kmoad
commented
1 year ago There was an bug with the variant report app. It's been fixed here https://github.com/KarchinLab/open-cravat-modules-karchinlab/commit/19684ad095c235fcba5827b65595aed7a8c17f4b
Please update variant report to version 1.1.1 using oc module update variantreport
Thanks for catching this.
I am trying to get the VariantReport webapp up and running. I am running OpenCravat locally using the Docker image (ver. 2.3)
1. I have installed all required modules as per the documentation as well as the modules listed here: https://github.com/KarchinLab/open-cravat/issues/60
2. This shows the page when loaded
Screenshot 2023-05-03 at 09.08.38.pdf The basic variant info is shown correctly, but none of the report sections populate. The example shown is chr7:117592643:G:A:hg38
3. This is the url: http://localhost:8080/webapps/variantreport/index.html
4. Here is the list of all installed modules:
oc module ls Name Title Type Version Data source ver Size
abraom ABRaOM annotator 1.0.0 113.6 MB
aloft ALoFT annotator 1.1.0 v4.3a 450.8 MB
arrvars Arrhythmia Channelopathy Variants annotator 1.2.0 January 2020 2.1 MB
biogrid BioGRID annotator 3.8.0 v4.4.216 123.4 MB
cancer_genome_interpreter Cancer Genome Interpreter annotator 1.3.0 2018.01.17 562.9 kB
cancer_hotspots Cancer Hotspots annotator 1.2.1 December 2017 268.6 kB
cardioboost CardioBoost annotator 1.0.0 v2.1 18.2 MB
casecontrol Case-Control postaggregator 1.2.0 34.3 kB
ccre_screen Candidate cis-Regulatory Elements by ENCODE (SCREEN) annotator 1.0.1 2019.1 77.8 MB
cgc Cancer Gene Census annotator 85.0.12 2019-03-23 228.7 kB
cgl Cancer Gene Landscape annotator 1.1.0 v2013.03.29 479.6 kB
chasmplus CHASMplus annotator 1.3.0 v1.0.0 8.0 GB
chasmplus_group CHASMplus group 1.2.0 v1.0.0 77.0 kB
civic CIViC annotator 1.0.18 Latest Available 55.4 kB
clingen ClinGen Gene annotator 1.0.1 190.4 kB
clinvar ClinVar annotator 2023.02.01 2023.02.01 382.3 MB
clinvar_acmg ClinVar ACMG annotator 2023.02.01 2023.02.01 84.3 MB
cosmic COSMIC annotator 94.0.0 v94 1.6 GB
cravat-converter Cravat Converter converter 1.1.2 15.1 kB
csvreporter CSV Reporter reporter 2.1.0 267.7 kB
cvdkp Cardiovascular Disease Knowledge Portal annotator 1.0.0 27 March 2019 2.5 GB
dann_coding DANN Coding annotator 1.0.0 v4.1 4.3 GB
dbsnp dbSNP annotator 154.0.2 v154 31.9 GB
denovo Denovo-DB annotator 1.6.11 v161 38.9 MB
dgi DGIdb: The Drug Interaction Database annotator 1.0.0 Jan 2021 7.5 MB
encode_tfbs ENCODE TFBS annotator 1.0.2 2012-03 578.6 MB
ensembl_regulatory_build Ensembl Regulatory Build annotator 1.0.3 2020.06.09 49.6 MB
esp6500 ESP6500 annotator 6500.2.6 v0.0.30 116.1 MB
ess_gene Essential Genes annotator 3.5.8 dbNSFP v4.0b1 348.9 kB
excelreporter Excel Reporter reporter 2.1.1 107.2 kB
fathmm FATHMM annotator 2.3.7 v2.3 10.4 GB
fathmm_mkl FATHMM MKL annotator 1.0.0 v4.1 5.1 GB
fathmm_xf_coding FATHMM XF Coding annotator 1.0.0 v4.1 4.1 GB
fitcons fitCons annotator 1.0.0 v4.1 4.2 GB
genehancer GeneHancer annotator 1.1.0 v4.7 42.4 MB
gerp GERP++ annotator 3.6.2 dbNSFP v4.0b1 4.7 GB
geuvadis Geuvadis eQTLs annotator 0.0.1 296.0 kB
ghis GHIS annotator 3.6.0 dbNSFP v4.0b1 720.0 kB
gnomad gnomAD annotator 2.2.0 v2.1 17.4 GB
gnomad3 gnomAD3 annotator 1.1.0 v3 44.0 GB
gnomad_gene gnomAD Gene annotator 2.2.1 v2.1 10.6 MB
go Gene Ontology annotator 2022.11.01 2023.01.01 33.3 MB
grasp GRASP annotator 2.0.8 v2.0.0.0 715.0 MB
gtex GTEx eQTLs annotator 7.0.4 v7 14.7 MB
gwas_catalog GWAS Catalog annotator 1.0.0 39.0 MB
hereditary_cancer Hereditary Cancer package 1.0.0 343.6 kB
hg19 hg19 coordinates annotator 1.0.6 3.9 MB
hg38 UCSC hg38 Gene Mapper mapper 1.10.4 353.3 MB
hgdp HGDP annotator 1.0.0 63.4 MB
hpo Human Phenotype Ontology annotator 2.0.0 November 2022 19.0 MB
intact IntAct annotator 2019.08.23 2018.11.30 8.8 MB
interpro InterPro annotator 71.3.0 v71 7.3 GB
javierre_promoters Promoter IR annotator 2022.12.12 November 17, 2016 555.7 kB
linsight LINSIGHT annotator 2021.01.08 2018.10.19 9.2 GB
litvar LitVar annotator 1.1.0 Live 378.6 kB
loftool LoFtool annotator 3.6.1 dbNSFP v4.0b1 587.8 kB
lrt Likelihood Ratio Test annotator 1.0.0 v4.1 3.9 GB
mavedb MaveDB annotator 1.0.1 v1.7.2 2.1 MB
metalr MetaLR annotator 1.0.3 v4.1 4.0 GB
metasvm MetaSVM annotator 1.0.1 v4.1 4.0 GB
mirbase miRBase annotator 1.0.1 v3.0 646.2 kB
mupit MuPIT annotator 4.3.3 v5.2.4 5.6 MB
mutation_assessor Mutation Assessor annotator 3.1.0 Release 3 4.3 GB
mutationtaster MutationTaster annotator 1.0.0 v4.1a 12.1 GB
mutpred1 MutPred annotator 1.4.0 v4.1 15.6 GB
ncbigene NCBI Gene annotator 2022.08.30 2022.08.30 20.7 MB
ncrna ncRNA annotator 2022.12.12 hg38 5.8 MB
ndex NDEx NCI Cancer Pathways annotator 4.0.11 v2 797.3 kB
ndex_chd NDEx Congenital Heart Disease annotator 1.0.2 v2 397.7 kB
ndex_group NDEx group 1.0.0 2020.08 74.8 kB
ndex_signor NDEx SIGNOR annotator 1.0.2 v2 318.5 kB
oldcravat-converter OldCravat Converter converter 1.1.2 11.9 kB
omim OMIM annotator 1.0.0 v4.1 10.4 MB
oncokb OncoKB annotator 1.1.3 09.06.22 261.9 kB
pangalodb PangaloDB annotator 1.0.0 2020.03.27 1.3 MB
pharmgkb PharmGKB annotator 2.3.8 2023-02-01 3.7 MB
phastcons Phast Cons annotator 3.5.9 dbNSFP v4.0b1 6.3 GB
phdsnpg PhD-SNPg annotator 0.0.9 dbNSFP v4.0b1 5.3 GB
phi p(HI) annotator 3.6.1 dbNSFP v4.0b1 729.5 kB
phylop PhyloP annotator 3.5.10 dbNSFP v4.0b1 14.2 GB
polyphen2 PolyPhen-2 annotator 2022.10.13 2022.10.13 8.3 GB
prec P(rec) annotator 3.6.0 dbNSFP v4.0b1 611.1 kB
provean PROVEAN: Protein Variant Effect Analyzer annotator 1.1.0 v4.1a 12.5 GB
pseudogene Pseudogene annotator 42.0.1 hg38 1.4 MB
revel REVEL annotator 2022.11.29 v4.3a 7.0 GB
rvis RVIS annotator 3.1.0 v3 1.4 MB
segway Segway annotator 1.2.1 8.3 MB
segway_group Segway group 1.0.0 2019.09 6.9 kB
sift SIFT annotator 1.2.0 SIFT4G 2016-02-22 21.9 GB
siphy SiPhy annotator 3.5.5 dbNSFP v4.0b1 5.6 GB
swissprot_binding Swiss-Prot Binding annotator 1.0.0 12.02.2020 3.0 MB
swissprot_domains Swiss-Prot Domains annotator 1.0.0 12.02.2020 12.4 MB
swissprot_ptm Swiss-Prot PTM annotator 1.1.0 2018.04.10 12.6 MB
tagsampler Tag Sampler postaggregator 1.1.6 4.9 kB
target TARGET annotator 3.1.0 v3.0.1 63.0 kB
textreporter Text Reporter reporter 2.1.0 276.5 kB
thousandgenomes 1000 Genomes annotator 4.1.0 Phase 3 5.3 GB
thousandgenomes_group 1000 Genomes group 3.1.0 Phase 3 17.6 kB
trinity Trinity CTAT annotator 1.0.0 26 February 2020 175.6 kB
tsvreporter TSV Reporter reporter 2.1.0 259.8 kB
uk10k_cohort UK10k Cohorts annotator 3.5.9 dbNSFP v4.0b1 16.4 MB
uniprot UniProt annotator 2020.08.10 201809 793.1 kB
variantreport OpenCRAVAT Variant Report webapp 1.1.0 8.1 MB
vcf-converter VCF Converter converter 2.2.0 25.9 MB
vcfinfo VCF Info postaggregator 1.1.5 8.1 kB
vcfreporter VCF Reporter reporter 3.2.1 274.2 kB
vest VEST4 annotator 4.4.0 v4 9.7 GB
vista_enhancer VISTA Enhancer Browser annotator 2019.08.02 hg19 129.0 kB
wgallelefrequency Allele Frequency Spectrum webviewerwidget 1.1.0 109.2 kB
wgaloft ALoFT webviewerwidget 1.0.0 1.6 kB
wgcancer_genome_interpreter Cancer Genome Interpreter webviewerwidget 1.0.0 1.4 kB
wgcasecontrolsummary Case-Control Summary webviewerwidget 1.0.1 88.5 kB
wgcircossummary Circos Summary webviewerwidget 2.1.1 898.2 kB
wgcodingvsnoncodingsummary Coding vs Noncoding Summary webviewerwidget 2.0.0 2.6 kB
wgdgi DGIdb webviewerwidget 1.0.0 1.6 kB
wgenhancer Frequently Mutated Enhancers webviewerwidget 1.1.0 50.3 kB
wggosummary Gene Ontology Summary webviewerwidget 2.3.0 38.8 MB
wghpo Human Phenotype Ontology webviewerwidget 1.0.0 1.3 kB
wgigv IGV webviewerwidget 1.1.0 2.7 MB
wgmutationtaster MutationTaster webviewerwidget 1.0.0 1.4 kB
wgprovean PROVEAN webviewerwidget 1.0.0 1.3 kB
wgrankscore Rank Score Comparison webviewerwidget 1.0.2 71.4 kB
wgsosamplesummary Sequence Ontology Sample Summary webviewerwidget 2.1.0 15.2 kB
wgsosummary Sequence Ontology Summary webviewerwidget 1.5.0 4.4 kB
5. Module wghvs
I installed the module wghvs manually (as per #60). Interestingly, it does not show up when running oc module ls as above
oc module info wghgvs code_size: 2133 data_size: 0 data_versions: 1.0.0: null 1.0.1: null 1.0.2: null 1.0.3: null 1.0.4: null 1.2.0: null datasource: '' description: HGVS webviewer widget developer: name: Rick Kim email: rkim@insilico.us.com organization: In Silico Solutions citation: '' website: http://www.insilico.us.com hidden: true latest_version: 1.2.0 name: wghgvs publish_time: '2018-10-26T20:51:08.000000' size: 2133 tags:
Conclusion
I am now unsure how to proceed.