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authorAlyssa Ross <hi@alyssa.is>2024-01-10 01:11:23 +0100
committerAlyssa Ross <hi@alyssa.is>2024-01-10 01:11:23 +0100
commitc8d05d8abadb244bc4e6cee75d450978d1f09a61 (patch)
tree2d710425b8e3f78e84d5e46abb3397cb1b34ec18 /nixpkgs/pkgs/by-name
parentad899504860973e98351c922ecb934595f2c0f19 (diff)
parent0ed96eed101462bf05e1e99e1bbadcd49b4eb302 (diff)
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Merge branch 'nixos-unstable-small' of https://github.com/NixOS/nixpkgs
Diffstat (limited to 'nixpkgs/pkgs/by-name')
-rw-r--r--nixpkgs/pkgs/by-name/as/asn1editor/package.nix2
-rw-r--r--nixpkgs/pkgs/by-name/bi/bitwarden-directory-connector-cli/package.nix66
-rw-r--r--nixpkgs/pkgs/by-name/br/bruno/package.nix6
-rw-r--r--nixpkgs/pkgs/by-name/cp/cpu-x/package.nix4
-rw-r--r--nixpkgs/pkgs/by-name/ki/kikit/default.nix4
-rw-r--r--nixpkgs/pkgs/by-name/la/labwc-menu-generator/package.nix53
-rw-r--r--nixpkgs/pkgs/by-name/li/libgff/package.nix30
-rw-r--r--nixpkgs/pkgs/by-name/li/libstaden-read/libstaden-install-config-header.patch12
-rw-r--r--nixpkgs/pkgs/by-name/li/libstaden-read/package.nix47
-rw-r--r--nixpkgs/pkgs/by-name/me/memtree/package.nix6
-rw-r--r--nixpkgs/pkgs/by-name/ne/neural-amp-modeler-lv2/package.nix29
-rw-r--r--nixpkgs/pkgs/by-name/ni/nixseparatedebuginfod/package.nix49
-rw-r--r--nixpkgs/pkgs/by-name/qr/qrtool/package.nix6
-rw-r--r--nixpkgs/pkgs/by-name/sa/salmon/fetch-pufferfish.patch60
-rw-r--r--nixpkgs/pkgs/by-name/sa/salmon/package.nix84
15 files changed, 444 insertions, 14 deletions
diff --git a/nixpkgs/pkgs/by-name/as/asn1editor/package.nix b/nixpkgs/pkgs/by-name/as/asn1editor/package.nix
index a85d8f53fe6d..07941a7762c4 100644
--- a/nixpkgs/pkgs/by-name/as/asn1editor/package.nix
+++ b/nixpkgs/pkgs/by-name/as/asn1editor/package.nix
@@ -18,7 +18,7 @@ python3.pkgs.buildPythonApplication rec {
   propagatedBuildInputs = with python3.pkgs; [
     asn1tools
     coverage
-    wxPython_4_2
+    wxpython
   ];
 
   pythonImportsCheck = [ "asn1editor" ];
diff --git a/nixpkgs/pkgs/by-name/bi/bitwarden-directory-connector-cli/package.nix b/nixpkgs/pkgs/by-name/bi/bitwarden-directory-connector-cli/package.nix
new file mode 100644
index 000000000000..24376014a120
--- /dev/null
+++ b/nixpkgs/pkgs/by-name/bi/bitwarden-directory-connector-cli/package.nix
@@ -0,0 +1,66 @@
+{
+  lib,
+  buildNpmPackage,
+  fetchFromGitHub,
+  buildPackages,
+  python3,
+  pkg-config,
+  libsecret,
+  nodejs_18,
+}:
+buildNpmPackage rec {
+  pname = "bitwarden-directory-connector-cli";
+  version = "2023.10.0";
+  nodejs = nodejs_18;
+
+  src = fetchFromGitHub {
+    owner = "bitwarden";
+    repo = "directory-connector";
+    rev = "v${version}";
+    hash = "sha256-PlOtTh+rpTxAv8ajHBDHZuL7yeeLVpbAfKEDPQlejIg=";
+  };
+
+  postPatch = ''
+    ${lib.getExe buildPackages.jq} 'del(.scripts.preinstall)' package.json > package.json.tmp
+    mv -f package.json{.tmp,}
+  '';
+
+  npmDepsHash = "sha256-jBAWWY12qeX2EDhUvT3TQpnQvYXRsIilRrXGpVzxYvw=";
+
+  env.ELECTRON_SKIP_BINARY_DOWNLOAD = "1";
+
+  makeCacheWritable = true;
+  npmBuildScript = "build:cli:prod";
+
+  installPhase = ''
+    runHook preInstall
+    mkdir -p $out/libexec/bitwarden-directory-connector
+    cp -R {build-cli,node_modules} $out/libexec/bitwarden-directory-connector
+    runHook postInstall
+  '';
+
+  # needs to be wrapped with nodejs so that it can be executed
+  postInstall = ''
+    chmod +x $out/libexec/bitwarden-directory-connector/build-cli/bwdc.js
+    mkdir -p $out/bin
+    ln -s $out/libexec/bitwarden-directory-connector/build-cli/bwdc.js $out/bin/bitwarden-directory-connector-cli
+  '';
+
+  buildInputs = [
+    libsecret
+  ];
+
+  nativeBuildInputs = [
+    python3
+    pkg-config
+  ];
+
+  meta = with lib; {
+    description = "LDAP connector for Bitwarden";
+    homepage = "https://github.com/bitwarden/directory-connector";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [Silver-Golden];
+    platforms = platforms.linux;
+    mainProgram = "bitwarden-directory-connector-cli";
+  };
+}
diff --git a/nixpkgs/pkgs/by-name/br/bruno/package.nix b/nixpkgs/pkgs/by-name/br/bruno/package.nix
index 1687065fbd9b..dcacc86071b1 100644
--- a/nixpkgs/pkgs/by-name/br/bruno/package.nix
+++ b/nixpkgs/pkgs/by-name/br/bruno/package.nix
@@ -17,20 +17,20 @@
 
 buildNpmPackage rec {
   pname = "bruno";
-  version = "1.5.1";
+  version = "1.6.1";
 
   src = fetchFromGitHub {
     owner = "usebruno";
     repo = "bruno";
     rev = "v${version}";
-    hash = "sha256-GgXnsPEUurPHrijf966x5ldp+1lDrgS1iBinU+EkdYU=b";
+    hash = "sha256-Vf4UHN13eE9W4rekOEGAWIP3x79cVH3vI9sxuIscv8c=";
 
     postFetch = ''
       ${lib.getExe npm-lockfile-fix} $out/package-lock.json
     '';
   };
 
-  npmDepsHash = "sha256-R5dEL4QbwCSE9+HHCXlf/pYLmjCaD15tmdSSLbZgmt0=";
+  npmDepsHash = "sha256-pfV9omdJiozJ9VotTImfM/DRsBPNGAEzmSdj3/C//4A=";
 
   nativeBuildInputs = [
     (writeShellScriptBin "phantomjs" "echo 2.1.1")
diff --git a/nixpkgs/pkgs/by-name/cp/cpu-x/package.nix b/nixpkgs/pkgs/by-name/cp/cpu-x/package.nix
index aacb3ea75225..8171cfc78f2b 100644
--- a/nixpkgs/pkgs/by-name/cp/cpu-x/package.nix
+++ b/nixpkgs/pkgs/by-name/cp/cpu-x/package.nix
@@ -16,13 +16,13 @@
 
 stdenv.mkDerivation rec {
   pname = "cpu-x";
-  version = "5.0.2";
+  version = "5.0.3";
 
   src = fetchFromGitHub {
     owner = "X0rg";
     repo = "CPU-X";
     rev = "v${version}";
-    sha256 = "sha256-tdxIbs5jR4sQHt1ZLUmiAYszP2e5SCMqEFq+eW1k7+s=";
+    sha256 = "sha256-iaqqBeoack41D07Bbr0Fo1JXfF2ksXbqS5V5Ymt6Qvg=";
   };
 
   nativeBuildInputs = [ cmake pkg-config wrapGAppsHook nasm makeWrapper ];
diff --git a/nixpkgs/pkgs/by-name/ki/kikit/default.nix b/nixpkgs/pkgs/by-name/ki/kikit/default.nix
index 886cca973837..c32b89af37d0 100644
--- a/nixpkgs/pkgs/by-name/ki/kikit/default.nix
+++ b/nixpkgs/pkgs/by-name/ki/kikit/default.nix
@@ -12,7 +12,7 @@
 , markdown2
 , pytestCheckHook
 , commentjson
-, wxPython_4_2
+, wxpython
 , pcbnew-transition
 , pybars3
 , versioneer
@@ -42,7 +42,7 @@ buildPythonApplication rec {
     markdown2
     commentjson
     # https://github.com/yaqwsx/KiKit/issues/575
-    wxPython_4_2
+    wxpython
     pcbnew-transition
     pybars3
     # https://github.com/yaqwsx/KiKit/issues/574
diff --git a/nixpkgs/pkgs/by-name/la/labwc-menu-generator/package.nix b/nixpkgs/pkgs/by-name/la/labwc-menu-generator/package.nix
new file mode 100644
index 000000000000..331936ea5373
--- /dev/null
+++ b/nixpkgs/pkgs/by-name/la/labwc-menu-generator/package.nix
@@ -0,0 +1,53 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, glib
+, perl
+, pkg-config
+, unstableGitUpdater
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "labwc-menu-generator";
+  version = "unstable-2023-10-31";
+
+  src = fetchFromGitHub {
+    owner = "labwc";
+    repo = "labwc-menu-generator";
+    rev = "d7c81071f8b121ef83da32ae3fa16155d1a2ced9";
+    hash = "sha256-gZ0TuSVJwcKW4orawSmRQvoCfrpb8yLXlv81qCR86MU=";
+  };
+
+  nativeBuildInputs = [
+    pkg-config
+  ];
+
+  buildInputs = [
+    glib
+  ];
+
+  nativeCheckInputs = [
+    perl
+  ];
+
+  doCheck = true;
+
+  strictDeps = true;
+
+  installPhase = ''
+    runHook preInstall
+    install -Dm755 labwc-menu-generator -t $out/bin
+    runHook postInstall
+  '';
+
+  passthru.updateScript = unstableGitUpdater { };
+
+  meta = {
+    homepage = "https://github.com/labwc/labwc-menu-generator";
+    description = "Menu generator for labwc";
+    mainProgram = "labwc-menu-generator";
+    license = lib.licenses.gpl2Only;
+    platforms = lib.platforms.unix;
+    maintainers = with lib.maintainers; [ AndersonTorres romildo ];
+  };
+})
diff --git a/nixpkgs/pkgs/by-name/li/libgff/package.nix b/nixpkgs/pkgs/by-name/li/libgff/package.nix
new file mode 100644
index 000000000000..fe3473f2e4df
--- /dev/null
+++ b/nixpkgs/pkgs/by-name/li/libgff/package.nix
@@ -0,0 +1,30 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "libgff";
+  version = "2.0.0";
+
+  src = fetchFromGitHub {
+    owner = "COMBINE-lab";
+    repo = "libgff";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-ZCb3UyuB/+ykrYFQ9E5VytT65gAAULiOzIEu5IXISTc=";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  meta = {
+    description = "A lightweight GTF/GFF parsers exposing a C++ interface";
+    homepage = "https://github.com/COMBINE-lab/libgff";
+    downloadPage = "https://github.com/COMBINE-lab/libgff/releases";
+    changelog = "https://github.com/COMBINE-lab/libgff/releases/tag/" +
+                "v${finalAttrs.version}";
+    license = lib.licenses.boost;
+    platforms = lib.platforms.all;
+    maintainers = [ lib.maintainers.kupac ];
+  };
+})
diff --git a/nixpkgs/pkgs/by-name/li/libstaden-read/libstaden-install-config-header.patch b/nixpkgs/pkgs/by-name/li/libstaden-read/libstaden-install-config-header.patch
new file mode 100644
index 000000000000..39df97a508a3
--- /dev/null
+++ b/nixpkgs/pkgs/by-name/li/libstaden-read/libstaden-install-config-header.patch
@@ -0,0 +1,12 @@
+diff --git a/Makefile.am b/Makefile.am
+index 31286d1..2631af1 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -61,6 +61,7 @@ man_MANS = \
+ 	man/man4/Read.4
+ 
+ pkginclude_HEADERS = \
++        io_lib_config.h \
+ 	io_lib/Read.h \
+ 	io_lib/scf_extras.h \
+ 	io_lib/translate.h \
diff --git a/nixpkgs/pkgs/by-name/li/libstaden-read/package.nix b/nixpkgs/pkgs/by-name/li/libstaden-read/package.nix
new file mode 100644
index 000000000000..dd2d93ae30a3
--- /dev/null
+++ b/nixpkgs/pkgs/by-name/li/libstaden-read/package.nix
@@ -0,0 +1,47 @@
+{ lib
+, stdenv
+, autoreconfHook
+, fetchFromGitHub
+, bzip2
+, xz
+, zlib
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  # Same name as the Debian library
+  pname = "libstaden-read";
+  version = "1.15.0";
+
+  src = fetchFromGitHub {
+    owner = "jkbonfield";
+    repo = "io_lib";
+    rev = "io_lib-" + builtins.replaceStrings ["."] ["-"] finalAttrs.version;
+    fetchSubmodules = true;
+    hash = "sha256-2Dlx+MXmqar81/Xmf0oE+6lWX461EDYijiZsZf/VD28=";
+  };
+
+  patches = [
+    # Needed so that the lib can be detected
+    ./libstaden-install-config-header.patch
+  ];
+
+  buildInputs = [ bzip2 xz zlib ];
+  nativeBuildInputs = [ autoreconfHook ];
+
+  # autoreconfHook does not descend into htscodecs folder
+  preAutoreconf = ''
+    pushd ./htscodecs
+    autoreconf --install --force --verbose
+    pushd
+  '';
+
+  meta = {
+    description = "C library for reading/writing various DNA sequence formats";
+    homepage = "https://staden.sourceforge.net";
+    downloadPage = "https://github.com/jkbonfield/io_lib/releases";
+    changelog = "https://github.com/jkbonfield/io_lib/blob/${finalAttrs.src.rev}/CHANGES";
+    license = with lib.licenses; [ bsd3 free ];
+    platforms = lib.platforms.all;
+    maintainers = [ lib.maintainers.kupac ];
+  };
+})
diff --git a/nixpkgs/pkgs/by-name/me/memtree/package.nix b/nixpkgs/pkgs/by-name/me/memtree/package.nix
index f69c3f8e95d3..528323624805 100644
--- a/nixpkgs/pkgs/by-name/me/memtree/package.nix
+++ b/nixpkgs/pkgs/by-name/me/memtree/package.nix
@@ -6,14 +6,14 @@
 
 python3Packages.buildPythonApplication {
   pname = "memtree";
-  version = "unstable-2023-11-22";
+  version = "unstable-2024-01-04";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "nbraud";
     repo = "memtree";
-    rev = "edc09d91dcd72f175d6adc1d08b261dd95cc4fbf";
-    hash = "sha256-YLZm0wjkjaTw/lHY5k4cqPXCgINe+49SGPLZq+eRdI4=";
+    rev = "97615952eabdc5e8e1a4bd590dd1f4971f3c5a24";
+    hash = "sha256-Ifp8hwkuyBw57fGer3GbDiJaRjL4TD3hzj+ecGXWqI0=";
   };
 
   nativeBuildInputs = with python3Packages; [
diff --git a/nixpkgs/pkgs/by-name/ne/neural-amp-modeler-lv2/package.nix b/nixpkgs/pkgs/by-name/ne/neural-amp-modeler-lv2/package.nix
new file mode 100644
index 000000000000..a414dc2e65d4
--- /dev/null
+++ b/nixpkgs/pkgs/by-name/ne/neural-amp-modeler-lv2/package.nix
@@ -0,0 +1,29 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "neural-amp-modeler-lv2";
+  version = "0.1.3";
+
+  src = fetchFromGitHub {
+    owner = "mikeoliphant";
+    repo = finalAttrs.pname;
+    rev = finalAttrs.version;
+    fetchSubmodules = true;
+    hash = "sha256-sRZngmivNvSWcjkIqcqjjaIgXFH8aMq+/caNroXmzIk=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+  ];
+
+  meta = {
+    maintainers = [ lib.maintainers.viraptor ];
+    description = "Neural Amp Modeler LV2 plugin implementation";
+    homepage = finalAttrs.src.meta.homepage;
+    license = [ lib.licenses.gpl3 ];
+  };
+})
diff --git a/nixpkgs/pkgs/by-name/ni/nixseparatedebuginfod/package.nix b/nixpkgs/pkgs/by-name/ni/nixseparatedebuginfod/package.nix
new file mode 100644
index 000000000000..faacd2330d3f
--- /dev/null
+++ b/nixpkgs/pkgs/by-name/ni/nixseparatedebuginfod/package.nix
@@ -0,0 +1,49 @@
+{ lib
+, fetchFromGitHub
+, rustPlatform
+, libarchive
+, openssl
+, sqlite
+, pkg-config
+, nixosTests
+}:
+
+rustPlatform.buildRustPackage rec {
+  pname = "nixseparatedebuginfod";
+  version = "0.3.2";
+
+  src = fetchFromGitHub {
+    owner = "symphorien";
+    repo = "nixseparatedebuginfod";
+    rev = "v${version}";
+    hash = "sha256-XSEHNoc3h21foVeR28KgfiBTRHyUh+GJ52LMD2xFHfA=";
+  };
+
+  cargoHash = "sha256-t6W6siHuga/T9kmanA735zH2i9eCOT7vD6v7E5LIp9k=";
+
+  # tests need a working nix install with access to the internet
+  doCheck = false;
+
+  buildInputs = [
+    libarchive
+    openssl
+    sqlite
+  ];
+
+  nativeBuildInputs = [ pkg-config ];
+
+  passthru = {
+    tests = {
+      inherit (nixosTests) nixseparatedebuginfod;
+    };
+  };
+
+  meta = with lib; {
+    description = "Downloads and provides debug symbols and source code for nix derivations to gdb and other debuginfod-capable debuggers as needed";
+    homepage = "https://github.com/symphorien/nixseparatedebuginfod";
+    license = licenses.gpl3Only;
+    maintainers = [ maintainers.symphorien ];
+    platforms = platforms.linux;
+    mainProgram = "nixseparatedebuginfod";
+  };
+}
diff --git a/nixpkgs/pkgs/by-name/qr/qrtool/package.nix b/nixpkgs/pkgs/by-name/qr/qrtool/package.nix
index 306950a51532..79791ddb0ca2 100644
--- a/nixpkgs/pkgs/by-name/qr/qrtool/package.nix
+++ b/nixpkgs/pkgs/by-name/qr/qrtool/package.nix
@@ -8,16 +8,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "qrtool";
-  version = "0.10.1";
+  version = "0.10.2";
 
   src = fetchFromGitHub {
     owner = "sorairolake";
     repo = "qrtool";
     rev = "v${version}";
-    sha256 = "sha256-96k3VgxVGuKPLA4rD9B20AigFW03YvedT04UUzzmX38=";
+    sha256 = "sha256-caQoV0qAj2VXbEaYHsGOqCZCVyb4s1JJbBl7H0X5xEI=";
   };
 
-  cargoHash = "sha256-nAfW66vasnR0JHhz7n1XGA+OpPavOnGB6D6TfK9cr9Y=";
+  cargoHash = "sha256-V9TopADUGBR0MdOTIq1Tiee3NEzLa76zRq5bjULoLVI=";
 
   nativeBuildInputs = [ asciidoctor installShellFiles ];
 
diff --git a/nixpkgs/pkgs/by-name/sa/salmon/fetch-pufferfish.patch b/nixpkgs/pkgs/by-name/sa/salmon/fetch-pufferfish.patch
new file mode 100644
index 000000000000..7010a1a69fac
--- /dev/null
+++ b/nixpkgs/pkgs/by-name/sa/salmon/fetch-pufferfish.patch
@@ -0,0 +1,60 @@
+diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
+index bf2574e0..42582806 100755
+--- a/scripts/fetchPufferfish.sh
++++ b/scripts/fetchPufferfish.sh
+@@ -11,10 +11,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+ EXTERNAL_DIR=${CURR_DIR}/../external
+ INSTALL_DIR=${CURR_DIR}/../external/install
+ 
+-if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then
+-    rm -fr ${EXTERNAL_DIR}/pufferfish
+-fi
+-
+ if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then
+     rm -fr ${INSTALL_DIR}/include/pufferfish
+ fi
+@@ -23,42 +19,10 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
+     rm -fr ${INSTALL_DIR}/src/pufferfish
+ fi
+ 
+-SVER=salmon-v1.10.2
+-#SVER=develop
+-#SVER=sketch-mode
+-
+-EXPECTED_SHA256=f225b74833f71dcf767a565345224357fb091f90ce79717abc836814d9ccd101
+-
+-mkdir -p ${EXTERNAL_DIR}
+-curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip
+-
+-hashcheck=""
+-if exists sha256sum; then
+-	hashcheck="sha256sum"
+-elif exists shasum; then
+-	hashcheck="shasum -a256"
+-else
+-	unset hashcheck
+-fi
+-
+-
+-if [ -z "${hashcheck-}" ]; then
+-    echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";
+-else
+-
+-    if [[ $SVER != develop && $SVER != onetbb ]]; then
+-        echo "${EXPECTED_SHA256}  ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; }
+-    else
+-        echo "not testing sha since pulling from develop"
+-    fi
+-fi
+-
+-
+-rm -fr ${EXTERNAL_DIR}/pufferfish
+-unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR}
+-mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish
+ 
+ mkdir -p ${INSTALL_DIR}/include/pufferfish
++# This is needed later when pufferfish is compiled for Salmon
++cp -r ${pufferFishSrc} ${EXTERNAL_DIR}/pufferfish
+ 
+ cp ${EXTERNAL_DIR}/pufferfish/include/ProgOpts.hpp ${INSTALL_DIR}/include/pufferfish
+ cp ${EXTERNAL_DIR}/pufferfish/include/BooPHF.hpp ${INSTALL_DIR}/include/pufferfish
diff --git a/nixpkgs/pkgs/by-name/sa/salmon/package.nix b/nixpkgs/pkgs/by-name/sa/salmon/package.nix
new file mode 100644
index 000000000000..e4442e96fd6f
--- /dev/null
+++ b/nixpkgs/pkgs/by-name/sa/salmon/package.nix
@@ -0,0 +1,84 @@
+{ lib
+, stdenv
+, autoreconfHook
+, bash
+, boost
+, bzip2
+, cereal_1_3_2
+, cmake
+, curl
+, fetchFromGitHub
+, jemalloc
+, libgff
+, libiconv
+, libstaden-read
+, pkg-config
+, tbb_2021_8
+, xz
+, zlib
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "salmon";
+  version = "1.10.2";
+
+  pufferFishSrc = fetchFromGitHub {
+    owner = "COMBINE-lab";
+    repo = "pufferfish";
+    rev = "salmon-v${finalAttrs.version}";
+    hash = "sha256-JKbUFBEsqnENl4vFqve1FCd4TI3n9bRi2RNHC8QGQGc=";
+  };
+
+  src = fetchFromGitHub {
+    owner = "COMBINE-lab";
+    repo = "salmon";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-kwqoUmVCqjr/xRxJjQKaFjjCQW+MFASHJ2f9OiAumNU=";
+  };
+
+  patches = [
+    # Use pufferfish source fetched by nix
+    ./fetch-pufferfish.patch
+  ];
+
+  postPatch = "patchShebangs .";
+
+  buildInputs = [
+    (boost.override { enableShared = false; enabledStatic = true; })
+    bzip2
+    cereal_1_3_2
+    curl
+    jemalloc
+    libgff
+    libstaden-read
+    tbb_2021_8
+    xz
+    zlib
+  ] ++ lib.optionals stdenv.isDarwin [ libiconv ];
+
+  nativeBuildInputs = [ cmake pkg-config ];
+
+  strictDeps = true;
+
+  meta = {
+    description =
+      "Tool for quantifying the expression of transcripts using RNA-seq data";
+    longDescription = ''
+      Salmon is a tool for quantifying the expression of transcripts
+      using RNA-seq data. Salmon uses new algorithms (specifically,
+      coupling the concept of quasi-mapping with a two-phase inference
+      procedure) to provide accurate expression estimates very quickly
+      and while using little memory. Salmon performs its inference using
+      an expressive and realistic model of RNA-seq data that takes into
+      account experimental attributes and biases commonly observed in
+      real RNA-seq data.
+    '';
+    homepage = "https://combine-lab.github.io/salmon";
+    downloadPage = "https://github.com/COMBINE-lab/salmon/releases";
+    changelog = "https://github.com/COMBINE-lab/salmon/releases/tag/" +
+                "v${finalAttrs.version}";
+    license = lib.licenses.gpl3Only;
+    platforms = lib.platforms.all;
+    maintainers = [ lib.maintainers.kupac ];
+  };
+})