Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 481519) +++ head/biology/Makefile (revision 481520) @@ -1,145 +1,146 @@ # $FreeBSD$ # COMMENT = Biology 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 += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += clustalx SUBDIR += consed SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa 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 += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ + SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += njplot SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene 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 += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pysam 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 += 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 SUBDIR += xmolwt .include Index: head/biology/ncbi-cxx-toolkit/Makefile =================================================================== --- head/biology/ncbi-cxx-toolkit/Makefile (nonexistent) +++ head/biology/ncbi-cxx-toolkit/Makefile (revision 481520) @@ -0,0 +1,31 @@ +# $FreeBSD$ + +PORTNAME= ncbi-cxx-toolkit +DISTVERSION= 21_0_0 +CATEGORIES= biology science devel +MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/2018/Apr_2_2018/ +DISTNAME= ncbi_cxx--${DISTVERSION} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= NCBI C++ Toolkit + +LICENSE= PD +LICENSE_FILE= ${WRKSRC}/doc/public/LICENSE + +LIB_DEPENDS= libpcre.so:devel/pcre +RUN_DEPENDS= bash:shells/bash + +USES= compiler:c++11-lang gmake mysql perl5 python shebangfix ssl +SHEBANG_FILES= src/app/blast/get_species_taxids.sh src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl src/app/winmasker/windowmasker_2.2.22_adapter.py +USE_XORG= x11 xpm + +GNU_CONFIGURE= yes +CONFIGURE_ARGS= --without-debug --with-dll --without-static + +post-install: # autoplist: thousands of files + @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/run_with_lock + @cd ${STAGEDIR}${PREFIX} && \ + ${RMDIR} include/ncbi-tools++/algo/blast/bl2api include/ncbi-tools++/objtools/test && \ + ${FIND} * -type f -or -type l >> ${TMPPLIST} + +.include Property changes on: head/biology/ncbi-cxx-toolkit/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/ncbi-cxx-toolkit/distinfo =================================================================== --- head/biology/ncbi-cxx-toolkit/distinfo (nonexistent) +++ head/biology/ncbi-cxx-toolkit/distinfo (revision 481520) @@ -0,0 +1,3 @@ +TIMESTAMP = 1538937167 +SHA256 (ncbi_cxx--21_0_0.tar.gz) = 48cc3ae24ca63d1ab1be148e7525e8c5b9f4eaa5eb36d172800784b640a84a4f +SIZE (ncbi_cxx--21_0_0.tar.gz) = 52661343 Property changes on: head/biology/ncbi-cxx-toolkit/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/ncbi-cxx-toolkit/files/patch-src_build-system_Makefile.in.top =================================================================== --- head/biology/ncbi-cxx-toolkit/files/patch-src_build-system_Makefile.in.top (nonexistent) +++ head/biology/ncbi-cxx-toolkit/files/patch-src_build-system_Makefile.in.top (revision 481520) @@ -0,0 +1,11 @@ +--- src/build-system/Makefile.in.top.orig 2018-10-08 01:14:08 UTC ++++ src/build-system/Makefile.in.top +@@ -4,7 +4,7 @@ + # include @builddir@/Makefile.mk + include @build_root@/build/Makefile.mk + +-prefix = @prefix@ ++prefix = $(DESTDIR)@prefix@ + exec_prefix = @exec_prefix@ + PACKAGE_NAME = @PACKAGE_NAME@ + bindir = @bindir@ Property changes on: head/biology/ncbi-cxx-toolkit/files/patch-src_build-system_Makefile.in.top ___________________________________________________________________ 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/ncbi-cxx-toolkit/pkg-descr =================================================================== --- head/biology/ncbi-cxx-toolkit/pkg-descr (nonexistent) +++ head/biology/ncbi-cxx-toolkit/pkg-descr (revision 481520) @@ -0,0 +1,24 @@ +NCBI C++ Toolkit provides free, portable, public domain libraries with no +restrictions use. It has been written in the National Center for Biotechnology +Information in Bethesda, MD. + +It is vaguely a successor, or a new generation of biology/ncbi-toolkit. + +It contains: +* Networking and Interprocess Communication (IPC) library +* MultiThreading Library +* CGI and Fast-CGI Library, HTML Generation Library +* SQL Database Access Library, C++ wrapper library for BerkeleyDB +* C++ IOSTREAM Adaptor/Wrapper Library +* GZIP and BZ2 C++ Wrapper Library with IOSTREAM adaptors +* ASN.1 and XML Serialization Library with C++ Code Generator Tool (datatool) +* Date and Time Library +* File System Function Library +* Command-Line Argument, Configuration and Environment Processing Library +* Sequence Alignment Algorithms Library +* BLAST Engine Library +* Biological Sequences Retrieval and Processing Library +* Portable FLTK and OpenGL based GUI and graphic libraries +* XmlWrapp (XML parsing and handling, XSLT, XPath) + +WWW: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ Property changes on: head/biology/ncbi-cxx-toolkit/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