Remove duplicate entries in Data Manager: all

Question: Remove duplicate entries in Data Manager: all_fasta

3.3 years ago by

vebaev • 130

vebaev • 130 wrote:

Hi,

I have fetched a duplicate reference genome, is it possible to remove it?

Data Manager: all_fasta 
value    dbkey    name    path
hg19    hg19    Human Feb. 2009 (GRCh37/hg19) (hg19)    /galaxy-central/tool-data/hg19/seq/hg19.fa

Tomato24    Tomato24    Solanum lycopersicon 2.40    /galaxy-central/tool-data/Tomato24/seq/Tomato24.fa

tomato24    tomato24    Solanum lycopersicon (tomato ITAG2.40)    /galaxy-central/tool-data/tomato24/seq/tomato24.fa

data manager • 974 views

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modified 2.6 years ago by chaoyuan • 80 • written 3.3 years ago by vebaev • 130

3.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There is no automatic way to remove reference genomes using a Data Manager at this time. However, this is functionality that the team is considering adding in. For now, the duplication can be either left in place (it shouldn't harm anything) or the genome can be removed by altering the files/tables directly as an administrator on the command-line (if you familiar with the data structure). That said, it is probably best just to simply leave the extra genome alone since the removal process is non-trivial and a problem could be accidentally introduced.

If our team has other suggestions, we will post an update to this reply.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

2.6 years ago by

chaoyuan • 80

chaoyuan • 80 wrote:

I just ran into a problem caused by duplicate entries. It caused error for RNA STAR index builder. see the post here

The information is stored in all_fasta.loc, which, in my case is located at ~/galaxy-dev/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/fb744a070bee/all_fasta.loc )

You can remove duplicate entries by editing the file.

ADD COMMENT • link written 2.6 years ago by chaoyuan • 80

Do you need to change something in the galaxy database to make it properly ?

ADD REPLY • link written 2.6 years ago by christophe.habib • 340

No. After I edited the file, I clicked the reload all_fasta tool data table under Data Manager : all_fasta and it appears normal.

ADD REPLY • link written 2.6 years ago by chaoyuan • 80

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