From e03a013c18b162c708539252481d905dc314f4c4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?L=C3=A1szl=C3=B3=20Kupcsik?= <dev@biobits.be>
Date: Sat, 20 Jun 2026 22:03:45 +0200
Subject: [PATCH] salmon: 1.11.4 -> 1.12.0

- Last release of the C++ -based salmon.
- Updated pufferfish
- Prevented downloading missing deps (fails faster)

The author released the 2.0.0 series, which is an LLM-assisted rust
rewrite. Due to the overly active release frequency, I don't intend to
maintain this package any longer (excelpt maybe security fixes for the
C++-branch, if any)
---
 pkgs/by-name/sa/salmon/package.nix | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/pkgs/by-name/sa/salmon/package.nix b/pkgs/by-name/sa/salmon/package.nix
index 4caba4faf339..f63e4a0a48ef 100644
--- a/pkgs/by-name/sa/salmon/package.nix
+++ b/pkgs/by-name/sa/salmon/package.nix
@@ -26,15 +26,15 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "salmon";
-  version = "1.11.4";
+  version = "1.12.1";
 
   # SALMON_PUFFERFISH_GIT_TAG defined in cmake/SalmonDependencies.cmake
   pufferFishSrc = fetchFromGitHub {
     owner = "COMBINE-lab";
     repo = "pufferfish";
     fetchSubmodules = true;
-    rev = "ace68c1c022816ba8c50a1a07c5d08f2abd597d6";
-    hash = "sha256-Zwl45sUYSmHOqsYLZPscigjgd1V3Waza0jRvhvNh7jU=";
+    rev = "1c788594cef77f0558b183281f32152e0ed22ba9";
+    hash = "sha256-N9KYmFsl90eY8R1wH1Jbi3nnNld6YVGeQjqoxYxPqtE=";
   };
 
   # SALMON_FQFEEDER_GIT_TAG defined in cmake/SalmonDependencies.cmake
@@ -49,7 +49,7 @@ stdenv.mkDerivation (finalAttrs: {
     owner = "COMBINE-lab";
     repo = "salmon";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-BjWXNQtycSwCTe40kujN/YzCNhGjkz2ULGOYtI01yos=";
+    hash = "sha256-ggFPp6sHPcR4Wq/B0AaMVf0LZVIz+QcvKMNrTfnAY4w=";
   };
 
   patches = [ ./fix_pufferfish.patch ];
@@ -92,6 +92,7 @@ stdenv.mkDerivation (finalAttrs: {
   cmakeFlags = [
     "-DSALMON_PUFFERFISH_SOURCE_DIR=${finalAttrs.pufferFishSrc}"
     "-DSALMON_FQFEEDER_SOURCE_DIR=${finalAttrs.FQFeederSrc}"
+    "-DSALMON_FETCH_MISSING_DEPS=OFF"
   ];
 
   # These are needed to please htslib
@@ -120,6 +121,6 @@ stdenv.mkDerivation (finalAttrs: {
     changelog = "https://github.com/COMBINE-lab/salmon/releases/tag/" + "v${finalAttrs.version}";
     license = lib.licenses.gpl3Only;
     platforms = lib.platforms.all;
-    maintainers = [ lib.maintainers.kupac ];
+    maintainers = [ ];
   };
 })