diff options
| author | Justin Bedo <cu@cua0.org> | 2021-12-03 09:42:04 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2021-12-03 09:42:04 +1100 |
| commit | 32c842e7c5fe1038cec73da3e07ba12df6295549 (patch) | |
| tree | 2418ebb61d450fe4c11be3659afb22156ab52a1b /tools | |
| parent | 7e9f9d84efbfa3ddcd1b41f410adc53daca3f405 (diff) | |
genmap: init
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/genmap-calcmap.nix | 22 | ||||
| -rw-r--r-- | tools/genmap-index.nix | 16 | ||||
| -rw-r--r-- | tools/genmap.nix | 9 |
3 files changed, 47 insertions, 0 deletions
diff --git a/tools/genmap-calcmap.nix b/tools/genmap-calcmap.nix new file mode 100644 index 0000000..df9ccc3 --- /dev/null +++ b/tools/genmap-calcmap.nix @@ -0,0 +1,22 @@ +{ bionix +, k ? 30 +, e ? 2 +}: + +with bionix; + +ref: stage { + name = "genmap-mappability"; + buildInputs = with pkgs; [ genmap ]; + buildCommand = '' + mkdir $out + genmap map \ + -K ${toString k} \ + -E ${toString e} \ + --wig \ + -I ${bionix.genmap.index {} ref} \ + -O $out \ + -T $NIX_BUILD_CORES + ''; + passthru.multicore = true; +} diff --git a/tools/genmap-index.nix b/tools/genmap-index.nix new file mode 100644 index 0000000..249f061 --- /dev/null +++ b/tools/genmap-index.nix @@ -0,0 +1,16 @@ +{ bionix }: + +with bionix; +with lib.types; + +let + fa = f: matchFiletype "genmap-index" { fa = _: f; } f; +in + +ref: stage { + name = "genmap-index"; + buildInputs = with pkgs; [ genmap ]; + buildCommand = '' + genmap index -F ${fa ref} -I $out + ''; +} diff --git a/tools/genmap.nix b/tools/genmap.nix new file mode 100644 index 0000000..c29d74c --- /dev/null +++ b/tools/genmap.nix @@ -0,0 +1,9 @@ +{ bionix }: + +with bionix; + +{ + index = callBionixE ./genmap-index.nix; + calcmap = callBionixE ./genmap-calcmap.nix; +} + |