From 25793d11a48df3101114229c1de75b6e4d80da12 Mon Sep 17 00:00:00 2001 From: Anna Cuomo Date: Tue, 16 Jan 2024 16:08:07 +1100 Subject: [PATCH] update saige-qtl image with new step3 (#127) * update saige-qtl image with new step3 * add test data files to image * update commit hash to trigger new build * input output files do not need to be executable --- images.toml | 2 +- images/saige-qtl/Dockerfile | 14 ++++++++++---- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/images.toml b/images.toml index 894c858..08cfcd9 100644 --- a/images.toml +++ b/images.toml @@ -20,7 +20,7 @@ peer = '1.3' picard = '2.27.4' reviewer = '0.2.7' reviewer_bw2 = '0.2.7-bw2-fork-0.2' -saige-qtl = '1bdfe8408a17f7da8b0453a697a867f412f48bcc' +saige-qtl = '41a4dcae69d83a2eb02fb4491a0148d25e4d46db' sambamba = '1.0.1' samblaster = '0.1.26' samtools = '1.18' diff --git a/images/saige-qtl/Dockerfile b/images/saige-qtl/Dockerfile index 4bd8848..388dbff 100644 --- a/images/saige-qtl/Dockerfile +++ b/images/saige-qtl/Dockerfile @@ -20,11 +20,17 @@ RUN apt-get update && \ R CMD INSTALL . && \ mv extdata/step1_fitNULLGLMM_qtl.R \ extdata/step2_tests_qtl.R \ - extdata/step3_LDmat.R \ - extdata/createSparseGRM.R /usr/local/bin/ && \ + extdata/step3_gene_pvalue_qtl.R \ + extdata/input/n.indep_100_n.cell_1_01.step1 \ + extdata/input/seed_1_100_nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_Poisson.txt \ + extdata/input/genotype_10markers.vcf.gz \ + extdata/input/genotype_10markers.vcf.gz.csi \ + extdata/input/gene_1_cis_region.txt \ + extdata/output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1 \ + extdata/output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1_cis \ + extdata/output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1_cis_genePval /usr/local/bin/ && \ chmod a+x /usr/local/bin/step1_fitNULLGLMM_qtl.R \ /usr/local/bin/step2_tests_qtl.R \ - /usr/local/bin/step3_LDmat.R \ - /usr/local/bin/createSparseGRM.R && \ + /usr/local/bin/step3_gene_pvalue_qtl.R && \ cd .. && \ rm -r qtl