merge conda-build, unbundle htslib/samtools

amkram · amkram · commit 88e207457504 · 2026-04-07T16:27:23.000-07:00
diff --git a/.gitignore b/.gitignore
@@ -83,3 +83,4 @@ src/3rdparty/samtools/htslib-1.20/**/*.pico
 
 # Generated docs
 site/
+output/
diff --git a/cmake/patch_panman.sh b/cmake/patch_panman.sh
@@ -28,4 +28,14 @@ HEREDOC
     sed -i.bak '1i\
 #include "pair_hash_compat.hpp"
 ' "$SRCDIR/src/common.hpp"
+
+    # Fix parallel_reduce identity type mismatch (oneTBB 2022+ C++20 concepts
+    # require exact type match: 0 is int but lambda returns size_t).
+    # Also fix lambda taking non-const range ref (oneTBB requires const Range&).
+    if [ -f "$SRCDIR/src/summary.cpp" ]; then
+        sed -i.bak \
+            -e 's/children\.size()), 0,/children.size()), (size_t)0,/g' \
+            -e 's/\](tbb::blocked_range<size_t>\& r,/](const tbb::blocked_range<size_t>\& r,/g' \
+            "$SRCDIR/src/summary.cpp"
+    fi
 fi
diff --git a/recipe/CMakeLists.txt b/recipe/CMakeLists.txt
@@ -4,9 +4,8 @@ project(panmap VERSION 0.1.0)
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -pipe -Wno-unused-function -Wno-deprecated-declarations -w")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17 -Wall -pipe -Wno-unused-function -Wno-deprecated-declarations -w")
 
-include(ExternalProject)
 include(GNUInstallDirs)
 
 # ===== Find all system packages =====
@@ -25,7 +24,8 @@ find_library(CAPNP_LIBRARY NAMES capnp REQUIRED)
 find_library(KJ_LIBRARY NAMES kj REQUIRED)
 find_library(DEFLATE_LIBRARY NAMES deflate REQUIRED)
 find_library(ZSTD_LIBRARY NAMES zstd REQUIRED)
-
+find_library(HTS_LIBRARY NAMES hts REQUIRED)
+find_path(HTS_INCLUDE_DIR htslib/hts.h REQUIRED)
 find_program(CAPNP_EXECUTABLE NAMES capnp REQUIRED)
 find_program(CAPNPC_CXX_EXECUTABLE NAMES capnpc-c++ REQUIRED)
 
@@ -102,7 +102,7 @@ execute_process(
 file(WRITE "${PANMAN_SOURCE_DIR}/CMakeLists.txt" [=[
 cmake_minimum_required(VERSION 3.8)
 project(panmanUtils)
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -pipe -Wno-unused-function -Wno-deprecated-declarations -w")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17 -Wall -pipe -Wno-unused-function -Wno-deprecated-declarations -w")
 set(CMAKE_INCLUDE_CURRENT_DIR ON)
 
 find_package(Protobuf REQUIRED)
@@ -190,7 +190,7 @@ endif()
 
 add_custom_command(
     OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/lib/libminimap2.a
-    COMMAND cd ${CMAKE_CURRENT_SOURCE_DIR}/src/3rdparty/minimap2 && make clean && make -j ${MINIMAP2_MAKE_ARGS}
+    COMMAND cd ${CMAKE_CURRENT_SOURCE_DIR}/src/3rdparty/minimap2 && make clean && make -j libminimap2.a "CPPFLAGS=-I${CMAKE_INSTALL_PREFIX}/include" ${MINIMAP2_MAKE_ARGS}
     COMMAND mkdir -p ${CMAKE_CURRENT_BINARY_DIR}/lib ${CMAKE_CURRENT_BINARY_DIR}/bin
     COMMAND cp ${CMAKE_CURRENT_SOURCE_DIR}/src/3rdparty/minimap2/libminimap2.a ${CMAKE_CURRENT_BINARY_DIR}/lib/libminimap2.a
     COMMAND rm -f ${CMAKE_CURRENT_SOURCE_DIR}/src/3rdparty/minimap2/*.o
@@ -202,41 +202,12 @@ add_custom_target(minimap2_target
     COMMENT "Building minimap2 library"
 )
 
-# Htslib
-set(HTSLIB_INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}/htslib_install)
-ExternalProject_Add(htslib_ext
-    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src/3rdparty/samtools/htslib-1.20
-    CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=${HTSLIB_INSTALL_DIR}
-        --disable-lzma --disable-bz2 --disable-libcurl --disable-libdeflate
-    BUILD_COMMAND make -j lib-static
-    INSTALL_COMMAND make install
-    BUILD_IN_SOURCE 1
-    UPDATE_COMMAND ""
-)
-add_library(htslib STATIC IMPORTED GLOBAL)
-set_target_properties(htslib PROPERTIES IMPORTED_LOCATION ${HTSLIB_INSTALL_DIR}/lib/libhts.a)
-add_dependencies(htslib htslib_ext)
-
-# Samtools
-set(SAMTOOLS_BUILD_DIR ${CMAKE_CURRENT_BINARY_DIR}/samtools_build)
-ExternalProject_Add(samtools_ext
-    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src/3rdparty/samtools
-    BINARY_DIR ${SAMTOOLS_BUILD_DIR}
-    CONFIGURE_COMMAND ${CMAKE_COMMAND} -E copy_directory
-        ${CMAKE_CURRENT_SOURCE_DIR}/src/3rdparty/samtools ${SAMTOOLS_BUILD_DIR}
-    BUILD_COMMAND ${CMAKE_COMMAND} -E env
-        "LDFLAGS=-L${HTSLIB_INSTALL_DIR}/lib -lz -lpthread"
-        LD_LIBRARY_PATH=${HTSLIB_INSTALL_DIR}/lib
-        CPPFLAGS=-I${HTSLIB_INSTALL_DIR}/include
-        sh -c "cd ${SAMTOOLS_BUILD_DIR} && autoheader && autoconf && ./configure --with-htslib=${HTSLIB_INSTALL_DIR} --disable-lzma --disable-bz2 --disable-libcurl --disable-shared --with-pic --without-curses && make libst.a"
-    INSTALL_COMMAND ""
-    BUILD_IN_SOURCE 0
-    UPDATE_COMMAND ""
-    DEPENDS htslib_ext
+# Htslib (system/conda package)
+add_library(htslib SHARED IMPORTED GLOBAL)
+set_target_properties(htslib PROPERTIES
+    IMPORTED_LOCATION "${HTS_LIBRARY}"
+    INTERFACE_INCLUDE_DIRECTORIES "${HTS_INCLUDE_DIR}"
 )
-add_library(samtools STATIC IMPORTED GLOBAL)
-set_target_properties(samtools PROPERTIES IMPORTED_LOCATION "${SAMTOOLS_BUILD_DIR}/libst.a")
-add_dependencies(samtools samtools_ext)
 
 # BWA
 set(BWA_SOURCES
@@ -263,7 +234,7 @@ set(BWA_SOURCES
 file(GLOB BCFTOOLS_SOURCES src/3rdparty/bcftools/*.c)
 
 # Build dependency targets
-add_custom_target(build-deps DEPENDS htslib_ext samtools_ext minimap2_target capnp_tools)
+add_custom_target(build-deps DEPENDS minimap2_target capnp_tools)
 
 add_library(minimap2 STATIC IMPORTED)
 set_target_properties(minimap2 PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/lib/libminimap2.a")
@@ -275,6 +246,7 @@ target_compile_options(bwa PRIVATE -fPIC -w)
 
 add_library(bcftools STATIC ${BCFTOOLS_SOURCES})
 target_include_directories(bcftools PUBLIC src/3rdparty/bcftools)
+target_include_directories(bcftools PRIVATE ${HTS_INCLUDE_DIR})
 target_compile_options(bcftools PRIVATE -fPIC -w)
 
 # ===== panmap executable =====
@@ -292,7 +264,7 @@ target_sources(panmap PRIVATE ${LITE_CAPNP_GEN_CPP})
 target_include_directories(panmap PRIVATE
     ${CMAKE_CURRENT_BINARY_DIR}
     ${CMAKE_CURRENT_SOURCE_DIR}/src/3rdparty
-    ${HTSLIB_INSTALL_DIR}/include
+    ${HTS_INCLUDE_DIR}
 )
 
 target_link_libraries(panmap PRIVATE
@@ -301,7 +273,6 @@ target_link_libraries(panmap PRIVATE
     bwa
     bcftools
     minimap2
-    samtools
     htslib
     ${CAPNP_LIBRARY}
     ${KJ_LIBRARY}
diff --git a/recipe/build.sh b/recipe/build.sh
@@ -1,5 +1,5 @@
-#!/bin/bash
-set -ex
+#!/usr/bin/env bash
+set -eux
 
 # Copy the recipe's CMakeLists.txt over the upstream one
 cp -f "${RECIPE_DIR}/CMakeLists.txt" "${SRC_DIR}/panmap/CMakeLists.txt"
@@ -20,6 +20,12 @@ cat > "${SRC_DIR}/panmap/external/panman/src/version.hpp" <<'VEOF'
 #endif
 VEOF
 
+# Revert bcftools include paths from vendored htslib to system htslib
+# (upstream bcftools uses <htslib/...>, panmap's fork rewrote them to relative paths)
+find "${SRC_DIR}/panmap/src/3rdparty/bcftools" \( -name "*.c" -o -name "*.h" \) \
+    -exec sed -i.bak 's|"../samtools/htslib-1.20/htslib/\([^"]*\)"|<htslib/\1>|g' {} +
+find "${SRC_DIR}/panmap/src/3rdparty/bcftools" -name "*.bak" -delete
+
 cd "${SRC_DIR}/panmap"
 
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
@@ -58,3 +64,4 @@ cmake --build build -j "${CPU_COUNT}"
 
 install -d "${PREFIX}/bin"
 install -v -m 0755 build/bin/panmap "${PREFIX}/bin/"
+install -v -m 0755 build/panman-build/panmanUtils "${PREFIX}/bin/"
diff --git a/recipe/meta.yaml b/recipe/meta.yaml
@@ -8,59 +8,48 @@ package:
 
 source:
   - url: https://github.com/amkram/panmap/archive/v{{ version }}.tar.gz
-    sha256: fd00bcf2bbf70918d2e79590975f973b653156c91e085b89fdba2b2b8917025e
+    sha256: 5f9d925c348331478fdaa6b1bda6c3f07fc7640c6abdb15024401fab129cd40b
     folder: panmap
   - url: https://github.com/TurakhiaLab/panman/archive/refs/tags/v{{ panman_version }}.tar.gz
     sha256: 6e987799cd4f713f88b6e3ddafa9b59798a210c8ff1d8b59381bbc5fd2661c72
     folder: panman
 
 build:
   number: 0
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - cmake
     - make
-    - autoconf
-    - automake
-    - libtool
   host:
     - zlib
-    - boost-cpp
+    - htslib
+    - libboost-devel
     - libprotobuf
     - tbb-devel
     - capnproto >=1.0
     - jsoncpp
     - spdlog
-    - abseil-cpp
     - zstd
     - libdeflate
     - eigen
-  run:
-    - boost-cpp
-    - libprotobuf
-    - tbb
-    - capnproto >=1.0
-    - jsoncpp
-    - spdlog
-    - fmt
-    - libabseil
-    - zstd
-    - libdeflate
 
 test:
   commands:
     - panmap --help
+    - panmanUtils --help
 
 about:
-  home: "https://github.com/amkram/panmap"
+  home: "https://github.com/amkram/{{ name }}"
   license: "MIT"
   license_family: MIT
   license_file: "panmap/LICENSE"
   summary: "Pangenome-based sequence placement, alignment, and genotyping"
-  dev_url: "https://github.com/amkram/panmap"
+  dev_url: "https://github.com/amkram/{{ name }}"
 
 extra:
   additional-platforms:
diff --git a/recipe/recipe.yaml b/recipe/recipe.yaml
@@ -0,0 +1,64 @@
+context:
+  version: "0.1.0"
+  panman_version: "0.1.4"
+
+package:
+  name: panmap
+  version: ${{ version }}
+
+source:
+  - url: https://github.com/amkram/panmap/archive/v${{ version }}.tar.gz
+    sha256: fd00bcf2bbf70918d2e79590975f973b653156c91e085b89fdba2b2b8917025e
+    target_directory: panmap
+  - url: https://github.com/TurakhiaLab/panman/archive/refs/tags/v${{ panman_version }}.tar.gz
+    sha256: 6e987799cd4f713f88b6e3ddafa9b59798a210c8ff1d8b59381bbc5fd2661c72
+    target_directory: panman
+
+build:
+  number: 0
+  script: build.sh
+
+requirements:
+  build:
+    - ${{ compiler('c') }}
+    - ${{ compiler('cxx') }}
+    - cmake
+    - make
+    - autoconf
+    - automake
+    - libtool
+  host:
+    - zlib
+    - boost-cpp
+    - libprotobuf
+    - tbb-devel
+    - capnproto >=1.0
+    - jsoncpp
+    - spdlog
+    - abseil-cpp
+    - zstd
+    - docopt.cpp
+    - libdeflate
+    - eigen
+  run:
+    - boost-cpp
+    - libprotobuf
+    - tbb
+    - capnproto >=1.0
+    - jsoncpp
+    - spdlog
+    - fmt
+    - libabseil
+    - zstd
+    - libdeflate
+
+tests:
+  - script:
+      - panmap --help
+
+about:
+  homepage: https://github.com/amkram/panmap
+  license: MIT
+  license_file: panmap/LICENSE
+  summary: Pangenome-based sequence placement, alignment, and genotyping
+  repository: https://github.com/amkram/panmap
diff --git a/src/pileup.h b/src/pileup.h
@@ -1,12 +1,4 @@
-#include <htslib/cram.h>
-#include <htslib/faidx.h>
-#include <htslib/hts.h>
-#include <htslib/khash_str2int.h>
-#include <htslib/klist.h>
-#include <htslib/kstring.h>
-#include <htslib/sam.h>
-#include <samtools/bam_plcmd.h>
-#include <samtools/samtools.h>
+#include "samtools_compat.h"
 
 void bam_and_ref_to_mplp(sam_hdr_t *header, bam1_t **bam_lines, int nbams,
                          char *ref_string, int lref, kstring_t *mplp_string);
diff --git a/src/samtools_compat.h b/src/samtools_compat.h

Original file line number	Diff line number	Diff line change
`@@ -83,3 +83,4 @@ src/3rdparty/samtools/htslib-1.20/*/.pico`
`83`	`83`
`84`	`84`	`# Generated docs`
`85`	`85`	`site/`
	`86`	`+output/`