search

bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
992 stars 354 forks source link

VEP data download link needs to be updated. #2883

Closed jxshi closed 5 years ago

jxshi commented 5 years ago

Hi,

I tried to upgrade bcbio-nextgen recently. But it encountered the following error.

List of genomes to get (from the config file at '{'genomes': [{'dbkey': 'rn6', 'name': 'Rat (rn6)', 'indexes': ['seq', 'twobit'], 'annotations': ['transcripts', 'mirbase']}], 'genome_indexes': ['bwa', 'bowtie2', 'star', 'hisat2', 'rtg', 'twobit', 'bowtie'], 'install_liftover': False, 'install_uniref': False}'): Rat (rn6)
--2019-07-18 14:16:49--  http://ftp.ensembl.org/pub/release-97/variation/VEP/homo_sapiens_merged_vep_97_GRCh37.tar.gz
Resolving ftp.ensembl.org... 193.62.193.8
Connecting to ftp.ensembl.org|193.62.193.8|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2019-07-18 14:16:54 ERROR 404: Not Found.

I found that the link to vep data needs to be updated. (VEP should be in lower case in current link).

Previous link: http://ftp.ensembl.org/pub/release-97/variation/VEP/homo_sapiens_merged_vep_97_GRCh37.tar.gz

Current link: http://ftp.ensembl.org/pub/release-97/variation/vep/homo_sapiens_merged_vep_97_GRCh37.tar.gz

Thank you!

Cheers!

Jianxiang

jxshi commented 5 years ago

Hi,

I have replaced VEP with vep in line 106 of the following file to solve this.

~/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/effects.py

Cheers!

Jianxiang

roryk commented 5 years ago

Thanks, it looks like they switched from VEP to having both VEP and vep to only having vep, so it seems like maybe they were transitioning off of VEP and moving to justvep. I added a check to check for the release version being >= 97, and if so using vep. Thanks!

erinijapranckeviciene commented 5 years ago

Hi @jxshi , @roryk

I just reinstalled bcbio_nextgen less than 9 days ago and was upgrading vep. I came across the same as jxshi , but in my case it is line 99 of effects.py :

url = "http://ftp.ensembl.org/pub/release-%s/variation/VEP/%s.tar.gz" % (eversion, ensembl_name)

Changing manually from VEP to vep fixed the issue. So perhaps this is still in the code.

roryk commented 5 years ago

Hi @erinijapranckeviciene,

If you upgrade to the development version with -u development you'll pull in this fix, I think you might be operating on the -u stable branch.

erinijapranckeviciene commented 5 years ago

Hi @roryk , yes, this is the case, thank you.

roryk commented 5 years ago

Great! Thanks for following up.