From c4777315bcb327e6cd1df9cc09c0afc49271769c Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 23 Oct 2018 22:43:03 +1100
Subject: Allow building bwa-mem with one core

---
 tools/bwa-mem.nix | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

(limited to 'tools')

diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 0d0f7d8..3208e48 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -29,8 +29,7 @@ in stdenv.mkDerivation {
     done
     cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
     if [[ $cores -lt 1 ]] ; then
-      >&2 echo "not enough build cores"
-      exit 1
+      cores=1
     fi
     bwa mem ${optionalString (flags != null) flags} -t $cores ref.fa ${fq input1} \
       ${optionalString (input2 != null) (fq input2)} \
-- 
cgit v1.2.3


From 94cff4f9e392911421cd8b94973b8c1e5698c430 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 24 Oct 2018 07:46:23 +1100
Subject: Fix platypus bug

---
 tools/platypus-callVariants.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'tools')

diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
index a3e3a65..a57aa83 100644
--- a/tools/platypus-callVariants.nix
+++ b/tools/platypus-callVariants.nix
@@ -14,7 +14,7 @@ with bionix.types;
 
 let
   filename = path: last (splitString "/" path);
-  getref = f: matchFiletype "platypus-callVariants" { bam = r: r; } f;
+  getref = f: matchFiletype "platypus-callVariants" { bam = {ref, ...}: ref; } f;
   refs = map getref inputs;
   ref = head refs;
 in
-- 
cgit v1.2.3