diff options
Diffstat (limited to 'biology/ncbi-toolkit/pkg-plist')
| -rw-r--r-- | biology/ncbi-toolkit/pkg-plist | 82 |
1 files changed, 68 insertions, 14 deletions
diff --git a/biology/ncbi-toolkit/pkg-plist b/biology/ncbi-toolkit/pkg-plist index cc64a829fb5c..6804d8608983 100644 --- a/biology/ncbi-toolkit/pkg-plist +++ b/biology/ncbi-toolkit/pkg-plist @@ -1,5 +1,4 @@ bin/bl2seq -bin/blast bin/blastall bin/blastcl3 bin/blastclust @@ -7,11 +6,13 @@ bin/blastpgp bin/copymat bin/fastacmd bin/formatdb +bin/formatrpsdb bin/impala bin/makemat bin/megablast bin/rpsblast bin/seedtop +bin/taxblast bin/asn2ff bin/asn2gb bin/asn2idx @@ -23,8 +24,6 @@ bin/debruijn bin/entrcmd bin/fa2htgs bin/findspl -bin/getseq -bin/getfeat bin/getmesh bin/getpub bin/ddv @@ -34,10 +33,16 @@ bin/indexpub bin/makeset bin/tbl2asn bin/vecscreen +bin/demo_regexp +bin/demo_regexp_grep +bin/errhdr +bin/gene2xml +bin/ncbisort +bin/seqtest +bin/test_regexp bin/Nentrez bin/Psequin bin/entrez2 -bin/netentcf bin/sbtedit bin/udv include/ncbi/connect/connect_export.h @@ -48,12 +53,14 @@ include/ncbi/connect/ncbi_comm.h include/ncbi/connect/ncbi_config.h include/ncbi/connect/ncbi_connection.h include/ncbi/connect/ncbi_connector.h +include/ncbi/connect/ncbi_connssl.h include/ncbi/connect/ncbi_connutil.h include/ncbi/connect/ncbi_core.h include/ncbi/connect/ncbi_core_c.h include/ncbi/connect/ncbi_dispd.h include/ncbi/connect/ncbi_file_connector.h include/ncbi/connect/ncbi_ftp_connector.h +include/ncbi/connect/ncbi_gnutls.h include/ncbi/connect/ncbi_heapmgr.h include/ncbi/connect/ncbi_host_info.h include/ncbi/connect/ncbi_host_infop.h @@ -68,11 +75,11 @@ include/ncbi/connect/ncbi_server_info.h include/ncbi/connect/ncbi_server_infop.h include/ncbi/connect/ncbi_service.h include/ncbi/connect/ncbi_service_connector.h -include/ncbi/connect/ncbi_service_misc.h include/ncbi/connect/ncbi_servicep.h include/ncbi/connect/ncbi_socket.h include/ncbi/connect/ncbi_socket_connector.h include/ncbi/connect/ncbi_socket_unix.h +include/ncbi/connect/ncbi_socketp.h include/ncbi/connect/ncbi_types.h include/ncbi/connect/ncbi_util.h include/ncbi/FSpCompat.h @@ -90,6 +97,8 @@ 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 @@ -125,11 +134,13 @@ 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 @@ -139,6 +150,7 @@ include/ncbi/asnres.h include/ncbi/asnseq.h include/ncbi/asnsset.h include/ncbi/asnsubmt.h +include/ncbi/asntable.h include/ncbi/asntax1.h include/ncbi/asntax3.h include/ncbi/asntaxon.h @@ -147,6 +159,7 @@ include/ncbi/bandalgn.h include/ncbi/binary.h include/ncbi/biosrc.h include/ncbi/blast.h +include/ncbi/blast_dust.h include/ncbi/blastconcat.h include/ncbi/blastconcatdef.h include/ncbi/blastdef.h @@ -255,6 +268,8 @@ include/ncbi/list.h include/ncbi/lnfac.h include/ncbi/lookup.h include/ncbi/lsqfetch.h +include/ncbi/macroapi.h +include/ncbi/macrodlg.h include/ncbi/mapcn3d.h include/ncbi/mapgene.h include/ncbi/mapmime.h @@ -275,6 +290,8 @@ include/ncbi/medview.h include/ncbi/mimapi.h include/ncbi/mkbioseq.h include/ncbi/mmdb1.h +include/ncbi/mla2api.h +include/ncbi/mlkludge.h include/ncbi/mmdb2.h include/ncbi/mmdb3.h include/ncbi/mmdbapi.h @@ -348,12 +365,14 @@ include/ncbi/objgbseq.h include/ncbi/objgen.h include/ncbi/objinsdseq.h include/ncbi/objloc.h +include/ncbi/objmacro.h include/ncbi/objmdrs.h include/ncbi/objmedli.h include/ncbi/objmgr.h include/ncbi/objmim.h include/ncbi/objmime.h include/ncbi/objmla.h +include/ncbi/objmla2.h include/ncbi/objmmdb1.h include/ncbi/objmmdb2.h include/ncbi/objmmdb3.h @@ -369,6 +388,7 @@ include/ncbi/objseq.h include/ncbi/objspell.h include/ncbi/objsset.h include/ncbi/objsub.h +include/ncbi/objtable.h include/ncbi/objtax1.h include/ncbi/objtax3.h include/ncbi/objtseq.h @@ -519,6 +539,7 @@ include/ncbi/vibfltr.h include/ncbi/vibforms.h include/ncbi/vibgraph.h include/ncbi/vibincld.h +include/ncbi/vibmain.h include/ncbi/vibmouse.h include/ncbi/vibpcc.h include/ncbi/vibprocs.h @@ -584,7 +605,6 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/blast/rpsblast.html %%PORTDOCS%%%%DOCSDIR%%/blast/scoring.pdf %%PORTDOCS%%%%DOCSDIR%%/blast/seedtop.html -%%PORTDOCS%%%%DOCSDIR%%/blast/update_blastdb.pl %%PORTDOCS%%%%DOCSDIR%%/blast/web_blast.pl %%PORTDOCS%%%%DOCSDIR%%/dispatcher.html %%PORTDOCS%%%%DOCSDIR%%/fa2htgs/README @@ -619,26 +639,30 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/images/update.png %%PORTDOCS%%%%DOCSDIR%%/images/validate.png %%PORTDOCS%%%%DOCSDIR%%/images/welcome.png -%%PORTDOCS%%%%DOCSDIR%%/man/asn2ff.1 -%%PORTDOCS%%%%DOCSDIR%%/man/Nentrez.1 %%PORTDOCS%%%%DOCSDIR%%/man/Psequin.1 +%%PORTDOCS%%%%DOCSDIR%%/man/asn2all.1 %%PORTDOCS%%%%DOCSDIR%%/man/asn2asn.1 +%%PORTDOCS%%%%DOCSDIR%%/man/asn2ff.1 +%%PORTDOCS%%%%DOCSDIR%%/man/asn2fsa.1 %%PORTDOCS%%%%DOCSDIR%%/man/asn2gb.1 +%%PORTDOCS%%%%DOCSDIR%%/man/asn2idx.1 %%PORTDOCS%%%%DOCSDIR%%/man/asn2xml.1 %%PORTDOCS%%%%DOCSDIR%%/man/asndhuff.1 %%PORTDOCS%%%%DOCSDIR%%/man/asntool.1 +%%PORTDOCS%%%%DOCSDIR%%/man/asnval.1 %%PORTDOCS%%%%DOCSDIR%%/man/bl2seq.1 %%PORTDOCS%%%%DOCSDIR%%/man/blast.1 %%PORTDOCS%%%%DOCSDIR%%/man/blastall.1 +%%PORTDOCS%%%%DOCSDIR%%/man/blastall_old.1 %%PORTDOCS%%%%DOCSDIR%%/man/blastcl3.1 %%PORTDOCS%%%%DOCSDIR%%/man/blastclust.1 %%PORTDOCS%%%%DOCSDIR%%/man/blastpgp.1 %%PORTDOCS%%%%DOCSDIR%%/man/cdscan.1 %%PORTDOCS%%%%DOCSDIR%%/man/checksub.1 +%%PORTDOCS%%%%DOCSDIR%%/man/cleanasn.1 %%PORTDOCS%%%%DOCSDIR%%/man/copymat.1 %%PORTDOCS%%%%DOCSDIR%%/man/ddv.1 %%PORTDOCS%%%%DOCSDIR%%/man/debruijn.1 -%%PORTDOCS%%%%DOCSDIR%%/man/entrcmd.1 %%PORTDOCS%%%%DOCSDIR%%/man/entrez2.1 %%PORTDOCS%%%%DOCSDIR%%/man/errhdr.1 %%PORTDOCS%%%%DOCSDIR%%/man/vecscreen.1 @@ -648,20 +672,27 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/man/fmerge.1 %%PORTDOCS%%%%DOCSDIR%%/man/formatdb.1 %%PORTDOCS%%%%DOCSDIR%%/man/getpub.1 +%%PORTDOCS%%%%DOCSDIR%%/man/formatrpsdb.1 %%PORTDOCS%%%%DOCSDIR%%/man/gbseqget.1 -%%PORTDOCS%%%%DOCSDIR%%/man/getfeat.1 +%%PORTDOCS%%%%DOCSDIR%%/man/gene2xml.1 %%PORTDOCS%%%%DOCSDIR%%/man/getmesh.1 %%PORTDOCS%%%%DOCSDIR%%/man/gil2bin.1 %%PORTDOCS%%%%DOCSDIR%%/man/idfetch.1 %%PORTDOCS%%%%DOCSDIR%%/man/impala.1 %%PORTDOCS%%%%DOCSDIR%%/man/indexpub.1 +%%PORTDOCS%%%%DOCSDIR%%/man/insdseqget.1 %%PORTDOCS%%%%DOCSDIR%%/man/makemat.1 %%PORTDOCS%%%%DOCSDIR%%/man/makeset.1 %%PORTDOCS%%%%DOCSDIR%%/man/megablast.1 -%%PORTDOCS%%%%DOCSDIR%%/man/netentcf.1 +%%PORTDOCS%%%%DOCSDIR%%/man/nps2gps.1 %%PORTDOCS%%%%DOCSDIR%%/man/rpsblast.1 +%%PORTDOCS%%%%DOCSDIR%%/man/sbtedit.1 %%PORTDOCS%%%%DOCSDIR%%/man/seedtop.1 +%%PORTDOCS%%%%DOCSDIR%%/man/sortbyquote.1 +%%PORTDOCS%%%%DOCSDIR%%/man/spidey.1 %%PORTDOCS%%%%DOCSDIR%%/man/tbl2asn.1 +%%PORTDOCS%%%%DOCSDIR%%/man/trna2sap.1 +%%PORTDOCS%%%%DOCSDIR%%/man/trna2tbl.1 %%PORTDOCS%%%%DOCSDIR%%/man/udv.1 %%PORTDOCS%%%%DOCSDIR%%/ncbixml.txt %%PORTDOCS%%%%DOCSDIR%%/sdk.doc @@ -702,17 +733,26 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/seq_install/win-netscape.css %%PORTDOCS%%%%DOCSDIR%%/sequin.htm %%PORTDOCS%%%%DOCSDIR%%/tbl2asn.txt -%%DATADIR%%/16Score.nhr -%%DATADIR%%/16Score.nin -%%DATADIR%%/16Score.nsq +%%DATADIR%%/16SCore.nhr +%%DATADIR%%/16SCore.nin +%%DATADIR%%/16SCore.nsq %%DATADIR%%/BLOSUM45 +%%DATADIR%%/BLOSUM50 %%DATADIR%%/BLOSUM62 %%DATADIR%%/BLOSUM80 +%%DATADIR%%/BLOSUM90 +%%DATADIR%%/Combined16SrRNA.nhr +%%DATADIR%%/Combined16SrRNA.nin +%%DATADIR%%/Combined16SrRNA.nsq +%%DATADIR%%/Combined16SrRNA_2-12-2008.nhr +%%DATADIR%%/Combined16SrRNA_2-12-2008.nin +%%DATADIR%%/Combined16SrRNA_2-12-2008.nsq %%DATADIR%%/ContactPotential %%DATADIR%%/KSat.flt %%DATADIR%%/KSchoth.flt %%DATADIR%%/KSesigc.mat %%DATADIR%%/KSesigl.mat +%%DATADIR%%/PAM250 %%DATADIR%%/KSgc.flt %%DATADIR%%/KShopp.flt %%DATADIR%%/KSkyte.flt @@ -725,8 +765,14 @@ lib/ncbi/libvibrant.a %%DATADIR%%/KSpsigl.mat %%DATADIR%%/KSpur.flt %%DATADIR%%/KSpyr.flt +%%DATADIR%%/LSURef_93.fasta.nhr +%%DATADIR%%/LSURef_93.fasta.nin +%%DATADIR%%/LSURef_93.fasta.nsq %%DATADIR%%/PAM30 %%DATADIR%%/PAM70 +%%DATADIR%%/SSURef_93.fasta.nhr +%%DATADIR%%/SSURef_93.fasta.nin +%%DATADIR%%/SSURef_93.fasta.nsq %%DATADIR%%/UniVec.nhr %%DATADIR%%/UniVec.nin %%DATADIR%%/UniVec.nsq @@ -737,11 +783,17 @@ lib/ncbi/libvibrant.a %%DATADIR%%/blast.prt %%DATADIR%%/bstdt.prt %%DATADIR%%/bstdt.val +%%DATADIR%%/country_lat_lon.txt +%%DATADIR%%/ecnum_ambiguous.txt +%%DATADIR%%/ecnum_deleted.txt +%%DATADIR%%/ecnum_replaced.txt +%%DATADIR%%/ecnum_specific.txt %%DATADIR%%/featdef.prt %%DATADIR%%/featdef.val %%DATADIR%%/gc.prt %%DATADIR%%/gc.val %%DATADIR%%/humrep.fsa +%%DATADIR%%/institution_codes.txt %%DATADIR%%/lineages.txt %%DATADIR%%/makerpt.prt %%DATADIR%%/ncbiendo.dat @@ -751,6 +803,8 @@ lib/ncbi/libvibrant.a %%DATADIR%%/ncbirnam.dat %%DATADIR%%/objprt.prt %%DATADIR%%/pubkey.enc +%%DATADIR%%/rRNA_blast.nal +%%DATADIR%%/rRNAstrand.nal %%DATADIR%%/seqcode.prt %%DATADIR%%/seqcode.val %%DATADIR%%/sequin.hlp |