BSD Portsbiology/ncbi-toolkit 2017.01.06_10 FreeBSD
NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
0a79467178- Categories
- biology
- Package size
- 102402.0 KiB, 597001.0 KiB installed
Description
The NCBI (National Center for Biotechnology Information) development toolkit, containing various libraries needed by NCBI applications, as well as a software suite containing, amongst other things, NCBI BLAST 2.0.
From the README:
The NCBI Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI. We make it freely available to the public without restriction to facilitate the use of NCBI by the scientific community. However, please understand that while we feel we have done a high quality job, this is not commercial software.
The documentation lags considerably behind the software and we must make any changes required by our data production needs. Nontheless, many people have found it a useful and stable basis for a number of tools and applications.
In the other systems
The newest version among them is 2017.01.06, as upstream numbers it.
| System | Port | Version | Vulnerabilities | Status | Maintainer | Last update |
|---|---|---|---|---|---|---|
| FreeBSD | biology/ncbi-toolkit | 2017.01.06_10 newest | none known | - | [email protected] | 2026-07-10 |
| DragonFly | biology/ncbi-toolkit | 2017.01.06_9 newest | none known | - | [email protected] | - |
| GhostBSD | biology/ncbi-toolkit | 2017.01.06_10 newest | no data | - | [email protected] | - |
Install
Binary package:
pkg install ncbi-toolkitFrom the ports tree:
cd /usr/ports/biology/ncbi-toolkit/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= ncbi-toolkit>0:biology/ncbi-toolkitPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 2017.01.06_10 | 2017.01.06_10 | 2017.01.06_7 | 2017.01.06_9 | 2017.01.06_10 |
| FreeBSD:14:quarterly | 2017.01.06_10 | 2017.01.06_10 | n/a | 2017.01.06_9 | 2017.01.06_10 |
| FreeBSD:15:latest | 2017.01.06_10 | 2017.01.06_10 | n/a | 2017.01.06_9 | 2017.01.06_9 |
| FreeBSD:15:quarterly | 2017.01.06_10 | 2017.01.06_10 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2017.01.06_10 | 2017.01.06_10 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependency graph
Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.
Dependencies
As this port's Makefile names them.
Library 11
libfontconfig.so: x11-fonts/fontconfiglibgmp.so: math/gmplibgnutls.so: security/gnutlslibhogweed.so: security/nettlelibidn2.so: dns/libidn2libnettle.so: security/nettlelibp11-kit.so: security/p11-kitlibpng.so: graphics/pnglibtasn1.so: security/libtasn1libtspi.so: security/trouserslibunistring.so: devel/libunistring
The full lists below include those, and their dependencies in turn.
Build dependencies 36
- archivers/brotli
- archivers/liblz4
- archivers/zstd
- devel/gettext-runtime
- devel/libffi
- devel/libunistring
- dns/libidn2
- emulators/tpm-emulator
- graphics/jpeg-turbo
- graphics/png
- math/gmp
- print/freetype2
- print/indexinfo
- security/gnutls
- security/libtasn1
- security/nettle
- security/p11-kit
- security/trousers
- textproc/expat2
- x11-fonts/fontconfig
- x11-fonts/libXft
- x11-toolkits/libXaw
- x11-toolkits/libXmu
- x11-toolkits/libXt
- x11-toolkits/open-motif
- x11/libICE
- x11/libSM
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libXpm
- x11/libXrender
- x11/libxcb
- x11/xbitmaps
- x11/xorgproto
Run dependencies 36
- archivers/brotli
- archivers/liblz4
- archivers/zstd
- devel/gettext-runtime
- devel/libffi
- devel/libunistring
- dns/libidn2
- emulators/tpm-emulator
- graphics/jpeg-turbo
- graphics/png
- math/gmp
- print/freetype2
- print/indexinfo
- security/gnutls
- security/libtasn1
- security/nettle
- security/p11-kit
- security/trousers
- textproc/expat2
- x11-fonts/fontconfig
- x11-fonts/libXft
- x11-toolkits/libXaw
- x11-toolkits/libXmu
- x11-toolkits/libXt
- x11-toolkits/open-motif
- x11/libICE
- x11/libSM
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libXpm
- x11/libXrender
- x11/libxcb
- x11/xbitmaps
- x11/xorgproto
No port depends on this one.
Configuration
Options name: biology_ncbi-toolkit
| Option | Default | Description |
|---|---|---|
| DOCS | off | Build and/or install documentation |
- USES
- gettext-runtime iconv jpeg motif xorg
- Service scripts
- none
- Conflicts with
- fhist
Message after installing
The data files are installed in "/usr/local/share/ncbi-toolkit". To use them you need to create a .ncbirc file in your home directory with the following lines: [NCBI] Data=/usr/local/share/ncbi-toolkit/
Files
Manual pages 43
- Psequin(1)
- asn2all(1)
- asn2asn(1)
- asn2ff(1)
- asn2fsa(1)
- asn2gb(1)
- asn2idx(1)
- asn2xml(1)
- asndhuff(1)
- asndisc(1)
- asnmacro(1)
- asntool(1)
- asnval(1)
- blastcl3(1)
- cdscan(1)
- checksub(1)
- cleanasn(1)
- ddv(1)
- debruijn(1)
- entrez2(1)
- errhdr(1)
- fa2htgs(1)
- findspl(1)
- fmerge(1)
- gbseqget(1)
- gene2xml(1)
- getmesh(1)
- getpub(1)
- gil2bin(1)
- idfetch(1)
- indexpub(1)
- insdseqget(1)
- makeset(1)
- nps2gps(1)
- sbtedit(1)
- sortbyquote(1)
- spidey(1)
- subfuse(1)
- tbl2asn(1)
- trna2sap(1)
- trna2tbl(1)
- udv(1)
- vecscreen(1)
pkg-plist 821
- bin/Nentrez
- bin/Psequin
- bin/asn2ff
- bin/asn2gb
- bin/asn2idx
- bin/asn2xml
- bin/asndhuff
- bin/asntool
- bin/blastcl3
- bin/cdscan
- bin/checksub
- bin/ddv
- bin/debruijn
- bin/demo_regexp
- bin/demo_regexp_grep
- bin/dosimple
- bin/entrcmd
- bin/entrez2
- bin/errhdr
- bin/fa2htgs
- bin/findspl
- bin/gene2xml
- bin/getmesh
- bin/getpub
- bin/gil2bin
- bin/idfetch
- bin/indexpub
- bin/makeset
- bin/ncbisort
- bin/sbtedit
- bin/seqtest
- bin/tbl2asn
- bin/test_regexp
- bin/testcore
- bin/testobj
- bin/testval
- bin/udv
- bin/vecscreen
- include/ncbi/FSpCompat.h
- include/ncbi/FullPath.h
- include/ncbi/MoreCarbonAccessors.h
- include/ncbi/MoreFilesExtras.h
- include/ncbi/MoreFilesX.h
- include/ncbi/Optimization.h
- include/ncbi/OptimizationEnd.h
- include/ncbi/PubStructAsn.h
- include/ncbi/a2ferr.h
- include/ncbi/a2ferrdf.h
- include/ncbi/a2fstruc.h
- include/ncbi/aacomp.h
- include/ncbi/accentr.h
- include/ncbi/accid1.h
- include/ncbi/accutils.h
- include/ncbi/acerdapi.h
- include/ncbi/aceread.h
- include/ncbi/actutils.h
- include/ncbi/algorend.h
- include/ncbi/alignloc.h
- include/ncbi/alignmgr.h
- include/ncbi/alignmgr2.h
- include/ncbi/alignval.h
- include/ncbi/aliparse.h
- include/ncbi/aliread.h
- include/ncbi/all.h
- include/ncbi/allpub.h
- include/ncbi/apparam.h
- include/ncbi/asn.h
- include/ncbi/asn2ff.h
- include/ncbi/asn2ff6.h
- include/ncbi/asn2ffg.h
- include/ncbi/asn2ffp.h
- include/ncbi/asn2gnbi.h
- include/ncbi/asn2gnbk.h
- include/ncbi/asn2gnbp.h
- include/ncbi/asn2graphic.h
- include/ncbi/asn2graphicp.h
- include/ncbi/asnacces.h
- include/ncbi/asnalign.h
- include/ncbi/asnbibli.h
- include/ncbi/asnblock.h
- include/ncbi/asncode.h
- include/ncbi/asnent2.h
- include/ncbi/asnentgene.h
- include/ncbi/asnfdef.h
- include/ncbi/asnfeat.h
- include/ncbi/asngbseq.h
- include/ncbi/asngen.h
- include/ncbi/asnid0.h
- include/ncbi/asninsdseq.h
- include/ncbi/asnloc.h
- include/ncbi/asnmacro.h
- include/ncbi/asnmdrs.h
- include/ncbi/asnmedli.h
- include/ncbi/asnmim.h
- include/ncbi/asnmime.h
- include/ncbi/asnmla.h
- include/ncbi/asnmla2.h
- include/ncbi/asnneten.h
- include/ncbi/asnproj.h
- include/ncbi/asnprt.h
The first 100 are listed.
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| ncbi-toolkit-2017.01.06/ncbi.tar.gz | 1.55731358e+08 | 4b88aaad8f953b1b50bc7d06f3a5920f0d589d2c9a26c709199f8347905f5867 |
Master sites 1
- ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/