refactor conda stuff

2 files changed, 35 insertions, 21 deletions

diff --git a/conda.nix b/conda.nix
index 4006218..daffc8e 100644
--- a/conda.nix
+++ b/conda.nix
@@ -1,19 +1,28 @@
-{pkgs ? import <nixpkgs> {}}:
+{ stdenv, lib, writeScript, conda }:
 
-with pkgs;
+{
+  buildCondaEnv = { depends ? [], run }: stdenv.mkDerivation {
+    name = "conda-env";
+    buildInputs = [ conda ] ++ depends;
+    buildCommand = ''
+      mkdir $out
+      HOME=$out
+      conda-shell-4.3.31 << EOF
+      conda-install
+      ${run}
+      EOF
+    '';
+  };
 
-stdenv.mkDerivation {
-  name = "conda";
-  src = ./conda.nix;
-  phases = [ "buildPhase" ];
-  buildInputs = [ conda ];
-  buildPhase = ''
-    HOME=$TMPDIR
-    conda-shell-4.3.31 << EOF
-    conda-install
-    conda config --add channels bioconda
-    conda install -y bwa
-    bwa
-    EOF
-  '';
+  withCondaEnv = env: run: stdenv.mkDerivation {
+    name = "with-conda-env";
+    buildCommand = ''
+      #!${stdenv.shell}
+      export HOME=${env}
+      ${conda}/bin/conda-shell-4.3.31 << EOF
+      ${run}
+      EOF
+    '';
+  };
 }
+
diff --git a/test.nix b/test.nix
index 84c95b3..dd5ce75 100644
--- a/test.nix
+++ b/test.nix
@@ -3,6 +3,7 @@
 with pkgs;
 
 let
+  conda = callPackage ./conda.nix {};
 
   qsub = drv: lib.overrideDerivation drv ({ ppn ? 1, mem ? 1, walltime ? "24:00:00", args, builder, ... }: {
     builder = "/bin/bash";
@@ -63,10 +64,14 @@ let
     buildCommand = "sleep 5 && echo ${toString x} > $out";
   };
 
+  condaEnv = conda.buildCondaEnv {
+    run = ''
+      conda config --add channels bioconda
+      conda install -y bwa
+    '';
+  };
+
+  condaTest = conda.withCondaEnv condaEnv "bwa";
 
-in stdenv.mkDerivation rec {
-  name = "dummies";
-  dummies = map dummy [1 2 3 4 5];
-  buildCommand = "for f in ${toString dummies} ; cat $f >> $out";
-}
 
+in condaTest