Galaxy not showing my reference genome in Drop down for BowTie
Hi guys, As shown in the attached screenshot I uploaded a fasta file. And I want to use it as my reference genome for running bow tie but it doesn't appear in the dropdown on the bow tie tool. I'm sure I'm missing something obvious. Thanks, Greg
Hi Greg, Nice pic, it helps! My guess is that the datatype is not assigned as "fasta". To do this, click on the pencil icon for the custom reference genome dataset (#1) to bring up the Edit Attributes forms in the center panel. Then click on the "Datatype" tab and change this to be "fasta" and save. Full help in our wiki with Custom genomes starts here: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome Please let us know if you need more help, Jen Galaxy team On 10/9/12 11:08 AM, greg wrote:
Hi guys,
As shown in the attached screenshot I uploaded a fasta file. And I want to use it as my reference genome for running bow tie but it doesn't appear in the dropdown on the bow tie tool.
I'm sure I'm missing something obvious.
Thanks,
Greg
___________________________________________________________ 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:
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-- Jennifer Jackson http://galaxyproject.org
Thanks Jen. But it looks like the datatype was already set to fasta. I tried setting it again and saving but it didn't seem to help. Is there anything else I can try? thanks, Greg On Tue, Oct 9, 2012 at 9:10 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Greg,
Nice pic, it helps! My guess is that the datatype is not assigned as "fasta". To do this, click on the pencil icon for the custom reference genome dataset (#1) to bring up the Edit Attributes forms in the center panel. Then click on the "Datatype" tab and change this to be "fasta" and save.
Full help in our wiki with Custom genomes starts here: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
Please let us know if you need more help,
Jen Galaxy team
On 10/9/12 11:08 AM, greg wrote:
Hi guys,
As shown in the attached screenshot I uploaded a fasta file. And I want to use it as my reference genome for running bow tie but it doesn't appear in the dropdown on the bow tie tool.
I'm sure I'm missing something obvious.
Thanks,
Greg
___________________________________________________________ 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:
-- Jennifer Jackson http://galaxyproject.org
Looking at your screenshot, you have "Use a built-in index" selected. If you change this to "Use one from the history", do you see your fasta file listed? -Dannon On Oct 10, 2012, at 9:02 AM, greg <margeemail@gmail.com> wrote:
Thanks Jen. But it looks like the datatype was already set to fasta. I tried setting it again and saving but it didn't seem to help.
Is there anything else I can try?
thanks,
Greg
On Tue, Oct 9, 2012 at 9:10 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Greg,
Nice pic, it helps! My guess is that the datatype is not assigned as "fasta". To do this, click on the pencil icon for the custom reference genome dataset (#1) to bring up the Edit Attributes forms in the center panel. Then click on the "Datatype" tab and change this to be "fasta" and save.
Full help in our wiki with Custom genomes starts here: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
Please let us know if you need more help,
Jen Galaxy team
On 10/9/12 11:08 AM, greg wrote:
Hi guys,
As shown in the attached screenshot I uploaded a fasta file. And I want to use it as my reference genome for running bow tie but it doesn't appear in the dropdown on the bow tie tool.
I'm sure I'm missing something obvious.
Thanks,
Greg
___________________________________________________________ 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:
-- Jennifer Jackson http://galaxyproject.org
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:
Yes that was it! I knew I was missing something obvious. Thanks, Greg On Wed, Oct 10, 2012 at 9:06 AM, Dannon Baker <dannonbaker@me.com> wrote:
Looking at your screenshot, you have "Use a built-in index" selected. If you change this to "Use one from the history", do you see your fasta file listed?
-Dannon
On Oct 10, 2012, at 9:02 AM, greg <margeemail@gmail.com> wrote:
Thanks Jen. But it looks like the datatype was already set to fasta. I tried setting it again and saving but it didn't seem to help.
Is there anything else I can try?
thanks,
Greg
On Tue, Oct 9, 2012 at 9:10 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Greg,
Nice pic, it helps! My guess is that the datatype is not assigned as "fasta". To do this, click on the pencil icon for the custom reference genome dataset (#1) to bring up the Edit Attributes forms in the center panel. Then click on the "Datatype" tab and change this to be "fasta" and save.
Full help in our wiki with Custom genomes starts here: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
Please let us know if you need more help,
Jen Galaxy team
On 10/9/12 11:08 AM, greg wrote:
Hi guys,
As shown in the attached screenshot I uploaded a fasta file. And I want to use it as my reference genome for running bow tie but it doesn't appear in the dropdown on the bow tie tool.
I'm sure I'm missing something obvious.
Thanks,
Greg
___________________________________________________________ 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:
-- Jennifer Jackson http://galaxyproject.org
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:
participants (3)
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Dannon Baker -
greg -
Jennifer Jackson