CVS commit: pkgsrc/biology/fasttree

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Wed Dec  4 13:38:32 UTC 2024

Added Files:
        pkgsrc/biology/fasttree: DESCR Makefile PLIST distinfo
        pkgsrc/biology/fasttree/files: Makefile
        pkgsrc/biology/fasttree/patches: patch-FastTree-2.1.11.c

Log Message:
biology/fasttree: Phylogenetic trees from alignments

FastTree infers approximately-maximum-likelihood phylogenetic trees
from alignments of nucleotide or protein sequences. FastTree can
handle alignments with up to a million of sequences in a reasonable
amount of time and memory.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/fasttree/DESCR \
    pkgsrc/biology/fasttree/Makefile pkgsrc/biology/fasttree/PLIST \
    pkgsrc/biology/fasttree/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/fasttree/files/Makefile
cvs rdiff -u -r0 -r1.1 \
    pkgsrc/biology/fasttree/patches/patch-FastTree-2.1.11.c

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Added files:

Index: pkgsrc/biology/fasttree/DESCR
diff -u /dev/null pkgsrc/biology/fasttree/DESCR:1.1
--- /dev/null   Wed Dec  4 13:38:32 2024
+++ pkgsrc/biology/fasttree/DESCR       Wed Dec  4 13:38:31 2024
@@ -0,0 +1,4 @@
+FastTree infers approximately-maximum-likelihood phylogenetic trees
+from alignments of nucleotide or protein sequences. FastTree can
+handle alignments with up to a million of sequences in a reasonable
+amount of time and memory.
Index: pkgsrc/biology/fasttree/Makefile
diff -u /dev/null pkgsrc/biology/fasttree/Makefile:1.1
--- /dev/null   Wed Dec  4 13:38:32 2024
+++ pkgsrc/biology/fasttree/Makefile    Wed Dec  4 13:38:32 2024
@@ -0,0 +1,31 @@
+# $NetBSD: Makefile,v 1.1 2024/12/04 13:38:32 bacon Exp $
+
+DISTNAME=      FastTree-2.1.11
+CATEGORIES=    biology
+MASTER_SITES=  http://www.microbesonline.org/fasttree/
+EXTRACT_SUFX=  .c
+
+MAINTAINER=    bacon%NetBSD.org@localhost
+HOMEPAGE=      http://www.microbesonline.org/fasttree/
+COMMENT=       Approximately-maximum-likelihood phylogenetic trees from alignments
+LICENSE=       gnu-gpl-v2
+
+WRKSRC=                ${WRKDIR}
+
+.include "../../mk/bsd.prefs.mk"
+
+# Xcode supports -Xpreprocessor -fopenmp, but does not supply OpenMP libs
+.if ${OPSYS} == Darwin
+SUBST_CLASSES+=                openmp
+SUBST_SED.openmp=      -e 's|-fopenmp|-Xpreprocessor &|g'
+SUBST_STAGE.openmp=    pre-configure
+SUBST_FILES.openmp=    Makefile
+LDFLAGS+=              -L${PREFIX}/lib -lomp -lm
+.include "../../parallel/openmp/buildlink3.mk"
+.endif
+
+do-extract:
+       ${CP} ${DISTDIR}/${DISTFILES} ${WRKSRC}
+       ${CP} ${FILESDIR}/Makefile ${WRKSRC}
+
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/fasttree/PLIST
diff -u /dev/null pkgsrc/biology/fasttree/PLIST:1.1
--- /dev/null   Wed Dec  4 13:38:32 2024
+++ pkgsrc/biology/fasttree/PLIST       Wed Dec  4 13:38:32 2024
@@ -0,0 +1,2 @@
+@comment $NetBSD: PLIST,v 1.1 2024/12/04 13:38:32 bacon Exp $
+bin/FastTree
Index: pkgsrc/biology/fasttree/distinfo
diff -u /dev/null pkgsrc/biology/fasttree/distinfo:1.1
--- /dev/null   Wed Dec  4 13:38:32 2024
+++ pkgsrc/biology/fasttree/distinfo    Wed Dec  4 13:38:32 2024
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2024/12/04 13:38:32 bacon Exp $
+
+BLAKE2s (FastTree-2.1.11.c) = 276512fabf950e9c592f2ca750e2bb0054b8970a997a5751b38f878b7b6a6d34
+SHA512 (FastTree-2.1.11.c) = 2bbb1cc078b04125a55b8c02f65c9fbfb6db894c2fbfdaac8f86cc0084f2579723cdc4f6aa63bf4338b767d0fdaffa8dd503e4126c3f5f700d4f3da9fc085ee5
+Size (FastTree-2.1.11.c) = 395543 bytes
+SHA1 (patch-FastTree-2.1.11.c) = 58b86d03fbc5b535503580222f91b1c1fc12b593

Index: pkgsrc/biology/fasttree/files/Makefile
diff -u /dev/null pkgsrc/biology/fasttree/files/Makefile:1.1
--- /dev/null   Wed Dec  4 13:38:32 2024
+++ pkgsrc/biology/fasttree/files/Makefile      Wed Dec  4 13:38:32 2024
@@ -0,0 +1,24 @@
+
+BIN =          FastTree
+SRC =          FastTree*.c
+CC ?=          gcc
+CFLAGS ?=      -O3
+CFLAGS +=      -DOPENMP -fopenmp
+
+MKDIR ?=       mkdir
+INSTALL ?=     install
+PREFIX ?=      /usr/local
+
+.PHONY:        all install clean
+
+all:   ${BIN}
+
+${BIN}: ${SRC} Makefile
+       ${CC} ${CFLAGS} ${SRC} -o ${BIN} ${LDFLAGS} -lm
+
+install: ${BIN}
+       ${MKDIR} -p ${DESTDIR}${PREFIX}/bin
+       ${INSTALL} -s -c ${BIN} ${DESTDIR}${PREFIX}/bin
+
+clean:
+       ${RM} -f ${BIN}

Index: pkgsrc/biology/fasttree/patches/patch-FastTree-2.1.11.c
diff -u /dev/null pkgsrc/biology/fasttree/patches/patch-FastTree-2.1.11.c:1.1
--- /dev/null   Wed Dec  4 13:38:32 2024
+++ pkgsrc/biology/fasttree/patches/patch-FastTree-2.1.11.c     Wed Dec  4 13:38:32 2024
@@ -0,0 +1,15 @@
+$NetBSD: patch-FastTree-2.1.11.c,v 1.1 2024/12/04 13:38:32 bacon Exp $
+
+# Ensure assumed alignment
+
+--- FastTree-2.1.11.c.orig     2024-12-03 14:56:25.897785201 +0000
++++ FastTree-2.1.11.c
+@@ -8782,7 +8782,7 @@ double pnorm(double x)
+ 
+ void *mymalloc(size_t sz) {
+   if (sz == 0) return(NULL);
+-  void *new = malloc(sz);
++  void *new = aligned_alloc(16, sz);
+   if (new == NULL) {
+     fprintf(stderr, "Out of memory\n");
+     exit(1);