Merge pull request #253179 from Kupac/salmon

salmon: init at 1.10.2

3 files changed, 89 insertions, 0 deletions

diff --git a/pkgs/by-name/li/libgff/package.nix b/pkgs/by-name/li/libgff/package.nix
new file mode 100644
index 000000000000..fe3473f2e4df
--- /dev/null
+++ b/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/pkgs/by-name/li/libstaden-read/libstaden-install-config-header.patch b/pkgs/by-name/li/libstaden-read/libstaden-install-config-header.patch
new file mode 100644
index 000000000000..39df97a508a3
--- /dev/null
+++ b/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/pkgs/by-name/li/libstaden-read/package.nix b/pkgs/by-name/li/libstaden-read/package.nix
new file mode 100644
index 000000000000..dd2d93ae30a3
--- /dev/null
+++ b/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 ];
+  };
+})