From feeb7d65852950b0bb24db64b75a99830dde3bf4 Mon Sep 17 00:00:00 2001
From: Jacob Morrison <jamorrison@users.noreply.github.com>
Date: Fri, 29 Sep 2023 17:18:37 -0500
Subject: [PATCH] Add dupsifter (#43279)

---
 recipes/dupsifter/build.sh  |  7 ++++++
 recipes/dupsifter/meta.yaml | 46 +++++++++++++++++++++++++++++++++++++
 recipes/dupsifter/patch     | 27 ++++++++++++++++++++++
 3 files changed, 80 insertions(+)
 create mode 100644 recipes/dupsifter/build.sh
 create mode 100644 recipes/dupsifter/meta.yaml
 create mode 100644 recipes/dupsifter/patch

diff --git a/recipes/dupsifter/build.sh b/recipes/dupsifter/build.sh
new file mode 100644
index 0000000000000..c34018d532433
--- /dev/null
+++ b/recipes/dupsifter/build.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+BIN=${PREFIX}/bin
+mkdir -p ${BIN}
+
+make CC="$CC $LDFLAGS" CFLAGS="$CFLAGS"
+cp dupsifter ${BIN}
diff --git a/recipes/dupsifter/meta.yaml b/recipes/dupsifter/meta.yaml
new file mode 100644
index 0000000000000..7a256ef424987
--- /dev/null
+++ b/recipes/dupsifter/meta.yaml
@@ -0,0 +1,46 @@
+{% set version = '1.2.0.20230926' %}
+
+package:
+  name: dupsifter
+  version: {{ version }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('dupsifter', max_pin='x') }}
+
+source:
+  url: https://github.com/huishenlab/dupsifter/releases/download/v{{ version }}/release-source.zip
+  sha256: 7a4dfe194d51ac09b30f85f6c77f9e8c31c62e636f56c09748688b32755d9521
+  patches:
+    - patch
+
+requirements:
+  build:
+    - make
+    - {{ compiler('c') }}
+  host:
+    - libcurl
+    - bzip2
+    - xz
+    - zlib
+    - libdeflate
+    - openssl # [not osx]
+    - pthread-stubs
+  run:
+    - libcurl
+    - bzip2
+    - xz
+    - zlib
+    - libdeflate
+    - openssl # [not osx]
+    - pthread-stubs
+
+test:
+  commands:
+    - dupsifter --help 2>&1 | grep dupsifter
+
+about:
+  home: https://github.com/huishenlab/dupsifter
+  license: MIT
+  summary: A tool for PCR duplicate marking of WGBS (and WGS) data
diff --git a/recipes/dupsifter/patch b/recipes/dupsifter/patch
new file mode 100644
index 0000000000000..aba337a5e6d8b
--- /dev/null
+++ b/recipes/dupsifter/patch
@@ -0,0 +1,27 @@
+diff --git a/Makefile b/Makefile
+index f786e73..32df980 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,6 +1,6 @@
+-CC = gcc
+-CFLAGS = -W -Wall -finline-functions -fPIC -std=gnu99 -Wno-unused-result -O3
+-CLIB = -lz -lm -llzma -lbz2 -lcurl
++CC ?= gcc
++CFLAGS ?= -W -Wall -finline-functions -fPIC -std=gnu99 -Wno-unused-result -O3
++CLIB = -lz -lm -llzma -lbz2 -lcurl -lpthread
+ CF_OPTIMIZE = 1
+ 
+ OS := $(shell uname)
+diff --git a/htslib-1.15.1/Makefile b/htslib-1.15.1/Makefile
+index 0871580..e7a313d 100644
+--- a/htslib-1.15.1/Makefile
++++ b/htslib-1.15.1/Makefile
+@@ -22,7 +22,7 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC     = gcc
++CC     ?= gcc
+ AR     = ar
+ RANLIB = ranlib
+