Date: Mon, 8 Oct 2018 07:54:49 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r481520 - in head/biology: . ncbi-cxx-toolkit ncbi-cxx-toolkit/files Message-ID: <201810080754.w987snhi064883@repo.freebsd.org>
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Author: yuri Date: Mon Oct 8 07:54:49 2018 New Revision: 481520 URL: https://svnweb.freebsd.org/changeset/ports/481520 Log: New port: biology/ncbi-cxx-toolkit: NCBI C++ Toolkit Added: head/biology/ncbi-cxx-toolkit/ head/biology/ncbi-cxx-toolkit/Makefile (contents, props changed) head/biology/ncbi-cxx-toolkit/distinfo (contents, props changed) head/biology/ncbi-cxx-toolkit/files/ head/biology/ncbi-cxx-toolkit/files/patch-src_build-system_Makefile.in.top (contents, props changed) head/biology/ncbi-cxx-toolkit/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Mon Oct 8 07:52:50 2018 (r481519) +++ head/biology/Makefile Mon Oct 8 07:54:49 2018 (r481520) @@ -65,6 +65,7 @@ SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ + SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += njplot Added: head/biology/ncbi-cxx-toolkit/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ncbi-cxx-toolkit/Makefile Mon Oct 8 07:54:49 2018 (r481520) @@ -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 <bsd.port.mk> Added: head/biology/ncbi-cxx-toolkit/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ncbi-cxx-toolkit/distinfo Mon Oct 8 07:54:49 2018 (r481520) @@ -0,0 +1,3 @@ +TIMESTAMP = 1538937167 +SHA256 (ncbi_cxx--21_0_0.tar.gz) = 48cc3ae24ca63d1ab1be148e7525e8c5b9f4eaa5eb36d172800784b640a84a4f +SIZE (ncbi_cxx--21_0_0.tar.gz) = 52661343 Added: head/biology/ncbi-cxx-toolkit/files/patch-src_build-system_Makefile.in.top ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ncbi-cxx-toolkit/files/patch-src_build-system_Makefile.in.top Mon Oct 8 07:54:49 2018 (r481520) @@ -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@ Added: head/biology/ncbi-cxx-toolkit/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ncbi-cxx-toolkit/pkg-descr Mon Oct 8 07:54:49 2018 (r481520) @@ -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/
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