diff options
| author | Justin Bedo <cu@cua0.org> | 2018-11-02 15:35:22 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-11-02 15:40:27 +1100 |
| commit | f416c145204765a1566782f0ff384d3f65d6ed35 (patch) | |
| tree | 0ce95603001956ac9941f95bd4870aa7a06cce28 /lib | |
| parent | ec77e9c3a9c2dc7425ee07474f525dd0a3d01fab (diff) | |
kallisto: init
Diffstat (limited to 'lib')
| -rwxr-xr-x | lib/references.nix | 22 | ||||
| -rw-r--r-- | lib/types.nix | 3 |
2 files changed, 24 insertions, 1 deletions
diff --git a/lib/references.nix b/lib/references.nix index 498cfd9..bdeefa6 100755 --- a/lib/references.nix +++ b/lib/references.nix @@ -46,6 +46,28 @@ rec { ''; passthru.filetype = filetype.vcf { ref = seq; }; }; + ensembl = { + cdna = stdenvNoCC.mkDerivation rec { + name = "ensembl-grch38-cdna-${version}"; + version = "94"; + src = fetchurl { + url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz"; + sha256 = "1fc5d6p2wlwsm49wnmxmm3byjx5jvr6z9fpzrq7v7fpb086adl0h"; + }; + buildCommand = "gunzip < $src > $out"; + passthru.filetype = filetype.fa {}; + }; + ncrna = stdenvNoCC.mkDerivation rec { + name = "ensembl-grch38-ncrna-${version}"; + version = "94"; + src = fetchurl { + url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz"; + sha256 = "1cpasykwriila52nqgvw6d3mjyh6d9qi613hvhn4h1dxkqzgnjff"; + }; + buildCommand = "gunzip < $src > $out"; + passthru.filetype = filetype.fa {}; + }; + }; }; grcm38 = grcm38-p6; diff --git a/lib/types.nix b/lib/types.nix index 4dbc6ff..ef9b1b7 100644 --- a/lib/types.nix +++ b/lib/types.nix @@ -21,7 +21,8 @@ let in rec { - matchFiletype = sym: y: x: if x ? filetype then match x.filetype (defError (idft sym) y filetype) else abort "unknown filetype for ${sym}"; + matchFiletype = sym: y: x: if x ? filetype then matchFiletype' sym y x.filetype else abort "unknown filetype for ${sym}"; + matchFiletype' = sym: y: x: match x (defError (idft sym) y filetype); filetype = make-type "filetype" { fa = {}; fq = {}; |