From 0b1c28d5a1c46a7a10aa518863b1bd532824495e Mon Sep 17 00:00:00 2001
From: Luis Pedro Coelho <luis@luispedro.org>
Date: Wed, 4 May 2022 02:13:31 +0200
Subject: [PATCH 1/4] Static build for megahit

---
 pkgs/applications/science/biology/megahit/default.nix | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pkgs/applications/science/biology/megahit/default.nix b/pkgs/applications/science/biology/megahit/default.nix
index ee2f16f389b..45cb7560502 100644
--- a/pkgs/applications/science/biology/megahit/default.nix
+++ b/pkgs/applications/science/biology/megahit/default.nix
@@ -14,6 +14,9 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake ];
   buildInputs = [ zlib ];
 
+  cmakeFlags = lib.optional stdenv.hostPlatform.isStatic [
+    "-DSTATIC_BUILD=ON"
+    ];
   meta = with lib; {
     description = "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph";
     license     = licenses.gpl3;

From 967a5d78962b88f4e91fe5e3e4497912556ea60b Mon Sep 17 00:00:00 2001
From: Luis Pedro Coelho <luis@luispedro.org>
Date: Wed, 4 May 2022 02:15:17 +0200
Subject: [PATCH 2/4] Static builds for HTSLIB

We need to disable curses support and replace the build and install
phases (otherwise, they expect that *.so files will be present).
---
 .../science/biology/htslib/default.nix        | 20 +++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/libraries/science/biology/htslib/default.nix b/pkgs/development/libraries/science/biology/htslib/default.nix
index d93b4fb2a5a..2e3f9dec319 100644
--- a/pkgs/development/libraries/science/biology/htslib/default.nix
+++ b/pkgs/development/libraries/science/biology/htslib/default.nix
@@ -14,9 +14,25 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ zlib bzip2 xz curl ];
 
-  configureFlags = [ "--enable-libcurl" ]; # optional but strongly recommended
+  configureFlags = if ! stdenv.hostPlatform.isStatic
+                    then [ "--enable-libcurl" ] # optional but strongly recommended
+                    else [ "--disable-libcurl" "--disable-plugins" ];
 
-  installFlags = [ "prefix=$(out)" ];
+
+  # In the case of static builds, we need to replace the build and install phases
+  buildPhase = lib.optional stdenv.hostPlatform.isStatic ''
+    make AR=$AR lib-static
+    make LDFLAGS=-static bgzip htsfile tabix
+  '';
+
+  installPhase = lib.optional stdenv.hostPlatform.isStatic ''
+    install -d $out/bin
+    install -d $out/lib
+    install -d $out/include/htslib
+    install -D libhts.a $out/lib
+    install  -m644 htslib/*h $out/include/htslib
+    install -D bgzip htsfile tabix $out/bin
+  '';
 
   preCheck = ''
     patchShebangs test/

From 47588733783c4133de4973caa466d52d9c04992a Mon Sep 17 00:00:00 2001
From: Luis Pedro Coelho <luis@luispedro.org>
Date: Wed, 4 May 2022 02:16:17 +0200
Subject: [PATCH 3/4] Static build for samtools

Curses is not supported (it may be possible to support it)
---
 pkgs/applications/science/biology/samtools/default.nix | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix
index 98b0394c35f..ec61e0bd7ce 100644
--- a/pkgs/applications/science/biology/samtools/default.nix
+++ b/pkgs/applications/science/biology/samtools/default.nix
@@ -22,8 +22,15 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ zlib ncurses htslib ];
 
+  preConfigure = lib.optional stdenv.hostPlatform.isStatic ''
+    export LIBS="-lz -lbz2 -llzma"
+  '';
+  makeFlags = lib.optional stdenv.hostPlatform.isStatic "AR=${stdenv.cc.targetPrefix}ar";
+
   configureFlags = [ "--with-htslib=${htslib}" ]
-    ++ lib.optional (ncurses == null) "--without-curses";
+    ++ lib.optional (ncurses == null) "--without-curses"
+    ++ lib.optional stdenv.hostPlatform.isStatic ["--without-curses" ]
+    ;
 
   preCheck = ''
     patchShebangs test/

From 596c5e7ea26ba8c0bcd6d2f09ca7cb8202c20e70 Mon Sep 17 00:00:00 2001
From: Luis Pedro Coelho <luis@luispedro.org>
Date: Wed, 4 May 2022 02:20:50 +0200
Subject: [PATCH 4/4] Static bwa

AR needs to be passed specifically on the command line
---
 pkgs/applications/science/biology/bwa/default.nix | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix
index a2a11b1d451..d4727b41bd0 100644
--- a/pkgs/applications/science/biology/bwa/default.nix
+++ b/pkgs/applications/science/biology/bwa/default.nix
@@ -17,6 +17,8 @@ stdenv.mkDerivation rec {
     sed -i '/^CC/d' Makefile
   '';
 
+  makeFlags = lib.optional stdenv.hostPlatform.isStatic "AR=${stdenv.cc.targetPrefix}ar";
+
   # it's unclear which headers are intended to be part of the public interface
   # so we may find ourselves having to add more here over time
   installPhase = ''