How to add a new dbkey (publicbuilds, manual_builds, builds.txt, data manager)

Question: How to add a new dbkey (publicbuilds, manual_builds, builds.txt, data manager)

4.0 years ago by

Brad Langhorst • 100

United States

Brad Langhorst • 100 wrote:

What is the current method I should be using to add builds to galaxy (galaxy dist from 10/6/2014).

E.g. adding a genome from plants.ensemble.org?

I read about plans to create db key from the data manager tools, but I can't find the relevant tool.

Do i need to make up a name, fetch the genome and count chromosome lengths so I can populate manual_builds txt?

Is there some data manager tool that I cant' find?

Is there a good way to add ensembl genomes like we have for ucsc?

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modified 4.0 years ago by Bjoern Gruening ♦ 5.1k • written 4.0 years ago by Brad Langhorst • 100

4.0 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi Brad,

have you tried data_manager_fetch_genome_all_fasta?

Cheers,

Bjoern

ADD COMMENT • link written 4.0 years ago by Bjoern Gruening ♦ 5.1k

Yep. But you have to specify a dbkey in the first dropdown, and I can't find e.g. glycine max in the big list.

Did I miss something about how this works?

ADD REPLY • link written 4.0 years ago by Brad Langhorst • 100

There is a better Data Manager available in the Test ToolShed that will add a dbkey, .len file, and fasta genome for use by tools. I've been meaning to move it over to the main toolshed after an enhancement to allow it it deal with downloading from UCSC using their new file naming structure for the most recent human genome release. But you can have a look at it here for now if you like: https://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_fetch_genome_dbkeys_all_fasta

ADD REPLY • link written 4.0 years ago by Daniel Blankenberg ♦♦ 1.7k

Thanks for the responses!

I just tried the new data manager from the test toolshed...

I think it's a bit buggy (or maybe I've done something wrong... )

Here's the traceback from the failed tool execution

Traceback (most recent call last): File "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_fetch_genome_dbkeys_all_fasta/d59e1d23b388/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 410, in <module> if __name__ == "__main__": main() File "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_fetch_genome_dbkeys_all_fasta/d59e1d23b388/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 405, in main REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ) File "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_fetch_genome_dbkeys_all_fasta/d59e1d23b388/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 251, in download_from_url for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ): NameError: global name 'fasta_readers' is not defined

ADD REPLY • link written 4.0 years ago by Brad Langhorst • 100

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