Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 500736) +++ head/biology/Makefile (revision 500737) @@ -1,162 +1,163 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += consed 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 += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm 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 += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac 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-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-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 += 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-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-xenaPython SUBDIR += pycogent 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 += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise .include Index: head/biology/fastp/Makefile =================================================================== --- head/biology/fastp/Makefile (nonexistent) +++ head/biology/fastp/Makefile (revision 500737) @@ -0,0 +1,30 @@ +# $FreeBSD$ + +PORTNAME= fastp +DISTVERSIONPREFIX= v +DISTVERSION= 0.20.0 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Ultra-fast all-in-one FASTQ preprocessor + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= compiler:c++11-lang gmake +USE_GITHUB= yes + +GH_ACCOUNT= OpenGene + +ALL_TARGET= fastp +INSTALL_TARGET= install-strip +PLIST_FILES= bin/fastp + +.include + +# Force newer compiler on platforms using GCC 4.2 as base +.if ${CHOSEN_COMPILER_TYPE} == gcc +USE_GCC= yes +.endif + +.include Property changes on: head/biology/fastp/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/fastp/distinfo =================================================================== --- head/biology/fastp/distinfo (nonexistent) +++ head/biology/fastp/distinfo (revision 500737) @@ -0,0 +1,3 @@ +TIMESTAMP = 1556889058 +SHA256 (OpenGene-fastp-v0.20.0_GH0.tar.gz) = 8d751d2746db11ff233032fc49e3bcc8b53758dd4596fdcf4b4099a4d702ac22 +SIZE (OpenGene-fastp-v0.20.0_GH0.tar.gz) = 139422 Property changes on: head/biology/fastp/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/fastp/files/patch-Makefile =================================================================== --- head/biology/fastp/files/patch-Makefile (nonexistent) +++ head/biology/fastp/files/patch-Makefile (revision 500737) @@ -0,0 +1,34 @@ +--- Makefile.orig 2019-04-17 03:23:22 UTC ++++ Makefile +@@ -3,9 +3,11 @@ DIR_SRC := ./src + DIR_OBJ := ./obj + + PREFIX ?= /usr/local ++DESTDIR ?= + BINDIR ?= $(PREFIX)/bin + INCLUDE_DIRS ?= + LIBRARY_DIRS ?= ++STRIP_CMD ?= strip + + SRC := $(wildcard ${DIR_SRC}/*.cpp) + OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC})) +@@ -15,7 +17,8 @@ TARGET := fastp + BIN_TARGET := ${TARGET} + + CXX ?= g++ +-CXXFLAGS := -std=c++11 -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS} ++CXXFLAGS ?= -g -O3 ++CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) + LIBS := -lz -lpthread + LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS) + +@@ -38,5 +41,8 @@ make_obj_dir: + fi + + install: +- install $(TARGET) $(BINDIR)/$(TARGET) ++ install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET) + @echo "Installed." ++ ++install-strip: install ++ $(STRIP_CMD) $(DESTDIR)$(BINDIR)/$(TARGET) Property changes on: head/biology/fastp/files/patch-Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/fastp/pkg-descr =================================================================== --- head/biology/fastp/pkg-descr (nonexistent) +++ head/biology/fastp/pkg-descr (revision 500737) @@ -0,0 +1,5 @@ +fastp is a tool designed to provide fast all-in-one preprocessing for FastQ +files. This tool is developed in C++ with multithreading supported to afford +high performance. + +WWW: https://github.com/OpenGene/fastp Property changes on: head/biology/fastp/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property