Check, and optionally build, tantale's external dependencies

Reports whether the external programs tantale drives are present and at the versions it expects, and can build or repair the conda environment that provides most of them. It also downloads the Java programs tantale wraps (AnnoTALE, PrediTALE, TALEcorrection) and the four example genomes of the articles (tantale_genome()), which are too large to be part of the package.

Called bare it changes nothing – it is a diagnostic. Pass install = TRUE to act on what it finds.

Usage

tantale_setup(
  install = FALSE,
  conda = FALSE,
  conda_bin = "auto",
  archive_dir = NULL
)

Arguments

install

Build the tantale environment if it is missing, and repair it if a pinned version is wrong. FALSE by default, so the function reports and changes nothing.

conda

Install a conda distribution if none is found. FALSE by default; see the section above.

conda_bin

Passed to reticulate. "auto" lets it choose.

archive_dir

A directory holding the archives tantale-tools-1.tar.gz and tantale-genomes-1.tar.gz, downloaded beforehand, to install them from instead of downloading them: for a machine without internet access, or to download once for several machines. NULL (default) downloads them.

Value

Invisibly, a list with conda, system and archives data frames of the checks, and prefix, so the result can be tested as well as read. conda is NULL and prefix is NA when no conda/mamba installation, or no tantale environment, was found at all; system is always a data frame, since Java is checked regardless.

Details

Why versions are checked as well as presence. MAFFT changed its --text mode gap handling after 7.4x, and later versions align TALE repeat-code strings differently, leaving the N- and C-termini unanchored. An environment built by an older version of this package can therefore produce different alignments from the same input, with nothing to indicate it. The pins in tantale_conda_env.yaml exist for that reason, and this function checks them.

Why three paths are reported. The conda binary, its default root, and the environment actually in use are three different things, and on a machine with any history they diverge – reticulate scans several known locations, so two roots can each hold an environment named tantale. When that happens, a rebuild can honestly report success while the package goes on using the other one. Everything here therefore works with the environment's prefix (its path), never its name.

Where the downloads go. The function checks two archives, attached to releases of tantale's GitHub repository, against a sha256 recorded in the package and unpacks them into tools::R_user_dir("tantale", "data") (~/.local/share/R/tantale on Linux), in one folder per archive version (tools-1/, genomes-1/). Set the environment variable TANTALE_DATA_DIR to use another directory, for instance one shared by a team. The tools take about 60 MB, the genomes 20 MB.

Java is checked too. It is a hard requirement of the AnnoTALE, PrediTALE and TALE-correction wrappers, it comes from outside conda, and without this check they fail deep inside a system() call.

Installing conda itself

conda = TRUE installs a conda distribution if none is found. It is deliberately opt-in and separate from install: putting a package manager on someone's machine is a larger side effect than building an environment in one that already exists. It installs miniconda, via reticulate::install_miniconda().

See also

tell_tales(), tales_align(), tales_compare_distal(), talvez() and correct_tales(), the entry points that need these tools.

Examples

# \donttest{
# A read-only diagnostic report; nothing is installed or changed.
tantale_setup()
#> ✔ tools-1  /home/cunnac/snap/codium/495/.local/share/R/tantale/tools-1
#> ✔ genomes-1  /home/cunnac/snap/codium/495/.local/share/R/tantale/genomes-1
#> ✔ conda binary    /home/cunnac/bin/micromamba
#> ℹ default root    /home/cunnac/micromamba
#> ✔ tantale env     /home/cunnac/mamba/envs/tantale
#> ✔ mmseqs2             14.7e284
#> ✔ perl-statistics-r   0.34
#> ✔ hmmer               3.3.2
#> ✔ clustalo            1.2.4
#> ✔ igvtools            2.16.2
#> ✔ mafft               7.453
#> ✔ perl-list-moreutils 0.430
#> ✔ java                /usr/bin/java
#> ✔ Everything tantale needs is present.
# }