diff --git a/biology/Makefile b/biology/Makefile index 43439e1f4a89..927e88c08f00 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,244 +1,245 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += atac-seq SUBDIR += augustus SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bamutil SUBDIR += barrnap SUBDIR += bbmap + SUBDIR += bcf-score SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bfc SUBDIR += bio-mocha SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc SUBDIR += biolibc-tools SUBDIR += bioparser SUBDIR += biosig SUBDIR += biosoup SUBDIR += biostar-tools SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += edlib SUBDIR += emboss SUBDIR += erminej SUBDIR += exonerate SUBDIR += fasda SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastq-trim SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += flash SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps SUBDIR += gffread SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan 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 += kmcp SUBDIR += lamarc SUBDIR += libbigwig SUBDIR += libcombine SUBDIR += libgff SUBDIR += libgtextutils SUBDIR += libneurosim SUBDIR += libnuml SUBDIR += libsbml SUBDIR += libsedml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += megahit SUBDIR += metaeuk SUBDIR += migrate SUBDIR += minimap2 SUBDIR += mmseqs2 SUBDIR += molden SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-entrez-direct SUBDIR += ncbi-toolkit SUBDIR += ncbi-vdb 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 += pbseqan SUBDIR += peak-classifier SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phyml SUBDIR += picard-tools SUBDIR += plink SUBDIR += pooler SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-PySCeS SUBDIR += py-bcbio-gff SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-biosig SUBDIR += py-bx-python SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-deeptools SUBDIR += py-deeptoolsintervals SUBDIR += py-dna-features-viewer SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-gffutils SUBDIR += py-goatools SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-libnuml SUBDIR += py-libsedml SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-mrcfile SUBDIR += py-multiqc SUBDIR += py-ont-fast5-api SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-py2bit SUBDIR += py-pybigwig SUBDIR += py-pyfaidx SUBDIR += py-pyrodigal SUBDIR += py-pysam SUBDIR += py-python-libsbml SUBDIR += py-pywgsim SUBDIR += py-resdk SUBDIR += py-scikit-bio SUBDIR += py-valerius SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler SUBDIR += readseq SUBDIR += recombine SUBDIR += rna-seq SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables SUBDIR += rubygem-bio-old-biofetch-emulator SUBDIR += rubygem-bio-shell SUBDIR += sam2pairwise SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqan3 SUBDIR += seqio SUBDIR += seqkit SUBDIR += seqtk SUBDIR += sigviewer SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += snpeff SUBDIR += spoa SUBDIR += sra-tools SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += taxonkit SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ucsc-userapps SUBDIR += ugene SUBDIR += unikmer SUBDIR += vcf-split SUBDIR += vcf2hap SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wfa2-lib SUBDIR += wise .include diff --git a/biology/bcf-score/Makefile b/biology/bcf-score/Makefile new file mode 100644 index 000000000000..96207e1f8f84 --- /dev/null +++ b/biology/bcf-score/Makefile @@ -0,0 +1,51 @@ +PORTNAME= bcf-score +DISTVERSION= 1.16 +CATEGORIES= biology +MASTER_SITES= https://software.broadinstitute.org/software/score/ +DISTFILES+= score_${DISTVERSION}-20221221.tar.gz + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Bcftools plugins for GWAS-VCF summary statistics files +WWW= https://software.broadinstitute.org/software/score/ + +LICENSE= MIT + +LIB_DEPENDS= libhts.so:biology/htslib +BUILD_DEPENDS= bash:shells/bash +RUN_DEPENDS= bcftools>=${PORTVERSION}:biology/bcftools + +USES= autoreconf gmake localbase perl5 python:env shebangfix +USE_GITHUB= yes +USE_PERL5= test + +GH_ACCOUNT= samtools +GH_PROJECT= bcftools +GH_TAGNAME= 1.17 +GNU_CONFIGURE= yes +SHEBANG_FILES= misc/* test/test.pl + +post-extract: + @${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins + @${MKDIR} ${WRKSRC}/bcf-score + @${CP} ${WRKDIR}/*.R ${WRKSRC}/bcf-score + +pre-configure: + @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \ + ${WRKSRC}/configure.ac + +# One .so for each .c in the score distfile +do-install: + ${MKDIR} ${STAGEDIR}${PREFIX}/libexec/bcftools + ${INSTALL_PROGRAM} ${WRKSRC}/plugins/blupx.so \ + ${STAGEDIR}${PREFIX}/libexec/bcftools + ${INSTALL_PROGRAM} ${WRKSRC}/plugins/liftover.so \ + ${STAGEDIR}${PREFIX}/libexec/bcftools + ${INSTALL_PROGRAM} ${WRKSRC}/plugins/metal.so \ + ${STAGEDIR}${PREFIX}/libexec/bcftools + ${INSTALL_PROGRAM} ${WRKSRC}/plugins/munge.so \ + ${STAGEDIR}${PREFIX}/libexec/bcftools + ${INSTALL_PROGRAM} ${WRKSRC}/plugins/score.so \ + ${STAGEDIR}${PREFIX}/libexec/bcftools + (cd ${WRKSRC}/bcf-score && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}) + +.include diff --git a/biology/bcf-score/distinfo b/biology/bcf-score/distinfo new file mode 100644 index 000000000000..d343300fb841 --- /dev/null +++ b/biology/bcf-score/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1677335027 +SHA256 (score_1.16-20221221.tar.gz) = f5f7331f2f670ea26cbc48a924e1467ac13c69aaf3b2a56599e3decda9375c0b +SIZE (score_1.16-20221221.tar.gz) = 61927 +SHA256 (samtools-bcftools-1.16-1.17_GH0.tar.gz) = e6fdb4c94b531671ea8a0b00cb9245aa2602f6c4480621e45dac76338f590b9e +SIZE (samtools-bcftools-1.16-1.17_GH0.tar.gz) = 3481344 diff --git a/biology/bcf-score/files/patch-Makefile b/biology/bcf-score/files/patch-Makefile new file mode 100644 index 000000000000..3299954ae45b --- /dev/null +++ b/biology/bcf-score/files/patch-Makefile @@ -0,0 +1,33 @@ +--- Makefile.orig 2021-03-17 09:16:18 UTC ++++ Makefile +@@ -58,13 +58,14 @@ pluginpath = $(plugindir) + # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) + misc_bindir = $(bindir) + +-MKDIR_P = mkdir -p +-INSTALL = install -p +-INSTALL_DATA = $(INSTALL) -m 644 +-INSTALL_DIR = $(MKDIR_P) -m 755 +-INSTALL_MAN = $(INSTALL_DATA) +-INSTALL_PROGRAM = $(INSTALL) +-INSTALL_SCRIPT = $(INSTALL_PROGRAM) ++# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set ++MKDIR_P = mkdir -p ++INSTALL = install -p ++INSTALL_DATA = ${BSD_INSTALL_DATA} ++INSTALL_DIR = $(MKDIR_P) ++INSTALL_MAN = ${BSD_INSTALL_MAN} ++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} ++INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT} + + PROGRAMS = bcftools + MISC_SCRIPTS = \ +@@ -142,7 +143,7 @@ print-version: + ifdef USE_GPL + main.o : EXTRA_CPPFLAGS += -DUSE_GPL + OBJS += polysomy.o peakfit.o +- GSL_LIBS ?= -lgsl -lcblas ++ GSL_LIBS ?= -lgslcblas + endif + + print-%: diff --git a/biology/bcf-score/files/patch-configure.ac b/biology/bcf-score/files/patch-configure.ac new file mode 100644 index 000000000000..ca845d2ad85f --- /dev/null +++ b/biology/bcf-score/files/patch-configure.ac @@ -0,0 +1,11 @@ +--- configure.ac.orig 2018-07-18 08:34:29 UTC ++++ configure.ac +@@ -23,7 +23,7 @@ + # DEALINGS IN THE SOFTWARE. + + dnl Process this file with autoconf to produce a configure script +-AC_INIT([BCFtools], m4_esyscmd_s([./version.sh 2>/dev/null]), ++AC_INIT([BCFtools], [@PORTVERSION@], + [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/]) + AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER + AC_CONFIG_SRCDIR([main.c]) diff --git a/biology/bcf-score/pkg-descr b/biology/bcf-score/pkg-descr new file mode 100644 index 000000000000..2d926613d77b --- /dev/null +++ b/biology/bcf-score/pkg-descr @@ -0,0 +1,3 @@ +Score is a set of tools in the form of a bcftools plugin, for handling +and converting summary statistics files following the GWAS-VCF +specification. diff --git a/biology/bcf-score/pkg-plist b/biology/bcf-score/pkg-plist new file mode 100644 index 000000000000..719a907bf251 --- /dev/null +++ b/biology/bcf-score/pkg-plist @@ -0,0 +1,6 @@ +libexec/bcftools/blupx.so +libexec/bcftools/liftover.so +libexec/bcftools/metal.so +libexec/bcftools/munge.so +libexec/bcftools/score.so +%%DATADIR%%/assoc_plot.R