NGS data library construction

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NGS data library construction

Terrence Barrette
Hi All,
I'm working on building a local instance of the galaxy server.  I've got the application up and its proxied behind a local apache.  The base OS is redhat 5.5 kernel 2.6.18-194, python 2.6, on an hp dl385 with 8 cores and 20 GB of ram.  The local drive is 1 TB SAS and I have a few TB of nfs space mounted as /exds/galaxy for holding the datafiles as a repository.
 
I've got about 1 TB of solexa seq I want to make available to the various tools, bowtie, bwa, ... for analysis by the group but I'm a little uncertain how to proceed.  It seems that I should make a file similar to faseq.loc in the tool-data folder that points to the individual files in a folder in the nfs space, but I'm not sure how that will make it available to the different tools that could use it and how to keep it a single copy as different users access it and choose from the fastq files to make datasets for analysis.
 
In the galaxy-wiki it said to write to [hidden email], on the galaxy site it links to [hidden email], at bitbucket I was just going to add this question as a issue.  What is the preferred way to ask questions like this?
Thanks
Terry
 
 
 
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Re: NGS data library construction

Nate Coraor (nate@bx.psu.edu)
Terrence Barrette wrote:

> Hi All,
> I'm working on building a local instance of the galaxy server.  I've got
> the application up and its proxied behind a local apache.  The base OS
> is redhat 5.5 kernel 2.6.18-194, python 2.6, on an hp dl385 with 8 cores
> and 20 GB of ram.  The local drive is 1 TB SAS and I have a few TB of
> nfs space mounted as /exds/galaxy for holding the datafiles as a repository.
>  
> I've got about 1 TB of solexa seq I want to make available to the
> various tools, bowtie, bwa, ... for analysis by the group but I'm a
> little uncertain how to proceed.  It seems that I should make a file
> similar to faseq.loc in the tool-data folder that points to the
> individual files in a folder in the nfs space, but I'm not sure how that
> will make it available to the different tools that could use it and how
> to keep it a single copy as different users access it and choose from
> the fastq files to make datasets for analysis.

Hi Terry,

Have a look at the library_import_dir and allow_library_path_paste
options in the config file.  This will allow you to symlink or directly
specify the path to your data, and import that data into a Galaxy Data
Library.  In addition, you can choose not to copy the files into
Galaxy's database/files/ directory so you can continue to manage them
externally.

> In the galaxy-wiki it said to write to [hidden email]
> <mailto:[hidden email]>, on the galaxy site it links to
> [hidden email] <mailto:[hidden email]>, at bitbucket I
> was just going to add this question as a issue.  What is the preferred
> way to ask questions like this?

For questions like this, galaxy-dev is the right place.  galaxy-bugs is
for reporting issues with the public Galaxy servers we run.

--nate

> Thanks
> Terry
>  
>  
>  
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-dev

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