add macos conda build

.gitlab-ci.yml

@@ -61,9 +61,16 @@ deploy-checks:
         - if: '$CI_COMMIT_TAG =~ /^v[[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+$/'
 
 conda:
-    extends: .deploy-conda
+    extends: .deploy-conda-linux
     before_script:
         - *prep-image
         - export CONDA_PKG=${CI_PROJECT_NAME}
         - export CONDA_PKG_VERSION=${CI_COMMIT_TAG/v/}
         - cd conda
+
+conda-mac:
+    extends: .deploy-conda-mac
+    before_script:
+        - export CONDA_PKG=${CI_PROJECT_NAME}
+        - export CONDA_PKG_VERSION=${CI_COMMIT_TAG/v/}
+        - cd conda

CHANGELOG.md

@@ -4,6 +4,14 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+
+## [v0.1.1]
+### Fixed
+- Check input files are present and readable rather than segfaulting.
+### Changed
+- Clearer error messaging.
+
+
 ## [v0.1.0]
 
 First release.

Makefile

@@ -1,12 +1,8 @@
 OS := $(shell uname)
 ifeq ($(OS), Darwin)
-	SEDI=sed -i '.bak'
 	# mainly for dev builds using homebrew things
-	export LIBRARY_PATH=/usr/local/Cellar/[email protected]/1.1.1k/lib
-	ARGP ?= /usr/local/Cellar/argp-standalone/1.3/lib/libargp.a
-else
-	SEDI=sed -i
-	ARGP ?=
+    EXTRA_LDFLAGS ?= -L/usr/local/Cellar/[email protected]/1.1.1k/lib
+    ARGP ?= /usr/local/Cellar/argp-standalone/1.3/lib/libargp.a
 endif
 
 CC ?= gcc
@@ -26,7 +22,7 @@ htslib/libhts.a:
 	cd htslib/ \
 		&& autoheader \
 		&& autoconf \
-		&& CFLAGS="$(CFLAGS)" ./configure $(HTS_CONF_ARGS) \
+		&& CFLAGS="$(CFLAGS) $(EXTRA_CFLAGS)" ./configure $(HTS_CONF_ARGS) \
 		&& make -j 4
 
 

README.md

@@ -1,7 +1,7 @@
 Modified-base BAM to bedMethyl
 ------------------------------
 
-Simple demonstration program of aggregating modified base counts stored in a
+Simple program to aggregate modified base counts stored in a
 [modified-base BAM](https://circle-production-customer-artifacts.s3.amazonaws.com/picard/548f4caff7d0cea1406e35e3/60e6b57a449db620ab0ea9b7-0-build/artifacts/pdfs/SAMtags.pdf?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20210725T133456Z&X-Amz-SignedHeaders=host&X-Amz-Expires=60&X-Amz-Credential=AKIAJR3Q6CR467H7Z55A%2F20210725%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Signature=0590263dd0113d97f83c533f1e3633cdba6a9652a8a9f457d6a0eb0d188037ef) (Section 2.1) file to 
 a [bedMethyl](https://www.encodeproject.org/data-standards/wgbs/) file.
 
@@ -10,7 +10,13 @@ The code uses the `methylation` branch of htslib from
 
 ### Installation
 
-Clone the repository and then use make:
+The program is available from our conda channel, so can be installed with:
+
+    mamba create -n modbam2bed -c conda-forge -c epi2melabs modbam2bed
+
+Packages are available for bothe Linux and MacOS.
+
+Alternatively to install from the source code, clone the repository and then use make:
 
     git clone --recursive <repository>
     make modbam2bed

conda/build.sh

@@ -6,6 +6,14 @@ export HTS_CONF_ARGS="--prefix=${PREFIX} --enable-libcurl --with-libdeflate --en
 export EXTRA_CFLAGS="-I$PREFIX/include"
 export EXTRA_LDFLAGS="-L$PREFIX/lib"
 export EXTRA_LIBS="-ldl -ldeflate"
+
+OS=$(uname)
+if [[ "$OS" == "Darwin" ]]; then
+    echo "Setting Darwin args"
+    export ARGP=${PREFIX}/lib/libargp.a
+    export EXTRA_CFLAGS="${EXTRA_CFLAGS} -isysroot ${CONDA_BUILD_SYSROOT} -mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}"
+fi
+
 make clean $NAME
 
 mkdir -p $PREFIX/bin

conda/conda_build_config.yaml

@@ -0,0 +1,2 @@
+CONDA_BUILD_SYSROOT:
+    - /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk  # [osx]

conda/meta.yaml

@@ -13,8 +13,9 @@ requirements:
         - {{ compiler('c') }}
     host:
         - autoconf
+        - argp-standalone # [osx]
         - make
-        - binutils
+        - binutils # [not osx]
         - libcurl
         - bzip2
         - xz
@@ -48,4 +49,3 @@ about:
 extra:
     recipe-maintainers:
         - cjw85
-

src/args.c

@@ -8,7 +8,7 @@
 #include "htslib/faidx.h"
 #include "args.h"
 
-const char *argp_program_version = "0.1.0";
+const char *argp_program_version = "0.1.1";
 const char *argp_program_bug_address = "[email protected]";
 static char doc[] = 
  "modbam2bed -- summarise a BAM with modified base tags to bedMethyl.\