From 33a121a7bad5b2608cc41ce60ab3d65676541fa6 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 20 Sep 2018 13:57:12 +1000
Subject: Wrap some tools and make an example pipeline

---
 test.nix | 89 +++++++++++++++-------------------------------------------------
 1 file changed, 20 insertions(+), 69 deletions(-)

(limited to 'test.nix')

diff --git a/test.nix b/test.nix
index c59f786..6c158c6 100644
--- a/test.nix
+++ b/test.nix
@@ -1,77 +1,28 @@
 {pkgs ? import <nixpkgs> {}}:
 
 with pkgs;
+with lib;
 
 let
-  conda = callPackage ./conda.nix {};
-
-  qsub = drv: lib.overrideDerivation drv ({ ppn ? 1, mem ? 1, walltime ? "24:00:00", args, builder, ... }: {
-    builder = "/bin/bash";
-    args = let
-      script = writeScript "qsub-script" ''
-        #!${stdenv.shell}
-        while [ ! -e /stornext/HPCScratch/$PBS_JOBID ] ; do
-          sleep 5
-        done
-        set -a
-        . /stornext/HPCScratch/$PBS_JOBID
-        set +a
-        TMPDIR=/tmp/$PBS_JOBID
-        TEMP=$TMPDIR
-        TMP=$TMPDIR
-        NIX_BUILD_TOP=$TMPDIR
-        mkdir $TMPDIR
-        cd $TMPDIR
-        rm /stornext/HPCScratch/$PBS_JOBID
-        ${builder} ${lib.escapeShellArgs args} && touch /stornext/HPCScratch/$PBS_JOBID
-        cd /
-        rm -rf $TMPDIR
-      '';
-
-      qsub = writeScript "qsub" ''
-        #!/bin/bash
-        PATH=/usr/bin:/bin:/usr/sbin:/sbin
-        SHELL=/bin/sh
-        NIX_BUILD_CORES=${toString ppn}
-	      id=$(qsub -l nodes=1:ppn=${toString ppn},mem=${toString mem}gb,walltime=${walltime} ${script})
-        set > /stornext/HPCScratch/$id
-        while qstat ''${id%%.} 2> /dev/null > /dev/null ; do
-          sleep 5
-        done
-        if [[ -e /stornext/HPCScratch/$id ]] ; then
-          rm /stornext/HPCScratch/$id
-          exit 0
-        fi
-        exit 1
-      '';
-
-      in [ "-c" qsub ];
-  });
-
-  qstat = stdenv.mkDerivation rec {
-    name = "qstat";
-    buildCommand = "/usr/bin/qstat  > $out";
-  };
-
-  grep = x: stdenv.mkDerivation rec {
-    name = "grep";
-    buildInputs = [ bwa ];
-    buildCommand = "/usr/bin/grep distefano.l ${x} > $out";
-  };
-
-  dummy = x: stdenv.mkDerivation rec {
-    name = "dummy";
-    buildCommand = "sleep 5 && echo ${toString x} > $out";
-  };
-
-  condaEnv = conda.buildCondaEnv {
-    run = ''
-      conda config --add channels bioconda
-      conda install -y bwa
+  ref = ../bioshake/examples/ref.fa;
+  alignWithRG = rg: callPackage ./tools/bwa.nix { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
+  sort = callPackage ./tools/samtools-sort.nix { };
+  callVariants = callPackage ./tools/platypus.nix { inherit ref; };
+
+  samples = [ {name = "mysample1"; files = {input1 = ./example/sample1-1.fq; input2 = ./example/sample1-2.fq;};}
+             {name = "mysample2"; files = {input1 = ./example/sample2-1.fq; input2 = ./example/sample2-1.fq;};} ];
+
+  alignments = map (i: sort (alignWithRG i.name i.files)) samples;
+  variants = callVariants alignments;
+
+  testNaming = stdenv.mkDerivation {
+    name = "test-naming";
+    buildCommand = ''
+      mkdir $out
+      ln -s ${variants} $out/myfancyname
+      mkdir $out/alignments
+      ${concatStringsSep "\n" (zipListsWith (s: a: "ln -s ${a} $out/alignments/${s.name}.bam") samples alignments)}
     '';
   };
 
-  condaTest = conda.inCondaEnv condaEnv "bwa";
-
-
-in condaTest
+in testNaming
-- 
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