diff --git a/biology/Makefile b/biology/Makefile index 6044da1ad279..e113e4078e36 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,176 +1,177 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += consed SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm SUBDIR += haplohseq SUBDIR += hhsuite SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-DB-EMBL SUBDIR += p5-Bio-DB-NCBIHelper SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-Bio-Variation SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml + SUBDIR += plink SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += tophat SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += wise .include diff --git a/biology/plink/Makefile b/biology/plink/Makefile new file mode 100644 index 000000000000..e8c5ee1d5c5b --- /dev/null +++ b/biology/plink/Makefile @@ -0,0 +1,57 @@ +# $FreeBSD$ + +PORTNAME= plink +DISTVERSIONPREFIX= v +DISTVERSION= 1.90b6.17 +CATEGORIES= biology + +MAINTAINER= mzaki@e-mail.ne.jp +COMMENT= Whole genome association analysis toolset + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +NOT_FOR_ARCHS= aarch64 mips64 powerpc64 sparc64 +NOT_FOR_ARCHS_REASON= 64bit code requires SSE2 instructions + +USES= gmake fortran + +USE_GITHUB= yes +GH_ACCOUNT= chrchang +GH_PROJECT= plink-ng +GH_TAGNAME= 79b2df8c + +WRKSRC_SUBDIR= 1.9 +MAKEFILE= Makefile.std +MAKE_ARGS= ZLIB=-lz BLASFLAGS="${BLASLIB} ${LAPACKLIB}" +CFLAGS+= -DDYNAMIC_ZLIB -I${LOCALBASE}/include +LDFLAGS+= -lthr +INSTALL_TARGET= install-strip + +OPTIONS_DEFINE= EXAMPLES +OPTIONS_SINGLE= BLAS +OPTIONS_SINGLE_BLAS= NETLIB OPENBLAS +OPTIONS_DEFAULT= OPENBLAS + +BLAS_DESC= BLAS/LAPACK implementation + +OPENBLAS_USES= blaslapack:openblas + +NETLIB_DESC= Netlib's reference +NETLIB_USES= blaslapack:netlib +NETLIB_LIB_DEPENDS= libcblas.so:math/cblas +NETLIB_LDFLAGS= -lcblas + +EXAMPLES= toy.map toy.ped + +post-build: + (cd ${WRKSRC}; ${CC} ${CFLAGS} prettify.c -o prettify) + +post-install: + ${INSTALL_PROGRAM} ${WRKSRC}/prettify ${STAGEDIR}${PREFIX}/bin + +post-install-EXAMPLES-on: + @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} + ${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/,} ${STAGEDIR}${EXAMPLESDIR} + +.include diff --git a/biology/plink/distinfo b/biology/plink/distinfo new file mode 100644 index 000000000000..619b5b786086 --- /dev/null +++ b/biology/plink/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1588630386 +SHA256 (chrchang-plink-ng-v1.90b6.17-79b2df8c_GH0.tar.gz) = 1207dcabb4bf3f3f4ec5b0e4e5d66ec14075e2cd6d45dd318f13dfb8b4e57116 +SIZE (chrchang-plink-ng-v1.90b6.17-79b2df8c_GH0.tar.gz) = 3013121 diff --git a/biology/plink/files/patch-plink__common.h b/biology/plink/files/patch-plink__common.h new file mode 100644 index 000000000000..60701bb60b4e --- /dev/null +++ b/biology/plink/files/patch-plink__common.h @@ -0,0 +1,20 @@ +--- plink_common.h.orig 2020-01-22 01:51:56 UTC ++++ plink_common.h +@@ -122,7 +122,7 @@ + #define EOLN_STR "\n" + #define FOPEN_RB "r" + #define FOPEN_WB "w" +- #ifndef __APPLE__ ++ #if !defined(__APPLE__) && !defined(__FreeBSD__) + // argh + // not sure what the right threshold actually is, but this works for now + // (may break on gcc <3.0? but that shouldn't matter anymore) +@@ -143,7 +143,7 @@ + #define CLZLU __builtin_clzl + #ifndef __LP64__ + // attempt to patch GCC 6 build failure +- #if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8) ++ #if !defined(__FreeBSD__) && (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8) + #ifndef uintptr_t + #define uintptr_t unsigned long + #endif diff --git a/biology/plink/pkg-descr b/biology/plink/pkg-descr new file mode 100644 index 000000000000..ba35b2b902ee --- /dev/null +++ b/biology/plink/pkg-descr @@ -0,0 +1,9 @@ +PLINK is a widely used toolset for genome-wide association studies (GWAS) and +research in population genetics. + +Citation: +Chang et al. (2015) +Second-generation PLINK: rising to the challenge of larger and richer datasets. +GigaScience 4(1) doi:10.1186/s13742-015-0047-8 + +WWW: https://www.cog-genomics.org/plink/ diff --git a/biology/plink/pkg-plist b/biology/plink/pkg-plist new file mode 100644 index 000000000000..c646d6a309ff --- /dev/null +++ b/biology/plink/pkg-plist @@ -0,0 +1,4 @@ +bin/plink +bin/prettify +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.map +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.ped