nim: patch to fix dynamic library loading

pkgs/applications/misc/nimmm/default.nix

@@ -36,8 +36,6 @@ in stdenv.mkDerivation rec {
   nativeBuildInputs = [ nim ];
   buildInputs = [ termbox pcre ];
 
-  NIX_LDFLAGS = "-lpcre";
-
   buildPhase = ''
     export HOME=$TMPDIR;
     nim -p:${noise} -p:${nimbox} -p:${lscolors}/src c -d:release src/nimmm.nim

pkgs/applications/science/biology/mosdepth/default.nix

@@ -26,14 +26,14 @@ in stdenv.mkDerivation rec {
     sha256 = "01gm9gj2x2zs4yx6wk761fi1papi7qr3gp4ln1kkn8n2f9y9h849";
   };
 
-  buildInputs = [ nim ];
+  buildInputs = [ nim htslib pcre ];
 
   buildPhase = ''
     HOME=$TMPDIR
     nim -p:${hts-nim}/src -p:${docopt}/src c --nilseqs:on -d:release mosdepth.nim
   '';
+
   installPhase = "install -Dt $out/bin mosdepth";
-  fixupPhase = "patchelf --set-rpath ${stdenv.lib.makeLibraryPath [ stdenv.cc.cc htslib pcre ]} $out/bin/mosdepth";
 
   meta = with stdenv.lib; {
     description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.";

pkgs/development/compilers/nim/default.nix

@@ -28,6 +28,10 @@ stdenv.mkDerivation rec {
     openssl pcre readline boehmgc sfml sqlite
   ];
 
+  patches = [ ./nixbuild.patch ];
+
+  postPatch = "echo define:nixbuild >> config/nim.cfg";
+
   buildPhase = ''
     runHook preBuild
 

pkgs/development/compilers/nim/nixbuild.patch

@@ -0,0 +1,51 @@
+commit 164ba50fc74b980f77047080b2ae1ea099ae9b27
+Author: Emery Hemingway <ehmry@posteo.net>
+Date:   Mon Sep 7 14:09:22 2020 +0200
+
+    Load libaries by absolute path on NixOS
+    
+    If "nixbuild" is defined then choose dynamic runtime libraries by
+    searching $NIX_LDFLAGS at compile-time.
+    
+    Fix #15194
+
+diff --git a/lib/pure/dynlib.nim b/lib/pure/dynlib.nim
+index f31ae94dd..debed9c07 100644
+--- a/lib/pure/dynlib.nim
++++ b/lib/pure/dynlib.nim
+@@ -56,6 +56,9 @@
+ 
+ import strutils
+ 
++when defined(nixbuild):
++  import os
++
+ type
+   LibHandle* = pointer ## a handle to a dynamically loaded library
+ 
+@@ -95,6 +98,25 @@ proc libCandidates*(s: string, dest: var seq[string]) =
+       libCandidates(prefix & middle & suffix, dest)
+   else:
+     add(dest, s)
++  when defined(nixbuild):
++    # Nix doesn't have a global library directory so
++    # load libraries using an absolute path if one
++    # can be derived from NIX_LDFLAGS.
++    #
++    # During Nix/NixOS packaging the line "define:nixbuild"
++    # should be appended to the ../../config/nim.cfg file
++    # to enable this behavior by default.
++    #
++    var libDirs = split(getEnv("LD_LIBRARY_PATH"), ':')
++    for flag in split(getEnv("NIX_LDFLAGS")):
++      if flag.startsWith("-L"):
++        libDirs.add(flag[2..flag.high])
++    for lib in dest:
++      for dir in libDirs:
++        let abs = dir / lib
++        if existsFile(abs):
++          dest = @[abs]
++          return
+ 
+ proc loadLibPattern*(pattern: string, globalSymbols = false): LibHandle =
+   ## loads a library with name matching `pattern`, similar to what `dlimport`