NGS data library construction
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 galaxy-dev@bx.psu.edu, on the galaxy site it links to galaxy-bugs@bx.psu.edu, 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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 galaxy-dev@bx.psu.edu <mailto:galaxy-dev@bx.psu.edu>, on the galaxy site it links to galaxy-bugs@bx.psu.edu <mailto:galaxy-bugs@bx.psu.edu>, 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
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participants (2)
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Nate Coraor -
Terrence Barrette