mirror of
https://github.com/macports/macports-ports.git
synced 2026-07-12 18:20:25 -07:00
Brian D. WeitznerandRenee Otten
5f7ee976cc
* update patch to enable compilation on macOS 15 * remove platform statement from portfile
135 lines
6.0 KiB
Tcl
135 lines
6.0 KiB
Tcl
# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
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PortSystem 1.0
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name ncbi_tools
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categories science
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license public-domain
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maintainers nomaintainer
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version 20120620
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revision 1
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description Blast is a set of tools for doing nucleotide and protein searches
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long_description \
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"${description}"
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homepage https://www.ncbi.nlm.nih.gov/blast/
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fetch.use_epsv no
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master_sites ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${version}
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distname ncbi
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checksums sha256 603c9a4ade2a6f2f8e412558b732924d78fae403d225706e2ac38d553b08073c \
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rmd160 b37a6eda9f370d02632c1497cd66a3ca64aa0a36 \
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size 68428744
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dist_subdir ${name}/${version}
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extract.mkdir yes
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patchfiles patch-fix-build.diff
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use_configure no
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depends_build-append \
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port:tcsh
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build.cmd ${prefix}/bin/tcsh
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build.target
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# Need to clear build args, pre and post, as we aren't using Make
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build.pre_args
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build.post_args
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build.args -f -c ./ncbi/make/makedis.csh
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set binaries \
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[list \
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blastall dosimple gil2bin \
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asn2ff entrcmd idfetch seedtop \
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asn2gb blastcl3 impala seqtest \
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asn2idx blastclust errhdr indexpub tbl2asn \
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asn2xml blastpgp fa2htgs makemat test_regexp \
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asndhuff cdscan fastacmd makeset testcore \
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asntool checksub findspl megablast testobj \
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bl2bag.cgi copymat formatdb ncbisort testval \
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bl2seq formatrpsdb nph-viewgif.cgi taxblast \
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debruijn gene2xml vecscreen \
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demo_regexp getmesh wblast2.REAL \
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demo_regexp_grep getpub rpsblast wblast2_cs.REAL \
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]
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set manpages \
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[list \
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Psequin.1 asnval.1 cleanasn.1 formatdb.1 insdseqget.1 tbl2asn.1 \
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asn2all.1 bl2seq.1 copymat.1 formatrpsdb.1 makemat.1 trna2sap.1 \
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asn2asn.1 ddv.1 gbseqget.1 makeset.1 trna2tbl.1 taxblast.1 \
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asn2ff.1 blastall.1 debruijn.1 gene2xml.1 megablast.1 udv.1 \
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asn2fsa.1 entrez2.1 getmesh.1 nps2gps.1 vecscreen.1 \
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asn2gb.1 blastcl3.1 errhdr.1 getpub.1 rpsblast.1 \
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asn2idx.1 blastclust.1 fa2htgs.1 gil2bin.1 sbtedit.1 \
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asn2xml.1 blastpgp.1 fastacmd.1 idfetch.1 seedtop.1 \
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asndhuff.1 cdscan.1 findspl.1 impala.1 sortbyquote.1 \
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asntool.1 checksub.1 fmerge.1 indexpub.1 spidey.1 \
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]
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set datafiles \
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[list \
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lat_lon_country.txt \
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16SCore.nhr KSesigc.mat UniVec.nhr lat_lon_island.txt \
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16SCore.nin KSesigl.mat UniVec.nin lat_lon_water.txt \
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16SCore.nsq KSgc.flt UniVec.nsq lineages.txt \
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64-matK-FINAL-aligned-DNA.fas.nhr KShopp.flt UniVec_Core.nhr makerpt.prt \
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64-matK-FINAL-aligned-DNA.fas.nin KSkyte.flt UniVec_Core.nin ncbiendo.dat \
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64-matK-FINAL-aligned-DNA.fas.nsq KSmtidk.mat UniVec_Core.nsq ncbipnam.dat \
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64-rbcL-FINAL-aligned-DNA.fas.nhr KSmtk.mat asn2ff.prt ncbipros.dat \
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64-rbcL-FINAL-aligned-DNA.fas.nin KSnsigc.mat autofix.prt ncbiren.dat \
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64-rbcL-FINAL-aligned-DNA.fas.nsq KSnsigl.mat blast.prt ncbirnam.dat \
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BLOSUM45 KSpcc.mat bstdt.prt objprt.prt \
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BLOSUM50 KSpsigc.mat bstdt.val organelle_products.prt \
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BLOSUM62 KSpsigl.mat country_lat_lon.txt product_rules.prt \
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BLOSUM80 KSpur.flt ecnum_ambiguous.txt pubkey.enc \
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BLOSUM90 KSpyr.flt ecnum_deleted.txt rRNA_blast.nal \
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Combined16SrRNA.nhr LSURef_93.fasta.nhr ecnum_replaced.txt rRNAstrand.nal \
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Combined16SrRNA.nin LSURef_93.fasta.nin ecnum_specific.txt seqcode.prt \
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Combined16SrRNA.nsq LSURef_93.fasta.nsq featdef.prt seqcode.val \
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Combined16SrRNA_2-12-2008.nhr PAM250 featdef.val sequin.hlp \
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Combined16SrRNA_2-12-2008.nin PAM30 gc.prt sgmlbb.ent \
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Combined16SrRNA_2-12-2008.nsq PAM70 gc.val taxlist.txt \
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ContactPotential SSURef_93.fasta.nhr humrep.fsa validrules.prt \
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KSat.flt SSURef_93.fasta.nin institution_codes.txt \
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KSchoth.flt SSURef_93.fasta.nsq \
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]
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set ncbi_dir_doc \
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${prefix}/share/doc/${name}
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set ncbi_dir_man \
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${prefix}/share/man/man1
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set ncbi_dir_data \
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${prefix}/share/${name}/data
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destroot {
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xinstall -m 755 -d ${destroot}${ncbi_dir_doc}
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file copy ${worksrcpath}/ncbi/doc ${destroot}${ncbi_dir_doc}
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foreach binary ${binaries} {
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xinstall -m 755 ${worksrcpath}/ncbi/bin/${binary} ${destroot}${prefix}/bin/
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}
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foreach manpage ${manpages} {
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xinstall -m 444 ${worksrcpath}/ncbi/doc/man/${manpage} ${destroot}${ncbi_dir_man}/
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}
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xinstall -m 755 -d ${destroot}${ncbi_dir_data}
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foreach datafile ${datafiles} {
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xinstall -m 444 ${worksrcpath}/ncbi/data/${datafile} ${destroot}${ncbi_dir_data}/
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}
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}
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notes "
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Data files have moved from ${prefix}/data to ${ncbi_dir_data}
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"
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livecheck.type regex
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livecheck.url ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/
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livecheck.regex old/(\[0-9\]+)
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