diff --git a/biology/salmon/files/patch-CMakeLists.txt b/biology/salmon/files/patch-CMakeLists.txt
index 36038f452843..91dbffab92c3 100644
--- a/biology/salmon/files/patch-CMakeLists.txt
+++ b/biology/salmon/files/patch-CMakeLists.txt
@@ -1,155 +1,178 @@
---- CMakeLists.txt.orig	2025-07-26 11:52:41 UTC
+--- CMakeLists.txt.orig	2024-03-15 20:01:14 UTC
 +++ CMakeLists.txt
+@@ -19,16 +19,16 @@ if(NOT DEFINED USE_ARM)
+ 
+ # detect host architecture 
+ if(NOT DEFINED USE_ARM)
+-  if(CMAKE_SYSTEM_PROCESSOR MATCHES "^(aarch64.*|AARCH64.*|arm64.*|ARM64.*)")
+-    message("Detected 64-bit ARM host. Setting USE_ARM to true.")
++  if(CMAKE_SYSTEM_PROCESSOR MATCHES "^(x86_64|amd64|AMD64|i[3-6]86)$")
++    message("Detected x86 host. Setting USE_ARM to false.")
++    set(USE_ARM FALSE)
++    set(SCHAR_FLAG "")
++  else()
++    message("Detected non-x86 host. Setting USE_ARM to true.")
+     set(USE_ARM TRUE)
+     # set char to be signed
+     add_compile_options(-fsigned-char)
+     set(SCHAR_FLAG "-fsigned-char")
+-  else()
+-    message("Detected non-ARM host. Setting USE_ARM to false.")
+-    set(USE_ARM FALSE)
+-    set(SCHAR_FLAG "")
+   endif()
+ endif()
+ 
 @@ -310,14 +310,16 @@ endif()
  #  Grab pufferfish source --- DURING CONFIGURE TIME!
  #
  ####
 -if(NOT FETCHED_PUFFERFISH)
 +# if(NOT FETCHED_PUFFERFISH)
 +# Fetched by GH_TUPLE in FreeBSD port
 +# if(NOT FETCHED_PUFFERFISH)
    exec_program(${CMAKE_CURRENT_SOURCE_DIR}/scripts/fetchPufferfish.sh RETURN_VALUE FETCH_PF_SCRIPT_RET)
    message(STATUS "fetch PUFFERFISH exit code ${FETCH_PF_SCRIPT_RET}")
    if(NOT (FETCH_PF_SCRIPT_RET EQUAL 0))
      message(FATAL_ERROR "Could not fetch pufferfish source [fetchPufferfish.sh returned exit code ${FETCH_PF_SCRIPT_RET}].")
    endif()
    set(FETCHED_PUFFERFISH TRUE CACHE BOOL "Has pufferfish been fetched?" FORCE)
 -endif()
 +# endif()
  
  ##
  # Super-secret override
 @@ -364,7 +366,11 @@ endif()
    set(ICONV_LIB Iconv::Iconv)
  endif()
  
 -find_package(LibLZMA)
 +# find_package(LibLZMA)
 +# lzma is in FreeBSD base
 +# find_package(LibLZMA)
 +set(LIBLZMA_FOUND TRUE)
 +set(LIBLZMA_LIBRARIES /usr/lib/liblzma.a /usr/lib/libmd.a)
  if(NOT LIBLZMA_FOUND)
    message("Will attempt to fetch and build liblzma")
    message("=======================================")
 @@ -381,8 +387,11 @@ externalproject_add(liblzma
    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
    BUILD_IN_SOURCE TRUE
    CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} CPPFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} LDFLAGS=${EXTRA_CMAKE_LIBRARY_FLAGS}
 -  BUILD_COMMAND make ${QUIET_MAKE}
 -  INSTALL_COMMAND make ${QUIET_MAKE} install
 +#  BUILD_COMMAND make ${QUIET_MAKE}
 +#  INSTALL_COMMAND make ${QUIET_MAKE} install
 +# FreeBSD make is bsdmake
 +  BUILD_COMMAND gmake ${QUIET_MAKE}
 +  INSTALL_COMMAND gmake ${QUIET_MAKE} install
  )
  
  # Tell cmake that the external project generated a library so we can
 @@ -411,8 +420,11 @@ externalproject_add(libbz2
    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
    BUILD_IN_SOURCE TRUE
    CONFIGURE_COMMAND ""
 -  BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
 -  INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR>
 +#  BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
 +#  INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR>
 +# FreeBSD make is bsdmake
 +  BUILD_COMMAND gmake ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
 +  INSTALL_COMMAND gmake ${QUIET_MAKE} install PREFIX=<INSTALL_DIR>
  )
  # Tell cmake that the external project generated a library so we can
  # add dependencies here instead of later
 @@ -577,9 +589,11 @@ endif()
  endif()
  
  ## Try and find TBB first
 -find_package(TBB 2021.4
 -  HINTS ${TBB_ROOT_SEARCH}
 -  COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
 +# find_package(TBB 2021.4
 +#   HINTS ${TBB_ROOT_SEARCH}
 +#   COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
 +# tbbmalloc_proxy is rolled into tbbmalloc in FreeBSD ports
 +find_package(TBB 2021.4 COMPONENTS tbb tbbmalloc)
  
  if (${TBB_FOUND})
    if (${TBB_VERSION} VERSION_GREATER_EQUAL 2021.4)
 @@ -761,25 +775,28 @@ if (NOT LIBSTADENIO_FOUND)
  if (NOT LIBSTADENIO_FOUND)
    message("Build system will compile Staden IOLib")
    message("==================================================================")
 +  # stadenio is downloaded by GH_TUPLE in FreeBSD port
    externalproject_add(libstadenio
 -    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
 -    DOWNLOAD_COMMAND curl -k -L https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-15-0/io_lib-1.15.0.tar.gz -o staden-io_lib-v1.15.0.tar.gz &&
 -      ${SHASUM} ad343dac7c77086db1b54585c5887b26eda6430d1639d111dd3304c3b749494f staden-io_lib-v1.15.0.tar.gz &&
 -      mkdir -p staden-io_lib-1.15.0 &&
 -      tar -xzf staden-io_lib-v1.15.0.tar.gz --strip-components=1 -C staden-io_lib-1.15.0 &&
 -      rm -fr staden-io_lib &&
 -      mv -f staden-io_lib-1.15.0 staden-io_lib &&
 -      curl -k -L https://github.com/samtools/htscodecs/releases/download/v1.6.0/htscodecs-1.6.0.tar.gz -o htscodecs-1.6.0.tar.gz &&
 -      mkdir -p htscodecs-1.6.0 &&
 -      tar -xzf htscodecs-1.6.0.tar.gz --strip-components=1 -C htscodecs-1.6.0 &&
 -      rm -fr staden-io_lib/htscodecs &&
 -      mv -f htscodecs-1.6.0 staden-io_lib/htscodecs
 +    # DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
 +    # DOWNLOAD_COMMAND curl -k -L https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-15-0/io_lib-1.15.0.tar.gz -o staden-io_lib-v1.15.0.tar.gz &&
 +      # ${SHASUM} ad343dac7c77086db1b54585c5887b26eda6430d1639d111dd3304c3b749494f staden-io_lib-v1.15.0.tar.gz &&
 +      # mkdir -p staden-io_lib-1.15.0 &&
 +      # tar -xzf staden-io_lib-v1.15.0.tar.gz --strip-components=1 -C staden-io_lib-1.15.0 &&
 +      # rm -fr staden-io_lib &&
 +      # mv -f staden-io_lib-1.15.0 staden-io_lib &&
 +      # curl -k -L https://github.com/samtools/htscodecs/releases/download/v1.6.0/htscodecs-1.6.0.tar.gz -o htscodecs-1.6.0.tar.gz &&
 +      # mkdir -p htscodecs-1.6.0 &&
 +      # tar -xzf htscodecs-1.6.0.tar.gz --strip-components=1 -C htscodecs-1.6.0 &&
 +      # rm -fr staden-io_lib/htscodecs &&
 +      # mv -f htscodecs-1.6.0 staden-io_lib/htscodecs
      SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
      INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
      CONFIGURE_COMMAND ./configure --enable-shared=no --without-libcurl --prefix=<INSTALL_DIR> LDFLAGS=${LIBSTADEN_LDFLAGS} CFLAGS=${LIBSTADEN_CFLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
 -    BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB} LDFLAGS+=${EXTRA_CMAKE_LIBRARY_FLAGS} CFLAGS+=${EXTRA_CMAKE_INCLUDE_FLAGS} CFLAGS+=${LZFLAG} CFLAGS+=${SCHAR_FLAG}
 +    # FreeBSD make is bsdmake
 +    BUILD_COMMAND gmake ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB} LDFLAGS+=${EXTRA_CMAKE_LIBRARY_FLAGS} CFLAGS+=${EXTRA_CMAKE_INCLUDE_FLAGS} CFLAGS+=${LZFLAG} CFLAGS+=${SCHAR_FLAG}
      BUILD_IN_SOURCE 1
 -    INSTALL_COMMAND make install
 +    # FreeBSD make is bsdmake
 +    INSTALL_COMMAND gmake install
    )
    if(NOT LIBLZMA_FOUND)
    	ExternalProject_Add_StepDependencies(libstadenio build liblzma)
 @@ -793,23 +810,26 @@ else()
    set(FAST_MALLOC_LIB "")
    set(HAVE_FAST_MALLOC TRUE)
  else()
 -  set(FAST_MALLOC_LIB "")
 -  set(HAVE_FAST_MALLOC FALSE)
 +  # set(FAST_MALLOC_LIB "")
 +  # set(HAVE_FAST_MALLOC FALSE)
  
    # See if we have Jemalloc
 -  find_package(Jemalloc)
 -  if(Jemalloc_FOUND)
 +  # find_package(Jemalloc)
 +  # if(Jemalloc_FOUND)
      ##
      # Don't be so stringent about the version yet
      ##
      #if (NOT (${JEMALLOC_VERSION} VERSION_LESS 5.2.1))
 -      message("Found Jemalloc library --- using this memory allocator")
 -      set(FAST_MALLOC_LIB ${JEMALLOC_LIBRARIES})
 -      set(HAVE_FAST_MALLOC TRUE)
 +      # message("Found Jemalloc library --- using this memory allocator")
 +      # set(FAST_MALLOC_LIB ${JEMALLOC_LIBRARIES})
 +      # set(HAVE_FAST_MALLOC TRUE)
      #else()
      #  message("Fond Jemalloc version ${JEMALLOC_VERSION}, but require >= 5.2.1. Downloading newer version")
      #endif()
 -  endif()
 +  # endif()
 +  # jemalloc is default on FreeBSD
 +  set(FAST_MALLOC_LIB "/usr/lib/libc.so")
 +  set(HAVE_FAST_MALLOC TRUE)
  endif()
  
  if(CONDA_BUILD)
diff --git a/biology/salmon/files/patch-external_pufferfish_CMakeLists.txt b/biology/salmon/files/patch-external_pufferfish_CMakeLists.txt
index d6c7695325fc..0db8319f2630 100644
--- a/biology/salmon/files/patch-external_pufferfish_CMakeLists.txt
+++ b/biology/salmon/files/patch-external_pufferfish_CMakeLists.txt
@@ -1,23 +1,41 @@
---- external/pufferfish/CMakeLists.txt.orig	2023-06-26 19:34:50 UTC
+--- external/pufferfish/CMakeLists.txt.orig	2024-03-15 14:14:23 UTC
 +++ external/pufferfish/CMakeLists.txt
-@@ -135,7 +135,7 @@ set(WARN_ALL_THINGS "-fdiagnostics-color=always;-Wall;
+@@ -15,12 +15,12 @@ if(NOT DEFINED USE_ARM)
+ message("CC version: ${CC_VERSION}")
+ 
+ if(NOT DEFINED USE_ARM)
+-  if(CMAKE_SYSTEM_PROCESSOR MATCHES "^(aarch64.*|AARCH64.*|arm64.*|ARM64.*)")
+-    message("Detected 64-bit ARM host. Setting USE_ARM to true.")
+-    set(USE_ARM TRUE)
+-  else()
+-    message("Detected non-ARM host. Setting USE_ARM to false.")
++  if(CMAKE_SYSTEM_PROCESSOR MATCHES "^(x86_64|amd64|AMD64|i[3-6]86)$")
++    message("Detected x86 host. Setting USE_ARM to false.")
+     set(USE_ARM FALSE)
++  else()
++    message("Detected non-x86 host. Setting USE_ARM to true.")
++    set(USE_ARM TRUE)
+   endif()
+ endif()
+ 
+@@ -135,7 +135,7 @@ set(OPT_FLAGS "-DHAVE_SIMDE;-D__STDC_FORMAT_MACROS;-DS
  
  
  set(OPT_FLAGS "-DHAVE_SIMDE;-D__STDC_FORMAT_MACROS;-DSTX_NO_STD_STRING_VIEW;-O3;-fPIC;-DNDEBUG;-funroll-loops;-ftree-vectorize;-fno-strict-aliasing")
 -set(DEBUG_FLAGS "-DHAVE_SIMDE;-D__STDC_FORMAT_MACROS;-DSTX_NO_STD_STRING_VIEW;-pg;-g;-gstabs")
 +set(DEBUG_FLAGS "-DHAVE_SIMDE;-D__STDC_FORMAT_MACROS;-DSTX_NO_STD_STRING_VIEW;-g")
  
  ##
  # OSX is strange (some might say, stupid in this regard).  Deal with it's quirkines here.
-@@ -188,11 +188,6 @@ endif()
+@@ -188,11 +188,6 @@ set(SHASUM ${CMAKE_CURRENT_SOURCE_DIR}/scripts/check_s
  ##
  set(SHASUM ${CMAKE_CURRENT_SOURCE_DIR}/scripts/check_shasum.sh)
  
 -
 -find_package(Jemalloc)
 -if(JEMALLOC_FOUND)
 -  include_directories(SYSTEM ${JEMALLOC_INCLUDE_DIRS})
 -endif()
  
  if(DO_QUIET_MAKE)
    set(QUIET_MAKE "--silent")