Re: [galaxy-dev] missing .fa files in rsync datacache indexes

2012-09-26 Thread Dave Bouvier

Kevin,

We decided to exclude fasta files mainly because 2bit is a lossless 
compression with a much lower file size, so it would be a waste of our 
users' bandwidth and time to include the (approximately) four times 
larger files when 2bit is available.


   --Dave B.

On 9/25/12 20:55:31.000, Kevin Y wrote:

Thanks Dave,
A question before we go ahead, why are they missing in the first place?

Does the main galaxy not actually need them? are the tools moving away
from fa?

Cheers,
Kevin.

On Tue, Sep 25, 2012 at 11:12 PM, Dave Bouvier d...@bx.psu.edu
mailto:d...@bx.psu.edu wrote:

Kevin,

Correct, converting from 2bit to fasta shouldn't cause any problems.

--Dave B.


On 9/25/12 03:20:14.000, Kevin Y wrote:

Hi,

Thanks for providing the indexes via rsync::
http://wiki.g2.bx.psu.edu/__Admin/Data%20Integration
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration

We've, noticed that despite soft links pointing to it, there are
no .fa
files for example in hg19/seq/
However there are 2bit files.

Would you guys recommend we convert them from 2bit to fasta?

Thanks,
Kevin.


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Re: [galaxy-dev] missing .fa files in rsync datacache indexes

2012-09-26 Thread Kevin Y
Thank again Dave,

For anyone who is interested, I've written a script for converting the
2bit's into fa's here:
https://bitbucket.org/gvl/gen_loc_files

Also packaged is a script to generate loc files by traversing the rsynced
folder, there is more work to be done on it though.

All feedback/contributions are welcome!
Kevin

On Wed, Sep 26, 2012 at 11:26 PM, Dave Bouvier d...@bx.psu.edu wrote:

 Kevin,

 We decided to exclude fasta files mainly because 2bit is a lossless
 compression with a much lower file size, so it would be a waste of our
 users' bandwidth and time to include the (approximately) four times larger
 files when 2bit is available.

--Dave B.


 On 9/25/12 20:55:31.000, Kevin Y wrote:

 Thanks Dave,
 A question before we go ahead, why are they missing in the first place?

 Does the main galaxy not actually need them? are the tools moving away
 from fa?

 Cheers,
 Kevin.

 On Tue, Sep 25, 2012 at 11:12 PM, Dave Bouvier d...@bx.psu.edu
 mailto:d...@bx.psu.edu wrote:

 Kevin,

 Correct, converting from 2bit to fasta shouldn't cause any problems.

 --Dave B.


 On 9/25/12 03:20:14.000, Kevin Y wrote:

 Hi,

 Thanks for providing the indexes via rsync::
 
 http://wiki.g2.bx.psu.edu/__**Admin/Data%20Integrationhttp://wiki.g2.bx.psu.edu/__Admin/Data%20Integration

 
 http://wiki.g2.bx.psu.edu/**Admin/Data%20Integrationhttp://wiki.g2.bx.psu.edu/Admin/Data%20Integration
 

 We've, noticed that despite soft links pointing to it, there are
 no .fa
 files for example in hg19/seq/
 However there are 2bit files.

 Would you guys recommend we convert them from 2bit to fasta?

 Thanks,
 Kevin.


 __**__**_

 Please keep all replies on the list by using reply all
 in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] missing .fa files in rsync datacache indexes

2012-09-25 Thread Dave Bouvier

Kevin,

Correct, converting from 2bit to fasta shouldn't cause any problems.

   --Dave B.

On 9/25/12 03:20:14.000, Kevin Y wrote:

Hi,

Thanks for providing the indexes via rsync::
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration

We've, noticed that despite soft links pointing to it, there are no .fa
files for example in hg19/seq/
However there are 2bit files.

Would you guys recommend we convert them from 2bit to fasta?

Thanks,
Kevin.


___
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

   http://lists.bx.psu.edu/


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Re: [galaxy-dev] missing .fa files in rsync datacache indexes

2012-09-25 Thread Kevin Y
Thanks Dave,
A question before we go ahead, why are they missing in the first place?

Does the main galaxy not actually need them? are the tools moving away from
fa?

Cheers,
Kevin.

On Tue, Sep 25, 2012 at 11:12 PM, Dave Bouvier d...@bx.psu.edu wrote:

 Kevin,

 Correct, converting from 2bit to fasta shouldn't cause any problems.

--Dave B.


 On 9/25/12 03:20:14.000, Kevin Y wrote:

 Hi,

 Thanks for providing the indexes via rsync::
 http://wiki.g2.bx.psu.edu/**Admin/Data%20Integrationhttp://wiki.g2.bx.psu.edu/Admin/Data%20Integration

 We've, noticed that despite soft links pointing to it, there are no .fa
 files for example in hg19/seq/
 However there are 2bit files.

 Would you guys recommend we convert them from 2bit to fasta?

 Thanks,
 Kevin.


 __**_
 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:

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