Rebuild MaSuRCA recipe (#51662)

* Rebuild MaSuRCA recipe * masurca: add aarch64 build * revert linux-aarch64
bioconda · Oct 25, 2024 · e455067 · e455067
1 parent e735f95
commit e455067
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Showing 3 changed files with 37 additions and 16 deletions.
diff --git a/recipes/masurca/0001-install.sh.patch b/recipes/masurca/0001-install.sh.patch
@@ -0,0 +1,14 @@
+diff --git a/install.sh b/install.sh
+index c30290e..0bce5d1 100755
+--- a/install.sh
++++ b/install.sh
+@@ -17,7 +17,7 @@ export NUM_THREADS=`grep -c '^processor' /proc/cpuinfo 2>/dev/null || sysctl -n
+ BINDIR=$DEST/bin
+ LIBDIR=$DEST/lib
+ export PKG_CONFIG_PATH=$LIBDIR/pkgconfig:$PKG_CONFIG_PATH
+-(cd global-1 && ./configure --prefix=$DEST --bindir=$BINDIR --libdir=$LIBDIR && make -j $NUM_THREADS install-special)
++(cd global-1 && autoreconf -if && ./configure --prefix=$DEST --bindir=$BINDIR --libdir=$LIBDIR && make -j $NUM_THREADS install-special)
+ echo "creating example config file masurca_config_example.txt"
+ $BINDIR/masurca -g masurca_config_example.txt
+-(cd Flye && make && cp -a ../Flye $DEST);
++(cd Flye && make && cp -arf ../Flye $DEST);
diff --git a/recipes/masurca/build.sh b/recipes/masurca/build.sh
@@ -1,13 +1,14 @@
 #!/usr/bin/env bash
 
 set -x -e
-BOOST_ROOT=${PREFIX}
-export DEST=${PREFIX}
+BOOST_ROOT="${PREFIX}"
+export DEST="${PREFIX}"
 export PERL_EXT_CPPFLAGS="-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector"
-export PERL_EXT_LDFLAGS="-shared -O2 -fstack-protector"
-export LDFLAGS="-L${PREFIX}/lib"
-export LIBRARY_PATH="$PREFIX/lib"
-export CPATH=${PREFIX}/include
-export CFLAGS="${CFLAGS} -std=gnu90 ${LDFLAGS}"
-export CXXFLAGS="$CXXFLAGS -std=gnu++14 ${LDFLAGS}"
+export PERL_EXT_LDFLAGS="-shared -O3 -fstack-protector"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export LIBRARY_PATH="${PREFIX}/lib"
+export INCLUDE_PATH="${PREFIX}/include"
+export CPATH="${PREFIX}/include"
+export CFLAGS="${CFLAGS} -O3 -std=gnu90 ${LDFLAGS}"
+export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -I${PREFIX}/include ${LDFLAGS}"
 ./install.sh
diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml
@@ -8,26 +8,30 @@ package:
 source:
   url: https://github.com/alekseyzimin/masurca/releases/download/v{{ version }}/MaSuRCA-{{ version }}.tar.gz
   sha256: 8758f6196bf7f57e24e08bda84abddfff08feb4cea204c0eb5e1cb9fe8198573
+  patches:
+    - 0001-install.sh.patch
 
 build:
-  number: 1
+  number: 2
   skip: True  # [osx]
   run_exports:
-    - {{ pin_subpackage(name, max_pin='x.x') }}
+    - {{ pin_subpackage(name, max_pin='x') }}
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - make
+    - automake
+    - autoconf
+    - libtool
+    - pkg-config
   host:
     - zlib
     - bzip2
     - boost-cpp
-    - perl
     - yaggo
   run:
-    - zlib
     - boost-cpp
     - perl
     - grep
@@ -40,10 +44,12 @@ test:
     - masurca --help
 
 about:
-  home: http://masurca.blogspot.co.uk/
-  license: GPL-3.0-only
-  license_family: GPL
-  license_file: LICENSE.txt
+  home: "https://masurca.blogspot.co.uk"
+  license: "GPL-3.0-only"
+  license_family: GPL3
+  license_file: "LICENSE.txt"
+  dev_url: "https://github.com/alekseyzimin/masurca"
+  doc_url: "https://github.com/alekseyzimin/masurca/blob/v{{ version }}/README.md"
   summary:
     MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software.
     MaSuRCA requires Illumina data, and supports third-generation PacBio/Nanopore