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Add the --skip-ssl option to mysql queries #45

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Add the --skip-ssl option to mysql queries #45

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10 changes: 5 additions & 5 deletions R/trackplot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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)
Expand All @@ -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")
Expand All @@ -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)
Expand Down Expand Up @@ -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)
Expand Down