From b597e2bcd5fced0e59813a30f548160c5fe4fbb9 Mon Sep 17 00:00:00 2001 From: JackieMium Date: Fri, 20 Feb 2026 17:43:33 -0600 Subject: [PATCH] add --skip-ssl option to mysql queries --- R/trackplot.R | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/R/trackplot.R b/R/trackplot.R index bc30308..1a64d00 100644 --- a/R/trackplot.R +++ b/R/trackplot.R @@ -1821,7 +1821,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = } cmd = paste0( - "mysql --user genome --host genome-mysql.soe.ucsc.edu -NAD ", + "mysql --user genome --host genome-mysql.soe.ucsc.edu --skip-ssl -NAD ", refBuild, " -e 'select chrom, chromStart, chromEnd, name, gieStain from ", tblName, " WHERE chrom =\"", chr, @@ -1897,7 +1897,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = .check_mysql() - cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu -NAD ", refBuild, " -e 'select chrom, chromStart, chromEnd, name from ", tbl, " WHERE chrom =\"", tar_chr, "\"'") + cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu --skip-ssl -NAD ", refBuild, " -e 'select chrom, chromStart, chromEnd, name from ", tbl, " WHERE chrom =\"", tar_chr, "\"'") message(paste0("Extracting chromHMM from UCSC:\n", " chromosome: ", tar_chr, "\n", " build: ", refBuild, "\n query: ", cmd)) #system(command = cmd) ucsc = data.table::fread(cmd = cmd) @@ -1921,7 +1921,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = .check_mysql() op_file = tempfile(pattern = "ucsc", fileext = ".tsv") - cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu -NAD ", refBuild, " -e 'select chrom, txStart, txEnd, strand, name, name2, exonStarts, exonEnds from refGene WHERE name2 =\"", genesymbol, "\"'") + cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu --skip-ssl -NAD ", refBuild, " -e 'select chrom, txStart, txEnd, strand, name, name2, exonStarts, exonEnds from refGene WHERE name2 =\"", genesymbol, "\"'") message(paste0("Extracting gene models from UCSC:\n", " Gene: ", genesymbol, "\n", " build: ", refBuild, "\n query: ", cmd)) ucsc = data.table::fread(cmd = cmd, sep = "\t") @@ -1946,7 +1946,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = tar_chr = chr } - cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu -NAD ", refBuild, " -e 'select chrom, txStart, txEnd, strand, name, name2, exonStarts, exonEnds from refGene WHERE chrom =\"", tar_chr, "\"'") + cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu --skip-ssl -NAD ", refBuild, " -e 'select chrom, txStart, txEnd, strand, name, name2, exonStarts, exonEnds from refGene WHERE chrom =\"", tar_chr, "\"'") message(paste0("Extracting gene models from UCSC:\n", " chromosome: ", tar_chr, "\n", " build: ", refBuild, "\n query: ", cmd)) #system(command = cmd) ucsc = data.table::fread(cmd = cmd) @@ -2159,7 +2159,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = temp_op_bed = tempfile(pattern = "profileplot_ucsc", tmpdir = op_dir, fileext = ".bed") - cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu -NAD ", refBuild, " -e 'select chrom, txStart, txEnd, strand, name, name2 from refGene'") + cmd = paste0("mysql --user genome --host genome-mysql.soe.ucsc.edu --skip-ssl -NAD ", refBuild, " -e 'select chrom, txStart, txEnd, strand, name, name2 from refGene'") message(paste0("Extracting gene models from UCSC:\n", " build: ", refBuild, "\n query: ", cmd)) #system(command = cmd) ucsc = data.table::fread(cmd = cmd)