lzma: deprecate alias

7 files changed, 15 insertions, 14 deletions

diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix
index 80506bb79b6c..46d39c1a7ba3 100644
--- a/pkgs/applications/science/biology/bcftools/default.nix
+++ b/pkgs/applications/science/biology/bcftools/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, python3, bash }:
+{ lib, stdenv, fetchurl, htslib, zlib, bzip2, xz, curl, perl, python3, bash }:
 
 stdenv.mkDerivation rec {
   pname = "bcftools";
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
     python3
   ];
 
-  buildInputs = [ htslib zlib bzip2 lzma curl ];
+  buildInputs = [ htslib zlib bzip2 xz curl ];
 
   strictDeps = true;
 
diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix
index f5aad5d05543..aac36d2af310 100644
--- a/pkgs/applications/science/biology/bedtools/default.nix
+++ b/pkgs/applications/science/biology/bedtools/default.nix
@@ -1,4 +1,4 @@
-{lib, stdenv, fetchFromGitHub, zlib, python3, bzip2, lzma}:
+{lib, stdenv, fetchFromGitHub, zlib, python3, bzip2, xz}:
 
 stdenv.mkDerivation rec {
   pname = "bedtools";
@@ -17,7 +17,8 @@ stdenv.mkDerivation rec {
     python3
   ];
 
-  buildInputs = [ zlib bzip2 lzma ];
+  buildInputs = [ zlib bzip2 xz ];
+
   cxx = if stdenv.cc.isClang then "clang++" else "g++";
   cc = if stdenv.cc.isClang then "clang" else "gcc";
   buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} -j $NIX_BUILD_CORES";
diff --git a/pkgs/applications/science/biology/delly/default.nix b/pkgs/applications/science/biology/delly/default.nix
index efaa4403f41d..fe81ff44d245 100644
--- a/pkgs/applications/science/biology/delly/default.nix
+++ b/pkgs/applications/science/biology/delly/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchpatch, fetchFromGitHub, htslib, zlib, bzip2, lzma, ncurses, boost }:
+{ lib, stdenv, fetchpatch, fetchFromGitHub, htslib, zlib, bzip2, xz, ncurses, boost }:
 
 stdenv.mkDerivation rec {
   pname = "delly";
@@ -11,7 +11,7 @@ stdenv.mkDerivation rec {
       sha256 = "sha256-DWwC35r8cQbePUzppkFQlev0YZdxk2+BSrNTW/DOY3M=";
   };
 
-  buildInputs = [ zlib htslib bzip2 lzma ncurses boost ];
+  buildInputs = [ zlib htslib bzip2 xz ncurses boost ];
 
   EBROOTHTSLIB = htslib;
 
diff --git a/pkgs/applications/science/biology/freebayes/default.nix b/pkgs/applications/science/biology/freebayes/default.nix
index 32ab614b9682..8646b8ca54a8 100644
--- a/pkgs/applications/science/biology/freebayes/default.nix
+++ b/pkgs/applications/science/biology/freebayes/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, zlib, bzip2, lzma }:
+{ lib, stdenv, fetchFromGitHub, zlib, bzip2, xz }:
 
 stdenv.mkDerivation rec {
   pname = "freebayes";
@@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
     fetchSubmodules = true;
   };
 
-  buildInputs = [ zlib bzip2 lzma ];
+  buildInputs = [ zlib bzip2 xz ];
 
   installPhase = ''
     install -vD bin/freebayes bin/bamleftalign scripts/* -t $out/bin
diff --git a/pkgs/applications/science/biology/kent/default.nix b/pkgs/applications/science/biology/kent/default.nix
index 26c55d3dc383..12bbfa09c251 100644
--- a/pkgs/applications/science/biology/kent/default.nix
+++ b/pkgs/applications/science/biology/kent/default.nix
@@ -3,7 +3,7 @@
 , libuuid
 , zlib
 , bzip2
-, lzma
+, xz
 , openssl
 , curl
 , libmysqlclient
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
     sha256 = "0l5lmqqc6sqkf4hyk3z4825ly0vdlj5xdfad6zd0708cb1v81nbx";
   };
 
-  buildInputs = [ libpng libuuid zlib bzip2 lzma openssl curl libmysqlclient ];
+  buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ];
 
   patchPhase = ''
     substituteInPlace ./src/checkUmask.sh \
diff --git a/pkgs/applications/science/biology/octopus/default.nix b/pkgs/applications/science/biology/octopus/default.nix
index fa88e5c47b47..0ef48ec6413b 100644
--- a/pkgs/applications/science/biology/octopus/default.nix
+++ b/pkgs/applications/science/biology/octopus/default.nix
@@ -1,4 +1,4 @@
-{lib, stdenv, fetchpatch, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, lzma, pkg-config}:
+{lib, stdenv, fetchpatch, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, xz, pkg-config}:
 
 stdenv.mkDerivation rec {
   pname = "octopus";
@@ -24,7 +24,7 @@ stdenv.mkDerivation rec {
   ];
 
   nativeBuildInputs = [ cmake pkg-config ];
-  buildInputs = [ boost gmp htslib zlib lzma ];
+  buildInputs = [ boost gmp htslib zlib xz ];
 
   postInstall = ''
     mkdir $out/bin
diff --git a/pkgs/applications/science/biology/svaba/default.nix b/pkgs/applications/science/biology/svaba/default.nix
index 87b77f6ac045..1aed501919f9 100644
--- a/pkgs/applications/science/biology/svaba/default.nix
+++ b/pkgs/applications/science/biology/svaba/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, zlib, bzip2, lzma, fetchFromGitHub } :
+{ lib, stdenv, zlib, bzip2, xz, fetchFromGitHub } :
 
 stdenv.mkDerivation rec {
   version = "1.1.0";
@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
     fetchSubmodules = true;
   };
 
-  buildInputs = [ zlib bzip2 lzma ];
+  buildInputs = [ zlib bzip2 xz ];
 
   installPhase = ''
     runHook preInstall