[Gmod-ajax] Deleting from JBrowse

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[Gmod-ajax] Deleting from JBrowse

bosborne
All,

I see bin/remove-track.pl, to remove a track. How do you remove a reference sequence and all of its tracks?

Thanks again,

Brian O.



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Re: Deleting from JBrowse

Colin
You can delete the whole data directory if you want to clear all tracks including the reference sequence. After doing that, you can re-run bin/prepare-refseqs.pl with your reference sequence and add tracks as usual.

-Colin


On Sat, Mar 29, 2014 at 1:41 PM, Brian Osborne <[hidden email]> wrote:
All,

I see bin/remove-track.pl, to remove a track. How do you remove a reference sequence and all of its tracks?

Thanks again,

Brian O.



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Re: Deleting from JBrowse

bosborne
Colin,

Got it. I’m wondering about situations with multiple genomes, where one may be re-annotating just one of the genomes, so the data’s changing. So say you have genomes A and B. Do you do something like this?

bin/prepare-refseqs.pl —fasta A.fa —out data/A
bin/biodb-to-json.pl —conf A.conf —out data/A
bin/prepare-refseqs.pl —fasta B.fa —out data/B
bin/biodb-to-json.pl —conf B.conf —out data/B

Or, is it best to just keep everything in the default data/ location, if you’re re-annotating A you just run this a second time with the new data:

bin/prepare-refseqs.pl —fasta A.fa —out data/A
bin/biodb-to-json.pl —conf A.conf —out data/A

This assumes that the old data is over-written. What is best?

Thanks again,

Brian O.

On Mar 29, 2014, at 4:12 PM, Colin <[hidden email]> wrote:

You can delete the whole data directory if you want to clear all tracks including the reference sequence. After doing that, you can re-run bin/prepare-refseqs.pl with your reference sequence and add tracks as usual.

-Colin


On Sat, Mar 29, 2014 at 1:41 PM, Brian Osborne <[hidden email]> wrote:
All,

I see bin/remove-track.pl, to remove a track. How do you remove a reference sequence and all of its tracks?

Thanks again,

Brian O.



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Re: Deleting from JBrowse

Colin
If you have a setup that has a one genome stored in data/A and another in data/B, and you only want to update data/A, then you can just delete the data/A directory and reload files for that genome only. You wouldn't have to delete data/B and you don't necessarily have to delete the 'root' data directory (in fact your data directories for different genomes can reside anywhere they want to). Also, I think that deleting the old data directory and then loading the new data is safer than trying to overwrite the old data.

Thanks,
-Colin



On Sat, Mar 29, 2014 at 4:33 PM, Brian Osborne <[hidden email]> wrote:
Colin,

Got it. I’m wondering about situations with multiple genomes, where one may be re-annotating just one of the genomes, so the data’s changing. So say you have genomes A and B. Do you do something like this?

bin/prepare-refseqs.pl —fasta A.fa —out data/A
bin/biodb-to-json.pl —conf A.conf —out data/A
bin/prepare-refseqs.pl —fasta B.fa —out data/B
bin/biodb-to-json.pl —conf B.conf —out data/B

Or, is it best to just keep everything in the default data/ location, if you’re re-annotating A you just run this a second time with the new data:

bin/prepare-refseqs.pl —fasta A.fa —out data/A
bin/biodb-to-json.pl —conf A.conf —out data/A

This assumes that the old data is over-written. What is best?

Thanks again,

Brian O.

On Mar 29, 2014, at 4:12 PM, Colin <[hidden email]> wrote:

You can delete the whole data directory if you want to clear all tracks including the reference sequence. After doing that, you can re-run bin/prepare-refseqs.pl with your reference sequence and add tracks as usual.

-Colin


On Sat, Mar 29, 2014 at 1:41 PM, Brian Osborne <[hidden email]> wrote:
All,

I see bin/remove-track.pl, to remove a track. How do you remove a reference sequence and all of its tracks?

Thanks again,

Brian O.



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Re: Deleting from JBrowse

bosborne
Colin,

I’m running commands like this now:


bin/prepare-refseqs.pl —fasta A.fa —out data/A
bin/biodb-to-json.pl —conf A.conf —out data/A

And I don’t get any errors, and I see the subdirectories in data/ being created. Unfortunately, I don’t see any visualizations. Do I have to change something in the *conf file to make this work?

Thanks again,

Brian O.


On Mar 29, 2014, at 7:02 PM, Colin <[hidden email]> wrote:

If you have a setup that has a one genome stored in data/A and another in data/B, and you only want to update data/A, then you can just delete the data/A directory and reload files for that genome only. You wouldn't have to delete data/B and you don't necessarily have to delete the 'root' data directory (in fact your data directories for different genomes can reside anywhere they want to). Also, I think that deleting the old data directory and then loading the new data is safer than trying to overwrite the old data.

Thanks,
-Colin



On Sat, Mar 29, 2014 at 4:33 PM, Brian Osborne <[hidden email]> wrote:
Colin,

Got it. I’m wondering about situations with multiple genomes, where one may be re-annotating just one of the genomes, so the data’s changing. So say you have genomes A and B. Do you do something like this?

bin/prepare-refseqs.pl —fasta A.fa —out data/A
bin/biodb-to-json.pl —conf A.conf —out data/A
bin/prepare-refseqs.pl —fasta B.fa —out data/B
bin/biodb-to-json.pl —conf B.conf —out data/B

Or, is it best to just keep everything in the default data/ location, if you’re re-annotating A you just run this a second time with the new data:

bin/prepare-refseqs.pl —fasta A.fa —out data/A
bin/biodb-to-json.pl —conf A.conf —out data/A

This assumes that the old data is over-written. What is best?

Thanks again,

Brian O.

On Mar 29, 2014, at 4:12 PM, Colin <[hidden email]> wrote:

You can delete the whole data directory if you want to clear all tracks including the reference sequence. After doing that, you can re-run bin/prepare-refseqs.pl with your reference sequence and add tracks as usual.

-Colin


On Sat, Mar 29, 2014 at 1:41 PM, Brian Osborne <[hidden email]> wrote:
All,

I see bin/remove-track.pl, to remove a track. How do you remove a reference sequence and all of its tracks?

Thanks again,

Brian O.



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Re: Deleting from JBrowse

Colin
You can use a specially crafted URL that specifies the data directory you are using "http://yourserver/jbrowse/index.html?data=data/A"

If the data directory is "outside" of the normal jbrowse directory it is probably best to create a symlink inside the jbrowse directory it so that this scheme can be used easily.

As far as configuration goes, you can also add these data directories to a "dataset selector" so that it is easier to access them, but it is not necessary to configure JBrowse this way to use the specially crafted URLs that I mentioned above : http://gmod.org/wiki/JBrowse_Configuration_Guide#Dataset_Selector


-Colin


On Thu, Apr 3, 2014 at 1:37 PM, Brian Osborne <[hidden email]> wrote:
Colin,

I’m running commands like this now:


bin/prepare-refseqs.pl —fasta A.fa —out data/A
bin/biodb-to-json.pl —conf A.conf —out data/A

And I don’t get any errors, and I see the subdirectories in data/ being created. Unfortunately, I don’t see any visualizations. Do I have to change something in the *conf file to make this work?

Thanks again,

Brian O.


On Mar 29, 2014, at 7:02 PM, Colin <[hidden email]> wrote:

If you have a setup that has a one genome stored in data/A and another in data/B, and you only want to update data/A, then you can just delete the data/A directory and reload files for that genome only. You wouldn't have to delete data/B and you don't necessarily have to delete the 'root' data directory (in fact your data directories for different genomes can reside anywhere they want to). Also, I think that deleting the old data directory and then loading the new data is safer than trying to overwrite the old data.

Thanks,
-Colin



On Sat, Mar 29, 2014 at 4:33 PM, Brian Osborne <[hidden email]> wrote:
Colin,

Got it. I’m wondering about situations with multiple genomes, where one may be re-annotating just one of the genomes, so the data’s changing. So say you have genomes A and B. Do you do something like this?

bin/prepare-refseqs.pl —fasta A.fa —out data/A
bin/biodb-to-json.pl —conf A.conf —out data/A
bin/prepare-refseqs.pl —fasta B.fa —out data/B
bin/biodb-to-json.pl —conf B.conf —out data/B

Or, is it best to just keep everything in the default data/ location, if you’re re-annotating A you just run this a second time with the new data:

bin/prepare-refseqs.pl —fasta A.fa —out data/A
bin/biodb-to-json.pl —conf A.conf —out data/A

This assumes that the old data is over-written. What is best?

Thanks again,

Brian O.

On Mar 29, 2014, at 4:12 PM, Colin <[hidden email]> wrote:

You can delete the whole data directory if you want to clear all tracks including the reference sequence. After doing that, you can re-run bin/prepare-refseqs.pl with your reference sequence and add tracks as usual.

-Colin


On Sat, Mar 29, 2014 at 1:41 PM, Brian Osborne <[hidden email]> wrote:
All,

I see bin/remove-track.pl, to remove a track. How do you remove a reference sequence and all of its tracks?

Thanks again,

Brian O.



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Re: Deleting from JBrowse

bosborne
Colin,

That works, of course.

BTW, this is all using the “new” driver, Bio::DB::Das::BioSQL.

Thanks again,

Brian O.

On Apr 3, 2014, at 2:49 PM, Colin <[hidden email]> wrote:

You can use a specially crafted URL that specifies the data directory you are using "http://yourserver/jbrowse/index.html?data=data/A"

If the data directory is "outside" of the normal jbrowse directory it is probably best to create a symlink inside the jbrowse directory it so that this scheme can be used easily.

As far as configuration goes, you can also add these data directories to a "dataset selector" so that it is easier to access them, but it is not necessary to configure JBrowse this way to use the specially crafted URLs that I mentioned above : http://gmod.org/wiki/JBrowse_Configuration_Guide#Dataset_Selector


-Colin


On Thu, Apr 3, 2014 at 1:37 PM, Brian Osborne <[hidden email]> wrote:
Colin,

I’m running commands like this now:


bin/prepare-refseqs.pl —fasta A.fa —out data/A
bin/biodb-to-json.pl —conf A.conf —out data/A

And I don’t get any errors, and I see the subdirectories in data/ being created. Unfortunately, I don’t see any visualizations. Do I have to change something in the *conf file to make this work?

Thanks again,

Brian O.


On Mar 29, 2014, at 7:02 PM, Colin <[hidden email]> wrote:

If you have a setup that has a one genome stored in data/A and another in data/B, and you only want to update data/A, then you can just delete the data/A directory and reload files for that genome only. You wouldn't have to delete data/B and you don't necessarily have to delete the 'root' data directory (in fact your data directories for different genomes can reside anywhere they want to). Also, I think that deleting the old data directory and then loading the new data is safer than trying to overwrite the old data.

Thanks,
-Colin



On Sat, Mar 29, 2014 at 4:33 PM, Brian Osborne <[hidden email]> wrote:
Colin,

Got it. I’m wondering about situations with multiple genomes, where one may be re-annotating just one of the genomes, so the data’s changing. So say you have genomes A and B. Do you do something like this?

bin/prepare-refseqs.pl —fasta A.fa —out data/A
bin/biodb-to-json.pl —conf A.conf —out data/A
bin/prepare-refseqs.pl —fasta B.fa —out data/B
bin/biodb-to-json.pl —conf B.conf —out data/B

Or, is it best to just keep everything in the default data/ location, if you’re re-annotating A you just run this a second time with the new data:

bin/prepare-refseqs.pl —fasta A.fa —out data/A
bin/biodb-to-json.pl —conf A.conf —out data/A

This assumes that the old data is over-written. What is best?

Thanks again,

Brian O.

On Mar 29, 2014, at 4:12 PM, Colin <[hidden email]> wrote:

You can delete the whole data directory if you want to clear all tracks including the reference sequence. After doing that, you can re-run bin/prepare-refseqs.pl with your reference sequence and add tracks as usual.

-Colin


On Sat, Mar 29, 2014 at 1:41 PM, Brian Osborne <[hidden email]> wrote:
All,

I see bin/remove-track.pl, to remove a track. How do you remove a reference sequence and all of its tracks?

Thanks again,

Brian O.



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