<pre style='margin:0'>
Christopher Nielsen (mascguy) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/61c92540243c366ae3841db58da2940d0e6327fe">https://github.com/macports/macports-ports/commit/61c92540243c366ae3841db58da2940d0e6327fe</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit 61c92540243c366ae3841db58da2940d0e6327fe
</span>Author: Christopher Nielsen <mascguy@github.com>
AuthorDate: Thu May 27 09:25:18 2021 -0400
<span style='display:block; white-space:pre;color:#404040;'> ncbi_tools: portfile cleanup
</span>---
science/ncbi_tools/Portfile | 142 ++++++++++++++++++++++++++------------------
1 file changed, 84 insertions(+), 58 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/ncbi_tools/Portfile b/science/ncbi_tools/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 9064a0d8db4..0741597574c 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/ncbi_tools/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/ncbi_tools/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,78 +1,105 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# -*- 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
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span> PortSystem 1.0
name ncbi_tools
<span style='display:block; white-space:pre;background:#ffe0e0;'>-version 20120620
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-description blast is a set of tools for doing nucleotide and protein searches
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-maintainers nomaintainer
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-license public-domain
</span> categories science
platforms darwin
<span style='display:block; white-space:pre;background:#e0ffe0;'>+license public-domain
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+maintainers nomaintainer
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+version 20120620
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description Blast is a set of tools for doing nucleotide and protein searches
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ "${description}"
</span> homepage https://www.ncbi.nlm.nih.gov/blast/
<span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span> fetch.use_epsv no
master_sites ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${version}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-distfiles ncbi.tar.gz
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums md5 e84826b8d390ca1ec6d0dfcaaf4cb6aa \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 603c9a4ade2a6f2f8e412558b732924d78fae403d225706e2ac38d553b08073c \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+distname ncbi
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums sha256 603c9a4ade2a6f2f8e412558b732924d78fae403d225706e2ac38d553b08073c \
</span> rmd160 b37a6eda9f370d02632c1497cd66a3ca64aa0a36 \
size 68428744
<span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span> dist_subdir ${name}/${version}
extract.mkdir yes
patchfiles patch-fix-build.diff
use_configure no
<span style='display:block; white-space:pre;background:#ffe0e0;'>-use_parallel_build no
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-build.cmd './ncbi/make/makedis.csh'
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_build-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:tcsh
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+build.cmd ${prefix}/bin/tcsh
</span> build.target
<span style='display:block; white-space:pre;background:#ffe0e0;'>-set binaries "blastall dosimple gil2bin \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asn2ff entrcmd idfetch seedtop \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asn2gb blastcl3 impala seqtest \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asn2idx blastclust errhdr indexpub tbl2asn \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asn2xml blastpgp fa2htgs makemat test_regexp \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asndhuff cdscan fastacmd makeset testcore \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asntool checksub findspl megablast testobj \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-bl2bag.cgi copymat formatdb ncbisort testval \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-bl2seq formatrpsdb nph-viewgif.cgi taxblast \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-debruijn gene2xml vecscreen \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-demo_regexp getmesh wblast2.REAL \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-demo_regexp_grep getpub rpsblast wblast2_cs.REAL"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-set manpages "Psequin.1 asnval.1 cleanasn.1 formatdb.1 insdseqget.1 tbl2asn.1 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asn2all.1 bl2seq.1 copymat.1 formatrpsdb.1 makemat.1 trna2sap.1 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asn2asn.1 ddv.1 gbseqget.1 makeset.1 trna2tbl.1 taxblast.1\
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asn2ff.1 blastall.1 debruijn.1 gene2xml.1 megablast.1 udv.1 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asn2fsa.1 entrez2.1 getmesh.1 nps2gps.1 vecscreen.1 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asn2gb.1 blastcl3.1 errhdr.1 getpub.1 rpsblast.1 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asn2idx.1 blastclust.1 fa2htgs.1 gil2bin.1 sbtedit.1 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asn2xml.1 blastpgp.1 fastacmd.1 idfetch.1 seedtop.1 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asndhuff.1 cdscan.1 findspl.1 impala.1 sortbyquote.1 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-asntool.1 checksub.1 fmerge.1 indexpub.1 spidey.1"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-set datafiles "lat_lon_country.txt \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-16SCore.nhr KSesigc.mat UniVec.nhr lat_lon_island.txt \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-16SCore.nin KSesigl.mat UniVec.nin lat_lon_water.txt \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-16SCore.nsq KSgc.flt UniVec.nsq lineages.txt \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-64-matK-FINAL-aligned-DNA.fas.nhr KShopp.flt UniVec_Core.nhr makerpt.prt \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-64-matK-FINAL-aligned-DNA.fas.nin KSkyte.flt UniVec_Core.nin ncbiendo.dat \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-64-matK-FINAL-aligned-DNA.fas.nsq KSmtidk.mat UniVec_Core.nsq ncbipnam.dat \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-64-rbcL-FINAL-aligned-DNA.fas.nhr KSmtk.mat asn2ff.prt ncbipros.dat \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-64-rbcL-FINAL-aligned-DNA.fas.nin KSnsigc.mat autofix.prt ncbiren.dat \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-64-rbcL-FINAL-aligned-DNA.fas.nsq KSnsigl.mat blast.prt ncbirnam.dat \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-BLOSUM45 KSpcc.mat bstdt.prt objprt.prt \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-BLOSUM50 KSpsigc.mat bstdt.val organelle_products.prt \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-BLOSUM62 KSpsigl.mat country_lat_lon.txt product_rules.prt \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-BLOSUM80 KSpur.flt ecnum_ambiguous.txt pubkey.enc \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-BLOSUM90 KSpyr.flt ecnum_deleted.txt rRNA_blast.nal \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Combined16SrRNA.nhr LSURef_93.fasta.nhr ecnum_replaced.txt rRNAstrand.nal \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Combined16SrRNA.nin LSURef_93.fasta.nin ecnum_specific.txt seqcode.prt \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Combined16SrRNA.nsq LSURef_93.fasta.nsq featdef.prt seqcode.val \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Combined16SrRNA_2-12-2008.nhr PAM250 featdef.val sequin.hlp \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Combined16SrRNA_2-12-2008.nin PAM30 gc.prt sgmlbb.ent \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Combined16SrRNA_2-12-2008.nsq PAM70 gc.val taxlist.txt \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-ContactPotential SSURef_93.fasta.nhr humrep.fsa validrules.prt \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-KSat.flt SSURef_93.fasta.nin institution_codes.txt \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-KSchoth.flt SSURef_93.fasta.nsq"
</span>
<span style='display:block; white-space:pre;background:#e0ffe0;'>+# Need to clear all build args, include pre and post, as we aren't using Make
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+build.pre_args
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+build.post_args
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+build.args -c ./ncbi/make/makedis.csh
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+set binaries \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+[list \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ blastall dosimple gil2bin \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asn2ff entrcmd idfetch seedtop \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asn2gb blastcl3 impala seqtest \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asn2idx blastclust errhdr indexpub tbl2asn \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asn2xml blastpgp fa2htgs makemat test_regexp \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asndhuff cdscan fastacmd makeset testcore \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asntool checksub findspl megablast testobj \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bl2bag.cgi copymat formatdb ncbisort testval \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bl2seq formatrpsdb nph-viewgif.cgi taxblast \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ debruijn gene2xml vecscreen \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ demo_regexp getmesh wblast2.REAL \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ demo_regexp_grep getpub rpsblast wblast2_cs.REAL\
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+set manpages \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+[list \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Psequin.1 asnval.1 cleanasn.1 formatdb.1 insdseqget.1 tbl2asn.1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asn2all.1 bl2seq.1 copymat.1 formatrpsdb.1 makemat.1 trna2sap.1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asn2asn.1 ddv.1 gbseqget.1 makeset.1 trna2tbl.1 taxblast.1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asn2ff.1 blastall.1 debruijn.1 gene2xml.1 megablast.1 udv.1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asn2fsa.1 entrez2.1 getmesh.1 nps2gps.1 vecscreen.1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asn2gb.1 blastcl3.1 errhdr.1 getpub.1 rpsblast.1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asn2idx.1 blastclust.1 fa2htgs.1 gil2bin.1 sbtedit.1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asn2xml.1 blastpgp.1 fastacmd.1 idfetch.1 seedtop.1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asndhuff.1 cdscan.1 findspl.1 impala.1 sortbyquote.1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ asntool.1 checksub.1 fmerge.1 indexpub.1 spidey.1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+set datafiles \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+[list \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ lat_lon_country.txt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 16SCore.nhr KSesigc.mat UniVec.nhr lat_lon_island.txt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 16SCore.nin KSesigl.mat UniVec.nin lat_lon_water.txt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 16SCore.nsq KSgc.flt UniVec.nsq lineages.txt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 64-matK-FINAL-aligned-DNA.fas.nhr KShopp.flt UniVec_Core.nhr makerpt.prt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 64-matK-FINAL-aligned-DNA.fas.nin KSkyte.flt UniVec_Core.nin ncbiendo.dat \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 64-matK-FINAL-aligned-DNA.fas.nsq KSmtidk.mat UniVec_Core.nsq ncbipnam.dat \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 64-rbcL-FINAL-aligned-DNA.fas.nhr KSmtk.mat asn2ff.prt ncbipros.dat \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 64-rbcL-FINAL-aligned-DNA.fas.nin KSnsigc.mat autofix.prt ncbiren.dat \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 64-rbcL-FINAL-aligned-DNA.fas.nsq KSnsigl.mat blast.prt ncbirnam.dat \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BLOSUM45 KSpcc.mat bstdt.prt objprt.prt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BLOSUM50 KSpsigc.mat bstdt.val organelle_products.prt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BLOSUM62 KSpsigl.mat country_lat_lon.txt product_rules.prt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BLOSUM80 KSpur.flt ecnum_ambiguous.txt pubkey.enc \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BLOSUM90 KSpyr.flt ecnum_deleted.txt rRNA_blast.nal \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Combined16SrRNA.nhr LSURef_93.fasta.nhr ecnum_replaced.txt rRNAstrand.nal \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Combined16SrRNA.nin LSURef_93.fasta.nin ecnum_specific.txt seqcode.prt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Combined16SrRNA.nsq LSURef_93.fasta.nsq featdef.prt seqcode.val \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Combined16SrRNA_2-12-2008.nhr PAM250 featdef.val sequin.hlp \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Combined16SrRNA_2-12-2008.nin PAM30 gc.prt sgmlbb.ent \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Combined16SrRNA_2-12-2008.nsq PAM70 gc.val taxlist.txt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ContactPotential SSURef_93.fasta.nhr humrep.fsa validrules.prt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ KSat.flt SSURef_93.fasta.nin institution_codes.txt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ KSchoth.flt SSURef_93.fasta.nsq \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+]
</span>
destroot {
xinstall -m 755 -d ${destroot}${prefix}/share/doc/${name}
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -89,7 +116,6 @@ destroot {
</span> }
}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-long_description ${description}
</span> livecheck.type regex
livecheck.url ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/
livecheck.regex old/(\[0-9\]+)
</pre><pre style='margin:0'>
</pre>