add gdrive downloader

- fetch dbNSFP automatically via gdrive.pl

3 files changed, 29 insertions, 12 deletions

diff --git a/default.nix b/default.nix
index 12ca5b3..ad8cecc 100644
--- a/default.nix
+++ b/default.nix
@@ -14,6 +14,7 @@ let
     callBionixE = p: exec (callBionix p);
 
     types = callBionix ./lib/types.nix {};
+    fetchgdrive = callBionix ./lib/google.nix {};
 
     bowtie = callBionix ./tools/bowtie.nix {};
     bwa = callBionix ./tools/bwa.nix {};
diff --git a/lib/google.nix b/lib/google.nix
new file mode 100644
index 0000000..354b5c5
--- /dev/null
+++ b/lib/google.nix
@@ -0,0 +1,20 @@
+{ bionix }:
+
+{ url, sha256 }:
+
+with bionix.pkgs;
+
+let
+  gdown = fetchurl {
+    url =
+      "https://raw.githubusercontent.com/circulosmeos/gdown.pl/master/gdown.pl";
+    sha256 = "1pw3vg70bgf33akbbphpr6zn3jndv0khmsa3k0m877hgzg1v52qv";
+  };
+in runCommand "gdown" {
+  nativeBuildInputs = [ perl wget ];
+  outputHashAlgo = "sha256";
+  outputHash = sha256;
+  outputHashMode = "flat";
+} ''
+  perl ${gdown} "${url}" $out
+''
diff --git a/lib/references.nix b/lib/references.nix
index c56ad0f..333888c 100644
--- a/lib/references.nix
+++ b/lib/references.nix
@@ -60,14 +60,12 @@ rec {
         '';
       };
       dbnsfp = {
-        db = pkgs.requireFile {
-          name = "dbNSFP.txt.gz";
-          message = "download the dbNSFP database manually from https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlSTY5dDJjcHVRZ3M and add to nix store";
+        db = fetchgdrive {
+          url = "https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlSTY5dDJjcHVRZ3M";
           sha256 = "0gfzbid3pc10zds7ya50w4qfynsxgpyh7dx35vhm5f3h64mw75pm";
         };
-        index = pkgs.requireFile {
-          name = "dbNSFP.txt.gz.tbi";
-          message = "download the dbNSFP index manually from https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlOTV5RllpRjNHU2s and add to nix store";
+        index = fetchgdrive {
+          url = "https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlOTV5RllpRjNHU2s";
           sha256 = "0bwwigbnz32mmc8bczidjf68vv8x8i28zwkl2kgcbpj542zk5q86";
         };
       };
@@ -146,14 +144,12 @@ rec {
         '';
       };
       dbnsfp = {
-        db = pkgs.requireFile {
-          name = "dbNSFP.txt.gz";
-          message = "download the dbNSFP database manually from https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlbTZodjlGUDZnTGc and add to nix store";
+        db = fetchgdrive {
+          url = "https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlbTZodjlGUDZnTGc";
           sha256 = "0gahnwkc7v2q6p6ixkhvsgqvvm6xf0c3bdh4nf0alih83h3wffd0";
         };
-        index = pkgs.requireFile {
-          name = "dbNSFP.txt.gz.tbi";
-          message = "download the dbNSFP index manually from https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlNVBJdFA5cFZRYkE and add to nix store";
+        index = fetchgdrive {
+          url = "https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlNVBJdFA5cFZRYkE";
           sha256 = "18blkly6gvg7r0sx968xlb1zl2kqg5j1kpbrm2r7ajlxlfyvrx3w";
         };
       };