# HG changeset patch # User iuc # Date 1545066705 18000 # Node ID 4a1e53517dbaf81ada6162704e63eb33054904ea # Parent 5fb59611125ed20f76f039111e9c1f8aa188ac14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f diff -r 5fb59611125e -r 4a1e53517dba gemini_actionable_mutations.xml --- a/gemini_actionable_mutations.xml Fri Dec 14 12:34:23 2018 -0500 +++ b/gemini_actionable_mutations.xml Mon Dec 17 12:11:45 2018 -0500 @@ -1,4 +1,4 @@ - + Retrieve genes with actionable somatic mutations via COSMIC and DGIdb gemini_macros.xml diff -r 5fb59611125e -r 4a1e53517dba gemini_macros.xml --- a/gemini_macros.xml Fri Dec 14 12:34:23 2018 -0500 +++ b/gemini_macros.xml Mon Dec 17 12:11:45 2018 -0500 @@ -1,15 +1,12 @@ - 0.18.1 + 0.20.1 - 181 + 200 gemini - tabix - - diff -r 5fb59611125e -r 4a1e53517dba test-data/gemini_amend_input.db Binary file test-data/gemini_amend_input.db has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/gemini_annotate_result.db Binary file test-data/gemini_annotate_result.db has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/gemini_auto_dom_input.db Binary file test-data/gemini_auto_dom_input.db has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/gemini_auto_rec_input.db Binary file test-data/gemini_auto_rec_input.db has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/gemini_comphets_input.db Binary file test-data/gemini_comphets_input.db has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/gemini_de_novo_input.db Binary file test-data/gemini_de_novo_input.db has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/gemini_is_somatic_result.db Binary file test-data/gemini_is_somatic_result.db has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/gemini_load_result1.db Binary file test-data/gemini_load_result1.db has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/gemini_load_result2.db Binary file test-data/gemini_load_result2.db has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/gemini_versioned_databases.loc --- a/test-data/gemini_versioned_databases.loc Fri Dec 14 12:34:23 2018 -0500 +++ b/test-data/gemini_versioned_databases.loc Mon Dec 17 12:11:45 2018 -0500 @@ -1,3 +1,3 @@ ## GEMINI versioned databases #DownloadDate dbkey DBversion Description Path -1999-01-01 hg19 181 GEMINI annotations (test snapshot) ${__HERE__}/test-cache +1999-01-01 hg19 200 GEMINI annotations (test snapshot) ${__HERE__}/test-cache diff -r 5fb59611125e -r 4a1e53517dba test-data/test-cache/gemini-config.yaml --- a/test-data/test-cache/gemini-config.yaml Fri Dec 14 12:34:23 2018 -0500 +++ b/test-data/test-cache/gemini-config.yaml Mon Dec 17 12:11:45 2018 -0500 @@ -2,12 +2,14 @@ versions: ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz: 4 ESP6500SI.all.snps_indels.tidy.v2.vcf.gz: 2 - ExAC.r0.3.sites.vep.tidy.vcf.gz: 3 + ExAC.r0.3.sites.vep.tidy.vcf.gz: 4 GRCh37-gms-mappability.vcf.gz: 2 - clinvar_20160203.tidy.vcf.gz: 5 + clinvar_20170130.tidy.vcf.gz: 5 cosmic-v68-GRCh37.tidy.vcf.gz: 3 - dbsnp.b141.20140813.hg19.tidy.vcf.gz: 4 + dbsnp.b147.20160601.tidy.vcf.gz: 1 detailed_gene_table_v75: 2 geno2mp.variants.tidy.vcf.gz: 1 + gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz: 2 hg19.rmsk.bed.gz: 2 summary_gene_table_v75: 2 + whole_genome_SNVs.tsv.compressed.gz: 2 diff -r 5fb59611125e -r 4a1e53517dba test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz Binary file test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz.tbi Binary file test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz.tbi has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz Binary file test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz.tbi Binary file test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz.tbi has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz Binary file test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz.tbi Binary file test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz.tbi has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz Binary file test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz.tbi Binary file test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz.tbi has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz Binary file test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz has changed diff -r 5fb59611125e -r 4a1e53517dba test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi Binary file test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi has changed