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| author | l-d-s <distefano.l@wehi.edu.au> | 2018-11-13 09:10:23 +1100 |
|---|---|---|
| committer | l-d-s <distefano.l@wehi.edu.au> | 2018-11-13 09:10:23 +1100 |
| commit | 2c92dd5c6425c67a18ab07eba7f15c07dbd4614a (patch) | |
| tree | 46be9656b500e38bd4aa47066ce8296a127dd5bf /lib | |
| parent | 886af7beaaa98ac32db88a7453d917409cf11ae8 (diff) | |
| parent | 4574deb8e1649eaf63df424585d11645c7cfa7dd (diff) | |
Merge branch 'master' of https://github.com/PapenfussLab/bionix
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 = {}; |