegalaxy, but I cannot find it.
I am wondering whether there is any way to directly call Table Recalibration without web-application wrapper.
Regards, Kaz
2014-04-12 7:26 GMT+09:00 Björn Grüning <bjoern.gruening@gmail.com>:
Hi Kaz,
you are searching for GATK tools, right? Please have a look at the GATK suites in the Tool Shed.
Cheers, Bjoern
Am 12.04.2014 00:16, schrieb KS:
Dear all,
I can't find either of Table Recalibration or Base Recalibrator on usegalaxy public server. I am defident this is right place to ask, but seqanswers is clouded with many other pipelines.
Is there an update of base recalibration tool on usegalaxy?
Best, Kaz ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
Hi Kaz, The issue with the Table Recalibration tool should now be resolved, you’ll need to refresh your Galaxy window if you haven’t already. Thanks for reporting the error and let us know if you find any more issues. Thanks for using Galaxy, Dan On Apr 12, 2014, at 2:27 AM, KS <ksf@kyudai.jp> wrote:
Hi Dan,
Thank you for informing.
I know I should install my own local galaxy server for repetitive analyses, but this is the first time for me to analyse exome. Thank you for giving me opportunity to use galaxy in public.
Hoping recovery of Table Recalibration tool.
Regards, Kaz
2014-04-12 13:08 GMT+09:00 Daniel Blankenberg <dan@bx.psu.edu>:
Hi Kaz,
We do have a problem with the Table Recalibration tool on Main right now. We'll let you know when we have a fix.
Thanks for using Galaxy,
Dan
On Apr 11, 2014, at 10:24 PM, KS <ksf@kyudai.jp> wrote:
Hi Bjoern,
Thank you for the reply.
I found Table Recalibration, probably from GATK, on Tool Shed as you informed. http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&advanced_search=false&operation=view_or_manage_repository&page=1&async=false&show_item_checkboxes=false&f-free-text-search=recalibration&id=797c55906a13241a But I am only a user of usegalaxy public server, so I am afraid I think I can't install tool from tool shed.
What I am doing is here: https://usegalaxy.org/u/ksfk/h/illumina-exome
I think I need Table Recalibration in "NGS: GATK Tools (beta)" tool group of left pane of usegalaxy, but I cannot find it.
I am wondering whether there is any way to directly call Table Recalibration without web-application wrapper.
Regards, Kaz
2014-04-12 7:26 GMT+09:00 Björn Grüning <bjoern.gruening@gmail.com>:
Hi Kaz,
you are searching for GATK tools, right? Please have a look at the GATK suites in the Tool Shed.
Cheers, Bjoern
Am 12.04.2014 00:16, schrieb KS:
Dear all,
I can't find either of Table Recalibration or Base Recalibrator on usegalaxy public server. I am defident this is right place to ask, but seqanswers is clouded with many other pipelines.
Is there an update of base recalibration tool on usegalaxy?
Best, Kaz ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
Hi Dan, Thank you for your quick handling of the issue. It seems I have connection problem with usegalaxy now, but I will try Table Recalibration later. Thank you again. Regards, Kaz 2014-04-16 0:09 GMT+09:00 Daniel Blankenberg <dan@bx.psu.edu>:
Hi Kaz,
The issue with the Table Recalibration tool should now be resolved, you’ll need to refresh your Galaxy window if you haven’t already. Thanks for reporting the error and let us know if you find any more issues.
Thanks for using Galaxy,
Dan
On Apr 12, 2014, at 2:27 AM, KS <ksf@kyudai.jp> wrote:
Hi Dan,
Thank you for informing.
I know I should install my own local galaxy server for repetitive analyses, but this is the first time for me to analyse exome. Thank you for giving me opportunity to use galaxy in public.
Hoping recovery of Table Recalibration tool.
Regards, Kaz
2014-04-12 13:08 GMT+09:00 Daniel Blankenberg <dan@bx.psu.edu>:
Hi Kaz,
We do have a problem with the Table Recalibration tool on Main right now. We'll let you know when we have a fix.
Thanks for using Galaxy,
Dan
On Apr 11, 2014, at 10:24 PM, KS <ksf@kyudai.jp> wrote:
Hi Bjoern,
Thank you for the reply.
I found Table Recalibration, probably from GATK, on Tool Shed as you informed. http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&advanced_search=false&operation=view_or_manage_repository&page=1&async=false&show_item_checkboxes=false&f-free-text-search=recalibration&id=797c55906a13241a But I am only a user of usegalaxy public server, so I am afraid I think I can't install tool from tool shed.
What I am doing is here: https://usegalaxy.org/u/ksfk/h/illumina-exome
I think I need Table Recalibration in "NGS: GATK Tools (beta)" tool group of left pane of usegalaxy, but I cannot find it.
I am wondering whether there is any way to directly call Table Recalibration without web-application wrapper.
Regards, Kaz
2014-04-12 7:26 GMT+09:00 Björn Grüning <bjoern.gruening@gmail.com>:
Hi Kaz,
you are searching for GATK tools, right? Please have a look at the GATK suites in the Tool Shed.
Cheers, Bjoern
Am 12.04.2014 00:16, schrieb KS:
Dear all,
I can't find either of Table Recalibration or Base Recalibrator on usegalaxy public server. I am defident this is right place to ask, but seqanswers is clouded with many other pipelines.
Is there an update of base recalibration tool on usegalaxy?
Best, Kaz ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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:
To search Galaxy mailing lists use the unified search at:
participants (3)
-
Björn Grüning -
Daniel Blankenberg -
KS