Add use_conda_env param and Fix mysql command bugs #41
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rainoffallingstar
commented
Nov 20, 2024
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rainoffallingstar
commented
- Add use_conda_env params to use certain conda envs with bwtool installed.
- Update mysql commands by adding "-A -P 3306" params for speed.
…and Update mysql commands to mariadb
R/trackplot.R
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| cmd = paste("bwtool summary -with-sum -keep-bed -header", bedSimple, bw, paste0(op_dir, bn, ".summary")) | ||
| if (!is.null(use_conda)){ | ||
| cmd_conda = paste0("conda run -n ", use_conda) |
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Hi,
what is the use_conda argument in this context? I guess it should be the environment name, but the main argument seems to be TRUE or FALSE.
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Hi!
Indeed, the use_conda argument should be designed to accept the name of the conda environment. It is not appropriate to simply name it use_conda, as this could potentially mislead users. I suggest renaming it to use_conda_env to avoid confusion and to clearly communicate the purpose of the argument.
I believe that bwtool is much easier to install via conda. I think this improvement would make this package more robust.
R/trackplot.R
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| @@ -2397,7 +2427,7 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = | |||
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| .check_mysql = function(warn = FALSE){ | |||
| check = as.character(Sys.which(names = 'mysql'))[1] | |||
| check = as.character(Sys.which(names = 'mariadb'))[1] | |||
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I am using MariaDB on Arch Linux, and the mysql package is being deprecated. It is expected to be removed in a future release, and it's suggested to use mariadb instead. By the way, MariaDB is a fork of MySQL , which is originated from the same source but has better performents and easy to install.
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Aye, by the way, I've retained the original mysql command in a separate commit.
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Yup. I will review them soon.
R/trackplot.R
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| #' @import data.table | ||
| #' @examples | ||
| #' bigWigs = system.file("extdata", "bw", package = "trackplot") |> list.files(pattern = "\\.bw$", full.names = TRUE) | ||
| #' cd = read_coldata(bws = bigWigs, build = "hg19") | ||
| #' oct4_loci = "chr6:31125776-31144789" | ||
| #' t = track_extract(colData = cd, loci = oct4_loci, build = "hg19") | ||
| #' @export | ||
| track_extract = function(colData = NULL, loci = NULL, gene = NULL, binsize = 10, nthreads = 1, query_ucsc = TRUE, gtf = NULL, build = "hg38", padding = 0, ideoTblName = "cytoBand"){ | ||
| track_extract = function(colData = NULL, loci = NULL, gene = NULL, binsize = 10, nthreads = 1, query_ucsc = TRUE, gtf = NULL, build = "hg38", padding = 0, ideoTblName = "cytoBand",use_conda = NULL){ |
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Again, use_conda shouldn't be the environment name instead of T/F.
…meter to use_conda_env for clarity.
rainoffallingstar
changed the title
