Genomes are missing from the dbdey table while present in bowtie2

usegalaxy.eu support
1

Hi,
I noticed that some genomes are not proposed in the bedtools slopbed: Galaxy
According to the wrapper it should use the dbkeys.loc table. I am suprised that so many genomes are missing, for example, for human there are only 2 proposed. For mouse, mm39 is missing.

Thanks,

Lucille

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2

Hi @lldelisle

It seems to be just the EU server with the problem. Ping @wm75

For comparison, the same ORG tool → Galaxy

3

Hi @lldelisle,
the __dbkeys__ data table on .eu turns out to really just contain a tiny subset of genomes we have a all_fasta record for.
I’ll clarify why.
In the meantime: any genome you need exposed urgently?

4

I have identifier 32 missing len files and have added them now.

The list is:

anoGam3
apiMel3
bosTau8
bosTau9
canFam6
ce10
ce11
ce6
danRer10
danRer11
danRer7
dm3
equCab3
eschColi_K12
felCat9
galGal6
hg19
hg38
macFas5
melGal5
mm39
oryCun2
oviAri4
pp1.2b
rheMac10
rn5
rn6
rn7
sacCer3
susScr11
susScr3
xenTro3
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5

Thank you very much.

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