biology/ncbi-toolkit: Update 2012.06.20 -> 2017.01.06

Port changes:
* Take maintainership
* Add to LIB_DEPENDS and USExx
* Remove lists of executables and manpages, use file listing instead (*)
* Update WWW

1 files changed, 55 insertions, 47 deletions

diff --git a/biology/ncbi-toolkit/pkg-plist b/biology/ncbi-toolkit/pkg-plist
index efd3cb71ee07..24f92e502b77 100644
--- a/biology/ncbi-toolkit/pkg-plist
+++ b/biology/ncbi-toolkit/pkg-plist
@@ -6,14 +6,9 @@ bin/asn2idx
 bin/asn2xml
 bin/asndhuff
 bin/asntool
-bin/bl2seq
-bin/blastall
 bin/blastcl3
-bin/blastclust
-bin/blastpgp
 bin/cdscan
 bin/checksub
-bin/copymat
 bin/ddv
 bin/debruijn
 bin/demo_regexp
@@ -23,27 +18,22 @@ bin/entrcmd
 bin/entrez2
 bin/errhdr
 bin/fa2htgs
-bin/fastacmd
 bin/findspl
-bin/formatdb
-bin/formatrpsdb
 bin/gene2xml
 bin/getmesh
 bin/getpub
 bin/gil2bin
 bin/idfetch
-bin/impala
 bin/indexpub
-bin/makemat
 bin/makeset
-bin/megablast
 bin/ncbisort
-bin/rpsblast
 bin/sbtedit
-bin/seedtop
 bin/seqtest
-bin/taxblast
 bin/tbl2asn
+bin/test_regexp
+bin/testcore
+bin/testobj
+bin/testval
 bin/udv
 bin/vecscreen
 include/ncbi/FSpCompat.h
@@ -186,7 +176,10 @@ include/ncbi/connect/ncbi_heapmgr.h
 include/ncbi/connect/ncbi_host_info.h
 include/ncbi/connect/ncbi_host_infop.h
 include/ncbi/connect/ncbi_http_connector.h
+include/ncbi/connect/ncbi_ipv6.h
 include/ncbi/connect/ncbi_lb.h
+include/ncbi/connect/ncbi_lbos.h
+include/ncbi/connect/ncbi_lbosp.h
 include/ncbi/connect/ncbi_lbsmd.h
 include/ncbi/connect/ncbi_local.h
 include/ncbi/connect/ncbi_memory_connector.h
@@ -564,6 +557,7 @@ include/ncbi/xmlblast.h
 lib/ncbi/libblast.a
 lib/ncbi/libblastapi.a
 lib/ncbi/libblastcompadj.a
+lib/ncbi/libconnssl.a
 lib/ncbi/libddvlib.a
 lib/ncbi/libncbi.a
 lib/ncbi/libncbiCacc.a
@@ -586,41 +580,46 @@ lib/ncbi/libvibgif.a
 lib/ncbi/libvibnet.a
 lib/ncbi/libvibrant.a
 man/man1/Psequin.1.gz
+man/man1/asn2all.1.gz
+man/man1/asn2asn.1.gz
 man/man1/asn2ff.1.gz
+man/man1/asn2fsa.1.gz
+man/man1/asn2gb.1.gz
 man/man1/asn2idx.1.gz
 man/man1/asn2xml.1.gz
 man/man1/asndhuff.1.gz
+man/man1/asndisc.1.gz
+man/man1/asnmacro.1.gz
 man/man1/asntool.1.gz
-man/man1/bl2seq.1.gz
-man/man1/blast.1.gz
-man/man1/blastall.1.gz
+man/man1/asnval.1.gz
 man/man1/blastcl3.1.gz
-man/man1/blastclust.1.gz
-man/man1/blastpgp.1.gz
 man/man1/cdscan.1.gz
 man/man1/checksub.1.gz
-man/man1/copymat.1.gz
+man/man1/cleanasn.1.gz
 man/man1/ddv.1.gz
 man/man1/debruijn.1.gz
 man/man1/entrez2.1.gz
 man/man1/errhdr.1.gz
 man/man1/fa2htgs.1.gz
-man/man1/fastacmd.1.gz
 man/man1/findspl.1.gz
-man/man1/formatdb.1.gz
-man/man1/formatrpsdb.1.gz
+man/man1/fmerge.1.gz
+man/man1/gbseqget.1.gz
+man/man1/gene2xml.1.gz
 man/man1/getmesh.1.gz
 man/man1/getpub.1.gz
 man/man1/gil2bin.1.gz
 man/man1/idfetch.1.gz
-man/man1/impala.1.gz
 man/man1/indexpub.1.gz
-man/man1/makemat.1.gz
-man/man1/megablast.1.gz
-man/man1/rpsblast.1.gz
-man/man1/seedtop.1.gz
-man/man1/taxblast.1.gz
+man/man1/insdseqget.1.gz
+man/man1/makeset.1.gz
+man/man1/nps2gps.1.gz
+man/man1/sbtedit.1.gz
+man/man1/sortbyquote.1.gz
+man/man1/spidey.1.gz
+man/man1/subfuse.1.gz
 man/man1/tbl2asn.1.gz
+man/man1/trna2sap.1.gz
+man/man1/trna2tbl.1.gz
 man/man1/udv.1.gz
 man/man1/vecscreen.1.gz
 %%PORTDOCS%%%%DOCSDIR%%/FAQ.txt
@@ -629,26 +628,8 @@ man/man1/vecscreen.1.gz
 %%PORTDOCS%%%%DOCSDIR%%/access.txt
 %%PORTDOCS%%%%DOCSDIR%%/asn2gb.txt
 %%PORTDOCS%%%%DOCSDIR%%/asn2gph.txt
-%%PORTDOCS%%%%DOCSDIR%%/blast/bl2seq.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/blast.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/blastall.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/blastclust.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/blastdb.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/blastftp.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/blastpgp.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/fastacmd.html
 %%PORTDOCS%%%%DOCSDIR%%/blast/filter.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/formatdb.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/formatrpsdb.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/history.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/impala.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/index.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/megablast.html
 %%PORTDOCS%%%%DOCSDIR%%/blast/netblast.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/rpsblast.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/scoring.pdf
-%%PORTDOCS%%%%DOCSDIR%%/blast/seedtop.html
-%%PORTDOCS%%%%DOCSDIR%%/blast/web_blast.pl
 %%PORTDOCS%%%%DOCSDIR%%/dispatcher.html
 %%PORTDOCS%%%%DOCSDIR%%/fa2htgs/README
 %%PORTDOCS%%%%DOCSDIR%%/fa2htgs/updateHtgsDoc
@@ -761,12 +742,36 @@ man/man1/vecscreen.1.gz
 %%DATADIR%%/LSURef_93.fasta.nhr
 %%DATADIR%%/LSURef_93.fasta.nin
 %%DATADIR%%/LSURef_93.fasta.nsq
+%%DATADIR%%/LSU_chloro_rRNA.nhr
+%%DATADIR%%/LSU_chloro_rRNA.nin
+%%DATADIR%%/LSU_chloro_rRNA.nsq
+%%DATADIR%%/LSU_mito_rRNA.nhr
+%%DATADIR%%/LSU_mito_rRNA.nin
+%%DATADIR%%/LSU_mito_rRNA.nsq
+%%DATADIR%%/LSU_nomito-nochloro-noplastid.nhr
+%%DATADIR%%/LSU_nomito-nochloro-noplastid.nin
+%%DATADIR%%/LSU_nomito-nochloro-noplastid.nsq
+%%DATADIR%%/LSU_plastid.nhr
+%%DATADIR%%/LSU_plastid.nin
+%%DATADIR%%/LSU_plastid.nsq
 %%DATADIR%%/PAM250
 %%DATADIR%%/PAM30
 %%DATADIR%%/PAM70
+%%DATADIR%%/SSU-mito-rRNA.nhr
+%%DATADIR%%/SSU-mito-rRNA.nin
+%%DATADIR%%/SSU-mito-rRNA.nsq
 %%DATADIR%%/SSURef_93.fasta.nhr
 %%DATADIR%%/SSURef_93.fasta.nin
 %%DATADIR%%/SSURef_93.fasta.nsq
+%%DATADIR%%/SSU_chloro_rRNA.nhr
+%%DATADIR%%/SSU_chloro_rRNA.nin
+%%DATADIR%%/SSU_chloro_rRNA.nsq
+%%DATADIR%%/SSU_nomito_nochloro_noplastid.nhr
+%%DATADIR%%/SSU_nomito_nochloro_noplastid.nin
+%%DATADIR%%/SSU_nomito_nochloro_noplastid.nsq
+%%DATADIR%%/SSU_plast_rRNA.nhr
+%%DATADIR%%/SSU_plast_rRNA.nin
+%%DATADIR%%/SSU_plast_rRNA.nsq
 %%DATADIR%%/UniVec.nhr
 %%DATADIR%%/UniVec.nin
 %%DATADIR%%/UniVec.nsq
@@ -775,6 +780,9 @@ man/man1/vecscreen.1.gz
 %%DATADIR%%/UniVec_Core.nsq
 %%DATADIR%%/asn2ff.prt
 %%DATADIR%%/autofix.prt
+%%DATADIR%%/bacteria-archea16SrRNA.nhr
+%%DATADIR%%/bacteria-archea16SrRNA.nin
+%%DATADIR%%/bacteria-archea16SrRNA.nsq
 %%DATADIR%%/blast.prt
 %%DATADIR%%/bstdt.prt
 %%DATADIR%%/bstdt.val