matmu / vep Goto Github PK

Sometimes an error occurs while building the singularity image:

Downloaded layer sha256:94da6cf6f5118f7b1daab46ec4470d1f17ef914933c005fd963f718c0c4c9424.tar.gz does not match checksum
Error during layer download - one or more layers failed to download correctly.

Hi @matmu,

is it possible to include samtools in the docker image in the next release. The LOFTEE plugin requires samtools and it would be interesting for us to include the information of LOFTEE as well.

Many thanks,
Axel

Hi,
I am trying to run VEP using this docker command:

docker run -v /home/dnanexus:/opt/data matmu/vep:105-GRCh37 vep --dir /opt/vep/.vep --offline --cache --input_file /opt/data/NGC00142_01.vcf.gz --vcf -o STDOUT --format vcf --offline --cache --dir_cache /opt/data/snv-master/demo/softwares/vep/grch37 --force_overwrite --species homo_sapiens --assembly GRCh37 --port 3337 --vcf_info_field ANN --sift b --polyphen b --humdiv --regulatory --allele_number --total_length --numbers --domains --hgvs --protein --symbol --ccds --uniprot --canonical --biotype --check_existing --af --af_1kg --pubmed --gene_phenotype --variant_class --plugin CADD,/opt/data/snv-master/demo/resources/cadd/grch37/whole_genome_SNVs.tsv.gz,/opt/data/snv-master/demo/resources/cadd/grch37/InDels.tsv.gz --plugin ExACpLI,/opt/data/snv-master/demo/resources/gnomad/grch37/gnomad.v2.1.1.lof_metrics.by_transcript_forVEP.txt --plugin REVEL,/opt/data/snv-master/demo/resources/revel/grch37/new_tabbed_revel.tsv.gz --plugin SpliceRegion --stats_text --stats_file /opt/data/tmpFile_1_AC0.exon.noGT.vep_stats.txt --output_file /opt/data/tmpFile_1_AC0.exon.noGT.new.vep.vcf

But, getting the following error:

Please let me know how to fix it.
Thanks with regards,
Ravi