Add FMSI (#51277)

* Initial version of adding FMSI to bioconda. * Corrected LICENSE. * FMSI recipe: do not build SDSL but have it as dependency. * clean up recipe * clean up recipe * clean up recipe * try patching makefile * add patches section * edit chmod command * do not build on aarch64/arm64 * add D_LIBCPP_DISABLE_AVAILABILITY * linux-aarch64 build --------- Co-authored-by: mencian <[email protected]> Co-authored-by: Joshua Zhuang <[email protected]>
bioconda · Oct 16, 2024 · a4d30f9 · a4d30f9
1 parent 5026036
commit a4d30f9
Show file tree

Hide file tree

Showing 4 changed files with 105 additions and 0 deletions.
diff --git a/recipes/fmsi/0001-Makefile.patch b/recipes/fmsi/0001-Makefile.patch
@@ -0,0 +1,29 @@
+diff --git a/src/Makefile b/src/Makefile
+index 6272ad5..473407a 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,10 +1,10 @@
+ .PHONY: all clean 
+-CXX=									g++
+-CXXFLAGS=							-g -Wall -Wno-unused-function -std=c++17 -O2
+-PROG=									../fmsi
+-INCLUDES-PATH?=.
++CXX=									${CXX}
++CXXFLAGS=							-g -Wall -Wno-unused-function -std=c++17 -O3
++PROG=									${PREFIX}/bin/fmsi
++INCLUDES-PATH?=							${PREFIX}
+ INCLUDES=							-I$(INCLUDES-PATH)/include -L$(INCLUDES-PATH)/lib 
+-LIBS=									-lz -lsdsl -ldivsufsort -ldivsufsort64
++LIBS+=									-lz -lsdsl -ldivsufsort -ldivsufsort64 -L${PREFIX}/lib
+
+ all:$(PROG)
+
+@@ -14,7 +14,7 @@ include/sdsl/suffix_arrays.hpp: sdsl-lite/build/Makefile
+ 	$(MAKE) -C sdsl-lite/build install
+
+ sdsl-lite/build/Makefile:
+-	cd sdsl-lite/build && cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=../.. ..
++	cd sdsl-lite/build && cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=${PREFIX} ..
+
+
+ $(PROG): $(wildcard *.cpp *.c *.h) ./include/sdsl/suffix_arrays.hpp version.h
diff --git a/recipes/fmsi/0002-version.patch b/recipes/fmsi/0002-version.patch
@@ -0,0 +1,7 @@
+diff --git a/src/version b/src/version
+index ee1372d..abd4105 100644
+--- a/src/version
++++ b/src/version
+@@ -1 +1 @@
+-0.2.2
++${PKG_VERSION}
diff --git a/recipes/fmsi/build.sh b/recipes/fmsi/build.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+mkdir -p ${PREFIX}/bin
+
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+else
+	export CXXFLAGS="${CXXFLAGS}"
+fi
+
+make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" \
+	CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}" \
+	-j"${CPU_COUNT}"
+
+chmod 0755 ${PREFIX}/bin/fmsi
diff --git a/recipes/fmsi/meta.yaml b/recipes/fmsi/meta.yaml
@@ -0,0 +1,49 @@
+{% set version = "0.2.4" %}
+{% set sha256 = "67c930b8bad30e786fb7a59cc8592e1a7231024debc95af7e2c203bb7022b0b3" %}
+
+package:
+  name: fmsi
+  version: {{ version }}
+
+source:
+  url: https://github.com/OndrejSladky/fmsi/archive/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+  patches:
+    - 0001-Makefile.patch
+    - 0002-version.patch
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('fmsi', max_pin="x.x") }}
+
+requirements:
+  build:
+    - make
+    - cmake
+    - {{ compiler('cxx') }}
+  host:
+    - zlib
+    - sdsl-lite
+  run:
+    - sdsl-lite
+
+test:
+  commands:
+    - fmsi -h 2>&1 | grep "FMSI"
+
+about:
+  home: "https://github.com/OndrejSladky/fmsi"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: "FMSI - memory efficient k-mer set index based on masked superstrings and Burrows-Wheeler transform."
+  dev_url: "https://github.com/OndrejSladky/fmsi"
+  doc_url: "https://github.com/OndrejSladky/fmsi/blob/v{{ version }}/README.md"
+
+extra:
+  identifiers:
+    - doi:10.1101/2024.03.06.583483
+    - doi:10.1101/2023.02.01.526717
+  additional-platforms:
+    - linux-aarch64