Question: How to install a genome (ce10) to local Galaxy
1
gravatar for meiemi2000
2.1 years ago by
meiemi200010
meiemi200010 wrote:

Hello,

I want to install a genome (ce10) to local galaxy instance. I am the admin of the local galaxy.

I obtained the ce10 genome using

rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/ce10

55 files were synced, but when I run Galaxy again, ce10 did not appear in the Genome dropbox selection. I guess there is another step to link the genome files to Galaxy, but HOW? Please help! Thank you!

 

galaxy • 1.1k views
ADD COMMENTlink modified 23 months ago by nitesh.turaga100 • written 2.1 years ago by meiemi200010
3
gravatar for nitesh.turaga
23 months ago by
nitesh.turaga100
United States
nitesh.turaga100 wrote:

Hi

Hope this helps. Parameters to fetch ce10 genome

http://imgur.com/ehU9rt5

ADD COMMENTlink modified 23 months ago • written 23 months ago by nitesh.turaga100

Thank you so much. This parameters actually solved my problem!

ADD REPLYlink written 23 months ago by meiemi200010
1
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Loading the data this way is not the best method anymore. However, if you do want to try it, instructions are here: https://wiki.galaxyproject.org/Admin/DataIntegration and https://wiki.galaxyproject.org/Admin/DataPreparation

A great way to load instead is to use Data Managers (available in the Tool Shed).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson24k
0
gravatar for meiemi2000
2.1 years ago by
meiemi200010
meiemi200010 wrote:

Hi Jennifer,

Thanks a lot for the pointer!

I installed Data Manager: data_manager_fetch_genome_all_fasta  and data_manager_bwa_index_builder.

Basically I follow this nice video by Daniel Blankenberg https://vimeo.com/74265510.

However, after installation, my desired genome C. elegans (WS220/ce10) is not listed in DBKEY drop-down menu. Can you tell me how to add ce10 to DBKEY?  

Mei

ADD COMMENTlink written 2.1 years ago by meiemi200010

Hello,

When adding a new genome that is not listed in the default list of genomes, this is a better data manager to use (it adds a new genome to the list): https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_fetch_genome_dbkeys_all_fasta/776bb1b478a0

I am not sure how you executed the other fasta-fetching data manager without a choosing an existing genome/dbkey on the form.

However, maybe you mean that the database is not included on the BWA tool form as a built-in reference? This seems like a index/tool mismatch. Note that there are two data managers to build BWA indexes. The BWA data manager you specify is for the older wrapped version of the tool (BWA for Illumina). The newer wrapped tools (BWA and BWA-MEM) require this data manager: https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_bwa_mem_index_builder/cb0147ade868

I should also mention that a server restart is necessary after indexing, just in case, even if that doesn't seem to be the core issue. Check into the tool/index dependencies and see if using the other data manager resolves the problem.

Please share back any details/updates or clarify if I didn't understand the problem correctly.

Thanks! Jen, Galaxy team

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson24k
0
gravatar for meiemi2000
2.1 years ago by
meiemi200010
meiemi200010 wrote:

Thanks Jen,

I installed the data_manager_fetch_genome_dbkeys_all_fasta/776bb1b478a0

Then I ran the Create DBKey and Reference Genome (Under Data Manager -> Run Data Manager Tool), and a window pops out containing the following lines:

Use exisiting dbkey or create a new one.

I choose : New (because ce10 is not in the drop down menu)

DBKEY to assign to data

I typed : C. elegans Oct. 2010 (WS220/ce10) (ce10)  (Does it matter what I typed here?)

Name of sequence

I left this blank

ID for sequence

I left this blank

Choose the source for the reference genome

I choose: UCSC

UCSC's DBKEY for source FASTA

I type: ce10

Sort by chromosome name

As is

Then execute.

This error message pops out (the whole message at the end of this post):

Traceback (most recent call last):
....
....
IOError: [Errno 2] No such file or directory: u'/Users/hueimeichen/galaxy/database/job_working_directory/000/32/dataset_30_files/C. elegans Oct. 2010 (WS220/ce10) (ce10).fa'

 

Does this mean I need to download the ce10 fasta file to a local directory? I thought this tool would pull data directly from USCS. Can you walk me through the steps? Sorry I am too new to this, I realize my questions may seem silly.

p.s. I will deal with BWA later after I get ce10 genome into the drop down menu with matching genome. 

Thanks again.

 

Whole error message:

Traceback (most recent call last):
  File "/Users/hueimeichen/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/776bb1b478a0/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 415, in <module>
    if __name__ == "__main__": main()
  File "/Users/hueimeichen/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/776bb1b478a0/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 410, 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 "/Users/hueimeichen/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/776bb1b478a0/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 217, in download_from_ucsc
    fasta_writer = open( fasta_filename, 'wb+' )
IOError: [Errno 2] No such file or directory: u'/Users/hueimeichen/galaxy/database/job_working_directory/000/32/dataset_30_files/C. elegans Oct. 2010 (WS220/ce10) (ce10).fa'

 

 

 

 

 

 

ADD COMMENTlink written 2.1 years ago by meiemi200010
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