kent: 468 -> 486 (#438937)

pkgs/by-name/ke/kent/package.nix

@@ -1,6 +1,7 @@
 {
   lib,
   stdenv,
+  writableTmpDirAsHomeHook,
   libpng,
   libuuid,
   zlib,
@@ -12,18 +13,23 @@
   bash,
   fetchFromGitHub,
   which,
+  writeShellScript,
+  jq,
+  nix-update,
 }:
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "kent";
-  version = "468";
+  version = "486";
 
   src = fetchFromGitHub {
     owner = "ucscGenomeBrowser";
     repo = "kent";
-    rev = "v${version}_base";
-    hash = "sha256-OM/noraW2X8WV5wqWEFiI5/JPOBmsp0fTeDdcZoXxAA=";
+    tag = "v${finalAttrs.version}_base";
+    hash = "sha256-NffQ04+5rMtG/VI7YFK4Ff39DDhdh9Wlc0i1iVbg8Js=";
   };
 
+  nativeBuildInputs = [ writableTmpDirAsHomeHook ];
+
   buildInputs = [
     libpng
     libuuid
@@ -37,10 +43,10 @@ stdenv.mkDerivation rec {
 
   postPatch = ''
     substituteInPlace ./src/checkUmask.sh \
-      --replace "/bin/bash" "${bash}/bin/bash"
+      --replace-fail "/bin/bash" "${bash}/bin/bash"
 
     substituteInPlace ./src/hg/sqlEnvTest.sh \
-      --replace "which mysql_config" "${which}/bin/which ${libmysqlclient}/bin/mysql_config"
+      --replace-fail "which mysql_config" "${which}/bin/which ${libmysqlclient}/bin/mysql_config"
   '';
 
   buildPhase = ''
@@ -50,7 +56,6 @@ stdenv.mkDerivation rec {
     export CFLAGS="-fPIC"
     export MYSQLINC=$(mysql_config --include | sed -e 's/^-I//g')
     export MYSQLLIBS=$(mysql_config --libs)
-    export HOME=$TMPDIR
     export DESTBINDIR=$HOME/bin
 
     mkdir -p $HOME/lib $HOME/bin/${stdenv.hostPlatform.parsed.cpu.name}
@@ -85,12 +90,17 @@ stdenv.mkDerivation rec {
     runHook postInstall
   '';
 
+  passthru.updateScript = writeShellScript "update-kent" ''
+    latestVersion=$(curl ''${GITHUB_TOKEN:+-u ":$GITHUB_TOKEN"} --fail --silent https://api.github.com/repos/ucscGenomeBrowser/kent/releases/latest | ${lib.getExe jq} --raw-output .tag_name | grep -oP '(?<=v)\d+')
+    ${lib.getExe nix-update} kent --version $latestVersion
+  '';
+
   meta = {
     description = "UCSC Genome Bioinformatics Group's suite of biological analysis tools, i.e. the kent utilities";
     homepage = "http://genome.ucsc.edu";
-    changelog = "https://github.com/ucscGenomeBrowser/kent/releases/tag/v${version}_base";
+    changelog = "https://github.com/ucscGenomeBrowser/kent/releases/tag/v${finalAttrs.version}_base";
     license = lib.licenses.unfree;
     maintainers = with lib.maintainers; [ scalavision ];
     platforms = lib.platforms.linux;
   };
-}
+})