Rebase onto c1a53897ad4290a1cbfa02fbe6f3869577b93744

Signed-off-by: Alyssa Ross <hi@alyssa.is>

13 files changed, 108 insertions, 40 deletions

diff --git a/pkgs/applications/science/biology/hmmer/default.nix b/pkgs/applications/science/biology/hmmer/default.nix
index 2a4df9d21db..243e067ddec 100644
--- a/pkgs/applications/science/biology/hmmer/default.nix
+++ b/pkgs/applications/science/biology/hmmer/default.nix
@@ -1,12 +1,12 @@
 { lib, stdenv, fetchurl }:
 
 stdenv.mkDerivation rec {
-  version = "3.3.2";
+  version = "3.4";
   pname = "hmmer";
 
   src = fetchurl {
     url = "http://eddylab.org/software/hmmer/${pname}-${version}.tar.gz";
-    sha256 = "0s9wf6n0qanbx8qs6igfl3vyjikwbrvh4d9d6mv54yp3xysykzlj";
+    sha256 = "sha256-ynDZT9DPJxvXBjQjqrsRbULeUzEXNDqbJ6ZcF/8G+/M=";
   };
 
   meta = with lib; {
@@ -18,6 +18,7 @@ stdenv.mkDerivation rec {
       HMMER can be downloaded and installed as a command line tool on your own hardware, and now it is also more widely accessible to the scientific community via new search servers at the European Bioinformatics Institute.
     '';
     homepage = "http://hmmer.org/";
+    changelog = "https://github.com/EddyRivasLab/hmmer/blob/hmmer-${version}/release-notes/RELEASE-${version}.md";
     license = licenses.gpl3;
     maintainers = [ maintainers.iimog ];
     # at least SSE is *required*
diff --git a/pkgs/applications/science/biology/trimmomatic/default.nix b/pkgs/applications/science/biology/trimmomatic/default.nix
new file mode 100644
index 00000000000..ad1dc45c5c2
--- /dev/null
+++ b/pkgs/applications/science/biology/trimmomatic/default.nix
@@ -0,0 +1,66 @@
+{ lib
+, stdenv
+, ant
+, fetchFromGitHub
+, jdk11_headless
+, jre
+, makeWrapper
+}:
+
+stdenv.mkDerivation rec {
+  pname = "trimmomatic";
+  version = "0.39";
+
+  src = fetchFromGitHub {
+    owner = "usadellab";
+    repo = "Trimmomatic";
+    rev = "v${version}";
+    hash = "sha256-u+ubmacwPy/vsEi0YQCv0fTnVDesQvqeQDEwCbS8M6I=";
+  };
+
+  # Set source and target version to 11
+  postPatch = ''
+    substituteInPlace ./build.xml \
+      --replace 'source="1.5" target="1.5"' 'release="11"'
+  '';
+
+  nativeBuildInputs = [ jdk11_headless ant makeWrapper ];
+
+  buildPhase = ''
+    runHook preBuild
+
+    ant
+
+    runHook postBuild
+  '';
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/bin $out/share
+    cp dist/jar/trimmomatic-${version}.jar $out/share/
+    cp -r adapters $out/share/
+    makeWrapper ${jre}/bin/java $out/bin/trimmomatic \
+      --add-flags "-cp $out/share/trimmomatic-${version}.jar org.usadellab.trimmomatic.Trimmomatic"
+
+    runHook postInstall
+  '';
+
+  meta = {
+    description = "A flexible read trimming tool for Illumina NGS data";
+    longDescription = ''
+      Trimmomatic performs a variety of useful trimming tasks for illumina
+      paired-end and single ended data: adapter trimming, quality trimming,
+      cropping to a specified length, length filtering, quality score
+      conversion.
+    '';
+    homepage = "http://www.usadellab.org/cms/?page=trimmomatic";
+    downloadPage = "https://github.com/usadellab/Trimmomatic/releases";
+    license = lib.licenses.gpl3Only;
+    sourceProvenance = [
+      lib.sourceTypes.fromSource
+      lib.sourceTypes.binaryBytecode  # source bundles dependencies as jars
+    ];
+    maintainers = [ lib.maintainers.kupac ];
+  };
+}
diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix
index 1b77cef6b80..5745b87a777 100644
--- a/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/pkgs/applications/science/chemistry/jmol/default.nix
@@ -25,14 +25,14 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "16.1.35";
+  version = "16.1.39";
   pname = "jmol";
 
   src = let
     baseVersion = "${lib.versions.major version}.${lib.versions.minor version}";
   in fetchurl {
     url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz";
-    hash = "sha256-r1ydAwAdXl5RRj64W0j8L7XbgnC7VOYjFNE019BcbpY=";
+    hash = "sha256-8M24VXMi7zHkTPNM5zd8nV4J0mXb3/MNIqqxfmlRt9M=";
   };
 
   patchPhase = ''
diff --git a/pkgs/applications/science/electronics/librepcb/default.nix b/pkgs/applications/science/electronics/librepcb/default.nix
index bd824ac2888..dfd679d4d53 100644
--- a/pkgs/applications/science/electronics/librepcb/default.nix
+++ b/pkgs/applications/science/electronics/librepcb/default.nix
@@ -1,21 +1,22 @@
 { stdenv, lib, fetchFromGitHub
-, qtbase, qttools, cmake, wrapQtAppsHook
+, qtbase, qttools, qtquickcontrols2, opencascade-occt, libGLU, libSM, freeimage, cmake, wrapQtAppsHook
 }:
 
 stdenv.mkDerivation rec {
   pname = "librepcb";
-  version = "0.1.7";
+  version = "1.0.0";
 
   src = fetchFromGitHub {
     owner  = pname;
     repo   = pname;
     rev    = version;
-    sha256 = "sha256-zqvvc3CHqdRWVUFt4BkH5Vq50/FKNvMNW2NvGyfWwFM=";
+    sha256 = "sha256-2o2Gue/RnDWxe8jk/Ehx9CM+B3ac5rEQn0H7yodUEZ8=";
     fetchSubmodules = true;
   };
 
-  nativeBuildInputs = [ cmake qttools wrapQtAppsHook ];
+  nativeBuildInputs = [ cmake qttools wrapQtAppsHook qtquickcontrols2 opencascade-occt libGLU ];
   buildInputs = [ qtbase ];
+  propagatedBuildInputs = [ libSM freeimage ];
 
   meta = with lib; {
     description = "A free EDA software to develop printed circuit boards";
diff --git a/pkgs/applications/science/electronics/nvc/default.nix b/pkgs/applications/science/electronics/nvc/default.nix
index dde8f05d623..94e0741f79a 100644
--- a/pkgs/applications/science/electronics/nvc/default.nix
+++ b/pkgs/applications/science/electronics/nvc/default.nix
@@ -16,13 +16,13 @@
 
 stdenv.mkDerivation rec {
   pname = "nvc";
-  version = "1.10.2";
+  version = "1.10.3";
 
   src = fetchFromGitHub {
     owner = "nickg";
     repo = "nvc";
     rev = "r${version}";
-    hash = "sha256-sAr51+8hFnpIq0jDd8dB5uiy00N09ufkFgWkFtW7ErU=";
+    hash = "sha256-0KLya2B+gs7aoOvkQdHuJuQtCHLUeSYATToBfIDhm/c=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix
index 86111327f06..fe8180899c0 100644
--- a/pkgs/applications/science/logic/coq/default.nix
+++ b/pkgs/applications/science/logic/coq/default.nix
@@ -55,7 +55,7 @@ let
    "8.16.1".sha256   = "sha256-n7830+zfZeyYHEOGdUo57bH6bb2/SZs8zv8xJhV+iAc=";
    "8.17.0".sha256   = "sha256-TGwm7S6+vkeZ8cidvp8pkiAd9tk008jvvPvYgfEOXhM=";
    "8.17.1".sha256   = "sha256-x+RwkbxMg9aR0L3WSCtpIz8jwA5cJA4tXAtHMZb20y4=";
-   "8.18+rc1".sha256   = "sha256-TmV0lzfzhpSnBoVyfTfVFUyBrXpUWSnyN1Le7b8IPTs=";
+   "8.18.0".sha256   = "sha256-WhiBs4nzPHQ0R24xAdM49kmxSCPOxiOVMA1iiMYunz4=";
   };
   releaseRev = v: "V${v}";
   fetched = import ../../../../build-support/coq/meta-fetch/default.nix
diff --git a/pkgs/applications/science/logic/cvc5/default.nix b/pkgs/applications/science/logic/cvc5/default.nix
index 24bcb16df9d..b8a05074aaa 100644
--- a/pkgs/applications/science/logic/cvc5/default.nix
+++ b/pkgs/applications/science/logic/cvc5/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "cvc5";
-  version = "1.0.7";
+  version = "1.0.8";
 
   src = fetchFromGitHub {
     owner  = "cvc5";
     repo   = "cvc5";
     rev    = "cvc5-${version}";
-    hash  = "sha256-0uT2Lzz0ZbfNWZBptjaGI1fN0mMniBz41eEwipGc5fc=";
+    hash  = "sha256-2sJKHD7Wzznut4hKOyxgc4LR4H+4u3m8Gq02+v+m5lM=";
   };
 
   nativeBuildInputs = [ pkg-config cmake flex ];
diff --git a/pkgs/applications/science/math/maxima/default.nix b/pkgs/applications/science/math/maxima/default.nix
index c102c645b3b..e7ac178cd5d 100644
--- a/pkgs/applications/science/math/maxima/default.nix
+++ b/pkgs/applications/science/math/maxima/default.nix
@@ -18,12 +18,12 @@ let
   searchPath = lib.makeBinPath
     (lib.filter (x: x != null) [ lisp-compiler rlwrap tk gnuplot ]);
 in
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "maxima";
   version = "5.46.0";
 
   src = fetchurl {
-    url = "mirror://sourceforge/${pname}/${pname}-${version}.tar.gz";
+    url = "mirror://sourceforge/${finalAttrs.pname}/${finalAttrs.pname}-${finalAttrs.version}.tar.gz";
     sha256 = "sha256-c5Dwa0jaZckDPosvYpuXi5AFZFSlQCLbfecOIiWqiwc=";
   };
 
@@ -52,11 +52,11 @@ stdenv.mkDerivation rec {
     done
     # Move emacs modules and documentation into the right place.
     mkdir -p $out/share/emacs $out/share/doc
-    ln -s ../maxima/${version}/emacs $out/share/emacs/site-lisp
-    ln -s ../maxima/${version}/doc $out/share/doc/maxima
+    ln -s ../maxima/${finalAttrs.version}/emacs $out/share/emacs/site-lisp
+    ln -s ../maxima/${finalAttrs.version}/doc $out/share/doc/maxima
   ''
    + (lib.optionalString (lisp-compiler.pname == "ecl") ''
-     cp src/binary-ecl/maxima.fas* "$out/lib/maxima/${version}/binary-ecl/"
+     cp src/binary-ecl/maxima.fas* "$out/lib/maxima/${finalAttrs.version}/binary-ecl/"
    '')
   ;
 
@@ -115,4 +115,4 @@ stdenv.mkDerivation rec {
     maintainers = with maintainers; [ doronbehar ];
     platforms = platforms.unix;
   };
-}
+})
diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix
index 405561510be..191ee7a00fd 100644
--- a/pkgs/applications/science/math/qalculate-gtk/default.nix
+++ b/pkgs/applications/science/math/qalculate-gtk/default.nix
@@ -1,14 +1,14 @@
 { lib, stdenv, fetchFromGitHub, intltool, autoreconfHook, pkg-config, libqalculate, gtk3, curl, wrapGAppsHook }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "qalculate-gtk";
-  version = "4.8.0";
+  version = "4.8.1";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-gtk";
-    rev = "v${version}";
-    sha256 = "sha256-GYy3Ot2vjXpCp89Rib3Ua0XeVGOOTejKcaqNZvPmxm0=";
+    rev = "v${finalAttrs.version}";
+    sha256 = "sha256-bG0hui5GjHWHny/8Rq5sZGz3s5rYnYlpc+K8I/LwDto=";
   };
 
   hardeningDisable = [ "format" ];
@@ -24,4 +24,4 @@ stdenv.mkDerivation rec {
     license = licenses.gpl2Plus;
     platforms = platforms.all;
   };
-}
+})
diff --git a/pkgs/applications/science/math/qalculate-qt/default.nix b/pkgs/applications/science/math/qalculate-qt/default.nix
index be9dd27695f..adc43b5f9da 100644
--- a/pkgs/applications/science/math/qalculate-qt/default.nix
+++ b/pkgs/applications/science/math/qalculate-qt/default.nix
@@ -1,14 +1,14 @@
 { lib, stdenv, fetchFromGitHub, intltool, pkg-config, qmake, wrapQtAppsHook, libqalculate, qtbase, qttools, qtsvg, qtwayland }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "qalculate-qt";
-  version = "4.8.0";
+  version = "4.8.1";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-qt";
-    rev = "v${version}";
-    hash = "sha256-7VlaoiY+HgHCMZCegUdy2wpgfx3fKaViMtkdNRleHaA=";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-hH+orU+5PmPcrhkLKCdsDhVCrD8Mvxp2RPTGSlsUP7Y=";
   };
 
   nativeBuildInputs = [ qmake intltool pkg-config qttools wrapQtAppsHook ];
@@ -33,4 +33,4 @@ stdenv.mkDerivation rec {
     license = licenses.gpl2Plus;
     platforms = platforms.unix;
   };
-}
+})
diff --git a/pkgs/applications/science/math/wxmaxima/default.nix b/pkgs/applications/science/math/wxmaxima/default.nix
index ee2f62317c0..c475dbd5ef2 100644
--- a/pkgs/applications/science/math/wxmaxima/default.nix
+++ b/pkgs/applications/science/math/wxmaxima/default.nix
@@ -10,14 +10,14 @@
 , glib
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs:{
   pname = "wxmaxima";
   version = "23.02.1";
 
   src = fetchFromGitHub {
     owner = "wxMaxima-developers";
     repo = "wxmaxima";
-    rev = "Version-${version}";
+    rev = "Version-${finalAttrs.version}";
     sha256 = "sha256-Lrj/oJNmKlCkNbnCGY2TewCospwajKdWgmKkreHzEIU=";
   };
 
@@ -51,4 +51,4 @@ stdenv.mkDerivation rec {
     maintainers = with maintainers; [ doronbehar ];
     platforms = platforms.linux;
   };
-}
+})
diff --git a/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/pkgs/applications/science/molecular-dynamics/lammps/default.nix
index 580dbb67968..f11e9bdeeb1 100644
--- a/pkgs/applications/science/molecular-dynamics/lammps/default.nix
+++ b/pkgs/applications/science/molecular-dynamics/lammps/default.nix
@@ -43,7 +43,7 @@
 , extraBuildInputs ? []
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   # LAMMPS has weird versioning converted to ISO 8601 format
   version = "2Aug2023";
   pname = "lammps";
@@ -51,7 +51,7 @@ stdenv.mkDerivation rec {
   src = fetchFromGitHub {
     owner = "lammps";
     repo = "lammps";
-    rev = "stable_${version}";
+    rev = "stable_${finalAttrs.version}";
     hash = "sha256-6T4YAa4iN3pJpODGPW+faR16xxyYYdkHLavtiPUbZ4o=";
   };
   preConfigure = ''
@@ -117,4 +117,4 @@ stdenv.mkDerivation rec {
     maintainers = [ maintainers.costrouc maintainers.doronbehar ];
     mainProgram = "lmp";
   };
-}
+})
diff --git a/pkgs/applications/science/physics/elmerfem/default.nix b/pkgs/applications/science/physics/elmerfem/default.nix
index 41a0e00ae78..e63203a93f2 100644
--- a/pkgs/applications/science/physics/elmerfem/default.nix
+++ b/pkgs/applications/science/physics/elmerfem/default.nix
@@ -1,14 +1,14 @@
-{ lib, stdenv, fetchFromGitHub, cmake, git, gfortran, mpi, blas, liblapack, pkg-config, libGL, libGLU, opencascade, libsForQt5, tbb, vtkWithQt5 }:
+{ lib, stdenv, fetchFromGitHub, cmake, git, gfortran, mpi, blas, liblapack, pkg-config, libGL, libGLU, opencascade-occt, libsForQt5, tbb, vtkWithQt5 }:
 
 stdenv.mkDerivation rec {
   pname = "elmerfem";
-  version = "unstable-2023-02-03";
+  version = "unstable-2023-09-18";
 
   src = fetchFromGitHub {
     owner = "elmercsc";
     repo = pname;
-    rev = "39c8784b6e4543a6bf560b5d597e0eec1eb06343";
-    hash = "sha256-yyxgFvlS+I4PouDL6eD4ZrXuONTDejCSYKq2AwQ0Iug=";
+    rev = "0fcced06f91c93f44557efd6a5f10b2da5c7066c";
+    hash = "sha256-UuARDYW7D3a4dB6I86s2Ed5ecQxc+Y/es3YIeF2VyTc=";
   };
 
   hardeningDisable = [ "format" ];
@@ -28,7 +28,7 @@ stdenv.mkDerivation rec {
     libsForQt5.qwt
     libGL
     libGLU
-    opencascade
+    opencascade-occt
     tbb
     vtkWithQt5
   ];