push sheeet

pkgs/by-name/as/astral/make-deterministic.patch

@@ -0,0 +1,21 @@
+diff --git a/make.sh b/make.sh
+index 3ff6529..937b1a2 100644
+--- a/make.sh
++++ b/make.sh
+@@ -17,6 +17,8 @@ jar cvfm ../astral.$version.jar ../manifest.text phylonet/util/BitSet.* phylonet
+ 
+ cd ..
+ 
++strip-nondeterminism --type jar astral.$version.jar
++
+ chmod +x astral.$version.jar
+ sed -e "s/__astral.jar__/astral.$version.jar/g" -e "s/__astral.zip__/Astral.$version.zip/g" README.template.md > README.md
+ sed -e "s/__astral.jar__/astral.$version.jar/g" -e "s/__astral.zip__/Astral.$version.zip/g" astral-tutorial-template.md > astral-tutorial.md
+@@ -32,6 +34,7 @@ ln -s ../astral-tutorial.pdf .
+ cd ..
+ rm -f Astral.$version.zip
+ zip -r Astral.$version.zip Astral 
++strip-nondeterminism --type zip Astral.$version.zip
+ 
+ set +x
+ echo "

pkgs/by-name/as/astral/package.nix

@@ -0,0 +1,83 @@
+{
+  lib,
+  stdenvNoCC,
+  fetchFromGitHub,
+  jdk8,
+  jre8,
+  strip-nondeterminism,
+  makeWrapper,
+  zip,
+}:
+
+let
+  jdk = jdk8;
+  jre = jre8;
+in
+stdenvNoCC.mkDerivation (finalAttrs: {
+  pname = "astral";
+  version = "5.7.1";
+
+  src = fetchFromGitHub {
+    owner = "smirarab";
+    repo = "ASTRAL";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-VhcsX9BxiZ0nISN6Xe4N+kq0iBMCtNhyxDrm9cwXfBA=";
+  };
+
+  patches = [
+    # we can't use stripJavaArchivesHook here, because the build process puts a .jar file into a zip file
+    # this patch calls strip-nondeterminism manually
+    ./make-deterministic.patch
+  ];
+
+  nativeBuildInputs = [
+    jdk
+    zip
+    strip-nondeterminism
+    makeWrapper
+  ];
+
+  buildPhase = ''
+    runHook preBuild
+    patchShebangs ./make.sh
+    ./make.sh
+    runHook postBuild
+  '';
+
+  doCheck = true;
+
+  checkPhase = ''
+    runHook preCheck
+    java -jar astral.${finalAttrs.version}.jar -i main/test_data/song_primates.424.gene.tre
+    runHook postCheck
+  '';
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm644 astral.${finalAttrs.version}.jar -t $out/share
+    install -Dm644 lib/*.jar -t $out/share/lib
+    install -Dm644 Astral.${finalAttrs.version}.zip -t $out/share
+    cp -a main/test_data $out/share
+
+    makeWrapper ${jre}/bin/java $out/bin/astral \
+        --add-flags "-jar $out/share/astral.${finalAttrs.version}.jar"
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/smirarab/ASTRAL";
+    description = "Tool for estimating an unrooted species tree given a set of unrooted gene trees";
+    mainProgram = "astral";
+    sourceProvenance = with sourceTypes; [
+      fromSource
+      binaryBytecode # source bundles dependencies as jars
+    ];
+    license = licenses.asl20;
+    maintainers = with maintainers; [
+      bzizou
+      tomasajt
+    ];
+  };
+})