update d4tools and d4binding (#48077)

* update build * fix lint * update build * update path * bump d4tools build number * bump d4binding to 0.3.11 * clean up recipe * clean up recipe --------- Co-authored-by: Joshua Zhuang <[email protected]> Co-authored-by: mencian <[email protected]>
bioconda · Oct 23, 2024 · cc53905 · cc53905
1 parent e6b4521
commit cc53905
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -772,9 +772,6 @@ recipes/perl-gd
 # sha mismatch when downloading source
 recipes/fmlrc2
 
-# tries to download zlib itself, which fails
-recipes/d4binding
-
 # no matching package named `quickersort` found
 recipes/mudskipper
 

diff --git a/recipes/d4binding/build.sh b/recipes/d4binding/build.sh
@@ -5,8 +5,10 @@ set -x
 # TODO: Remove the following export when pinning is updated and we use
 #       {{ compiler('rust') }} in the recipe.
 export \
-    CARGO_NET_GIT_FETCH_WITH_CLI=true \
-    CARGO_HOME="${BUILD_PREFIX}/.cargo"
+	CARGO_NET_GIT_FETCH_WITH_CLI=true \
+	CARGO_HOME="${BUILD_PREFIX}/.cargo"
+
+cp $RECIPE_DIR/build_htslib.sh d4-hts/build_htslib.sh
 
 cd d4binding 
 ./install.sh
diff --git a/recipes/d4binding/build_htslib.sh b/recipes/d4binding/build_htslib.sh
@@ -0,0 +1,63 @@
+#!/bin/bash
+
+if [ "${DOCS_RS}" = "1" ]
+then
+	exit 0
+fi
+
+set -ex
+
+pushd ${OUT_DIR}
+
+HTSLIB_VERSION=${1}
+
+rm -rf ${OUT_DIR}/htslib
+
+git clone -b ${HTSLIB_VERSION} http://github.com/samtools/htslib.git
+
+cd htslib
+
+cat > config.h << CONFIG_H
+#define HAVE_LIBBZ2 1
+#define HAVE_DRAND48 1
+CONFIG_H
+
+perl -i -pe 's/hfile_libcurl\.o//g' Makefile
+
+function is_musl() {
+	if [ ! -z $(echo $TARGET | grep musl) ]; then 
+		return 0
+	else
+		return 1
+	fi
+}
+
+is_musl && perl -i -pe 's/gcc/musl-gcc/g' Makefile
+
+
+if [ "x${ZLIB_SRC}" != "x" ]
+then
+	tar xz ${ZLIB_SRC}
+else
+	curl -L 'http://github.com/madler/zlib/archive/refs/tags/v1.2.11.tar.gz' | tar xz
+fi
+cd zlib-1.2.11
+is_musl && CC=musl-gcc ./configure || ./configure
+make libz.a
+cp libz.a ..
+cd ..
+
+#The original file in the repo is lacking -L in the curl command so it doen't work
+curl -L http://sourceware.org/pub/bzip2/bzip2-1.0.8.tar.gz | tar xz
+cd bzip2-1.0.8
+is_musl && perl -i -pe 's/gcc/musl-gcc/g' Makefile
+is_musl || perl -i -pe 's/CFLAGS=/CFLAGS=-fPIC /g' Makefile
+make
+cp libbz2.a ..
+cd ..
+
+perl -i -pe 's/CPPFLAGS =/CPPFLAGS = -Izlib-1.2.11 -Ibzip2-1.0.8/g' Makefile
+
+is_musl || perl -i -pe 's/CFLAGS *=/CFLAGS = -fPIC/g' Makefile
+
+make -j8 lib-static
diff --git a/recipes/d4binding/meta.yaml b/recipes/d4binding/meta.yaml
@@ -1,38 +1,44 @@
-{% set version = "0.3.4" %}
+{% set name = "d4binding" %}
+{% set version = "0.3.11" %}
 
 package:
-  name: d4binding
+  name: {{ name }}
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("d4binding", max_pin="x.x") }}
 
 source:
-  # TODO: use formal release number when 0.3.5 is released
-  url: https://github.com/38/d4-format/archive/refs/tags/v{{ version }}-3.tar.gz
-  sha256: 05e1a410b77c34d7d188e69ef607eaa9f0babcc9817c558362203fc3f1f2219c
+  url: https://github.com/38/d4-format/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 376e61c93cfe2efc15f5e74b75214e065e278146555e67b8769818bf49594726
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - rust >=1.30
-    - gcc #[not osx]
+    - gcc  # [not osx]
     - clangdev
     - pkg-config
     - make
     - cmake
   run:
     - starcode
+
 test:
   commands:
     - "true"
 
 about:
   home: https://github.com/38/d4-format
   license: MIT
+  license_family: MIT
   summary: |
-    The C/C++ binding for the D4 file format
+    The C/C++ binding for the D4 file format.
+  dev_url: https://github.com/38/d4-format
+
 extra:
   recipe-maintainers:
     - haohou

diff --git a/recipes/d4tools/meta.yaml b/recipes/d4tools/meta.yaml
@@ -1,15 +1,16 @@
+{% set name = "d4tools" %}
 {% set version = "0.3.11" %}
 
 package:
-  name: d4tools
+  name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/38/d4-format/archive/refs/tags/v{{ version }}.tar.gz
   sha256: 376e61c93cfe2efc15f5e74b75214e065e278146555e67b8769818bf49594726
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('d4tools', max_pin="x.x") }}
 
@@ -35,7 +36,7 @@ about:
   license: MIT
   license_family: MIT
   summary: |
-    The D4 command line utility program
+    The D4 command line utility program.
   dev_url: https://github.com/38/d4-format
 
 extra: