README.org

@@ -1,13 +1,6 @@
 * locigenesis
 
-locigenesis is a tool that generates a human T-cell receptor (TCR), runs it through a sequence reader simulation tool and extracts CDR3.
+locigenesis is a tool that generates an immune repertoire and runs it through a sequence reader simulation tool, to generate sequencing errors.
-
-The goal of this project is to generate both HVR sequences with and without sequencing errors, in order to create datasets for a Machine Learning algorithm.
-
-** Technologies
-
-- [[https://github.com/GreiffLab/immuneSIM/][immuneSIM]]: in silico generation of human and mouse BCR and TCR repertoires
-- [[http://www.pegase-biosciences.com/curesim-a-customized-read-simulator/][CuReSim]]: read simulator that mimics Ion Torrent sequencing
 
 ** Installation
 

shell.nix

@@ -21,10 +21,16 @@ let
     installPhase = ''
       mkdir -pv $out/share/java $out/bin
       cp -r ${src} $out/share/java/${name}
-      makeWrapper ${jre}/bin/java $out/bin/CuReSim --add-flags "-jar $out/share/java/${name}/${name}.jar"
+      makeWrapper ${pkgs.jdk}/bin/java $out/bin/CuReSim --add-flags "-jar $out/share/java/${name}/${name}.jar"
     '';
   };
 in mkShell {
-  buildInputs =
+  buildInputs = [
-    [ R rPackages.immuneSIM rPackages.Biostrings rPackages.stringr CuReSim ];
+    R
+    rPackages.immuneSIM
+    rPackages.Biostrings
+    rPackages.stringr
+    jdk
+    CuReSim
+  ];
 }