From 0e005735bcbe2207f2ba257984461edae6ed3eb0 Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Tue, 4 May 2021 00:57:35 +0200
Subject: [PATCH] Create a Nix derivation for CuReSim

---
 generation.sh |  2 +-
 shell.nix     | 34 +++++++++++++++++++++++++++++++---
 2 files changed, 32 insertions(+), 4 deletions(-)

diff --git a/generation.sh b/generation.sh
index ac50caa..63fd8d7 100755
--- a/generation.sh
+++ b/generation.sh
@@ -17,6 +17,6 @@ filename="sequence"
 prefix="curesim_"
 
 Rscript src/repertoire.r "$sequences" "$number_of_reads" &&
-	java -jar tools/CuReSim.jar -f "$data_directory$filename$fastq" -o "$data_directory$prefix$filename$fastq"
+	CuReSim -f "$data_directory$filename$fastq" -o "$data_directory$prefix$filename$fastq"
 Rscript src/alignment.r
 rm "$data_directory/log.txt"
diff --git a/shell.nix b/shell.nix
index a57793e..6057869 100644
--- a/shell.nix
+++ b/shell.nix
@@ -2,7 +2,35 @@
 
 with pkgs;
 
-mkShell {
-  buildInputs =
-    [ R rPackages.immuneSIM rPackages.Biostrings rPackages.stringr jdk ];
+let
+  CuReSim = stdenv.mkDerivation rec {
+    name = "CuReSim";
+    version = "1.3";
+    src = fetchzip {
+      url =
+        "http://www.pegase-biosciences.com/wp-content/uploads/2015/08/${name}${version}.zip";
+      sha256 = "1hvlpgy4haqgqq52mkxhcl9i1fx67kgwi6f1mijvqzk0xff77hkp";
+      stripRoot = true;
+      extraPostFetch = ''
+        chmod go-w $out
+      '';
+    };
+
+    nativeBuildInputs = [ makeWrapper ];
+
+    installPhase = ''
+      mkdir -pv $out/share/java $out/bin
+      cp -r ${src} $out/share/java/${name}
+      makeWrapper ${pkgs.jdk}/bin/java $out/bin/CuReSim --add-flags "-jar $out/share/java/${name}/${name}.jar"
+    '';
+  };
+in mkShell {
+  buildInputs = [
+    R
+    rPackages.immuneSIM
+    rPackages.Biostrings
+    rPackages.stringr
+    jdk
+    CuReSim
+  ];
 }