sci-biology/ncbi-blast+: treeclean

Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

9 files changed, 0 insertions, 2474 deletions

diff --git a/sci-biology/ncbi-blast+/Manifest b/sci-biology/ncbi-blast+/Manifest
deleted file mode 100644
index afe8a43ef..000000000
--- a/sci-biology/ncbi-blast+/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST ncbi-blast-2.11.0+-src.tar.gz 58493096 BLAKE2B cfd6e7c66b379bee7065d306d2e426b798ec13fea5ed736c05c48b45c2fd7389c5050cc920b67d5e0f58102a4ef1108decbde791012fab28fe7402f9c8747808 SHA512 617994a0e3a4675a5f7048f165ac405bbd6a715ece9aba115d7c26b6be446b889b817dd496a2e15673545e5b594684c83fc4edb22cb5ecca2fd6d342c3bd642e
-DIST ncbi-blast-2.2.30+-src.tar.gz 18985378 BLAKE2B 59e749964ee5c6e30ac0286fc928fa8806abfd01aa70d937751642929de4d4e8ebc2109061f5dc82baf7e517a8718e1e11b9372c84f8be3b4140f55708ab264b SHA512 501727486aaa384ee5c40368332243ec2e19f22ab88f50c9396b4d33738bde4dbb5d3a1025ae599c1b5f4b4dd3d065ba4d0eb30305f42bfc781c95bbc4140a17
-DIST ncbi-blast-2.2.31+-src.tar.gz 18971327 BLAKE2B 4f6b124ddf6c892a0be36cbdcb00fe20a15b6f7a49af3f022e31a757ebd48d95c52219ecb2d56fa7787f936dbc08853affe07250ddf5461aff2f7fa5a9742be7 SHA512 2681a4394cc250d1ee545cd85dc962d73b1dbbdd987790a029bf51a58e74cbb08b5c8cf4a02b9b7c95916e3fb0d1613e2ed8631bb7ad683156759421081bb4ca
-DIST ncbi-blast-2.6.0+-src.tar.gz 20025526 BLAKE2B d97d1245e3f2030025e99323d67d889e6cecaa719fe525dbe1574a916e5f8b7b620880d44efe51851d64b9d1cdd0538f13161bfea8e233dcca6a223548d5090d SHA512 ea6444892a0b10459193d33d243b5960ad206b702e01e94a554a5ebda0291ff45e1ce43479713c23a96eba676b40bb8c57a7ef9dd2118729feef6b2cd98560c6
-DIST ncbi-blast-2.8.1+-src.tar.gz 24973554 BLAKE2B d13dee5cdd0218cb409898ac999fe5613e534375958c4b814a4c52d9954152a8da491d4866d6090c11bbb94916542be4809744a7f474c189a3b2f3dc9bc8e207 SHA512 3f408c5f76704183578828df3272bab7d59dd6052364e73e1831cd005b87d87dcc086bb1799b316b09e639e4af0edea6404b93a4b3e3c159d27cef34fff93d6f
diff --git a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt
deleted file mode 100644
index aeaf75e45..000000000
--- a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-.*
--.*/test
--.*/unit_test
diff --git a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch b/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch
deleted file mode 100644
index 13dffeee7..000000000
--- a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch
+++ /dev/null
@@ -1,668 +0,0 @@
-Subject: ensure that all libraries link against all direct dependencies

-

- * src/**/Makefile.*.lib: set DLL_(D)LIB correctly.  Break the dependency

-   loop between libxblast and libxalgoblastdbindex by having the former

-   provide only the C++ BLAST API, leaving the C core only in libblast.

- * src/build-system/library_relations.txt: Change xblast's

-   relationship to blast from includes to needs, accordingly.

- * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect

-   rather than libconnect for consistency with libblast, which uses the

-   former to keep the aforementioned cycle-breaking from causing

-   inconsistency elsewhere.

-

-Debian-Bug: 633567.

-Author: Aaron M. Ucko <ucko@debian.org>

-Last-Update: 2014-12-02

---- a/c++/src/algo/blast/core/Makefile.blast.lib

-+++ b/c++/src/algo/blast/core/Makefile.blast.lib

-@@ -21,6 +21,7 @@ LIB = blast

- CFLAGS  = $(FAST_CFLAGS)  

- LDFLAGS = $(FAST_LDFLAGS) 

- 

-+DLL_LIB = composition_adjustment xconnect tables

- 

- WATCHERS = madden camacho

- 

---- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib

-+++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib

-@@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \

- CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)

- LDFLAGS  = $(FAST_LDFLAGS)

- 

-+DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi

-+

- ASN_DEP = seqset

- 

- WATCHERS = morgulis

---- a/c++/src/algo/blast/format/Makefile.xblastformat.lib

-+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib

-@@ -7,7 +7,8 @@ SRC = blastfmtutil blastxml_format blast

- 

- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)

- 

--DLL_LIB = align_format blastxml blastxml2 xhtml xcgi

-+DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \

-+          seq general xser tables xncbi blastxml2

- 

- WATCHERS = jianye zaretska madden camacho fongah2

- 

---- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib

-+++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib

-@@ -21,7 +21,7 @@ SRC = seq_masker seq_masker_score_mean s

- CXXFLAGS = $(FAST_CXXFLAGS)

- LDFLAGS  = $(FAST_LDFLAGS)

- 

--

-+DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi

- 

- USES_LIBRARIES =  \

-     seqmasks_io

---- a/c++/src/cgi/Makefile.cgi.lib

-+++ b/c++/src/cgi/Makefile.cgi.lib

-@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb

-       user_agent

- LIB = xcgi

- 

-+DLL_LIB = xutil xncbi

-+

- CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)

- 

- WATCHERS = vakatov

---- a/c++/src/html/Makefile.html.lib

-+++ b/c++/src/html/Makefile.html.lib

-@@ -7,6 +7,8 @@ SRC = node html htmlhelper page pager se

-       commentdiag indentstream html_exception writer_htmlenc

- LIB = xhtml

- 

-+DLL_LIB = xncbi

-+

- WATCHERS = ivanov

- 

- 

---- a/c++/src/objects/blast/Makefile.xnetblastcli.lib

-+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib

-@@ -3,6 +3,7 @@ ASN_DEP = xnetblast

- LIB = xnetblastcli

- SRC = blastclient blastclient_

- 

-+DLL_LIB = xnetblast xser xconnect xutil xncbi

- 

- USES_LIBRARIES =  \

-     xconnect xnetblast

---- a/c++/src/objtools/align_format/Makefile.align_format.lib

-+++ b/c++/src/objtools/align_format/Makefile.align_format.lib

-@@ -13,6 +13,10 @@ SRC = format_flags align_format_util sho

- 

- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)

- 

-+DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \

-+          xobjmgr xnetblast blastdb gene_info seqset seq general xser \

-+          xcgi xhtml tables xncbi

-+

- ###  EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST

- # CFLAGS   = $(FAST_CFLAGS)

- # CXXFLAGS = $(FAST_CXXFLAGS)

---- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib

-+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib

-@@ -12,7 +12,7 @@ SRC = aln_builders aln_converters aln_ge

- 

- WATCHERS = todorov dicuccio grichenk

- 

--

-+DLL_LIB = xobjmgr seqset seq xser tables xncbi

- 

- USES_LIBRARIES =  \

-     tables xobjutil

---- a/c++/src/objtools/readers/Makefile.xobjread.lib

-+++ b/c++/src/objtools/readers/Makefile.xobjread.lib

-@@ -21,7 +21,7 @@ SRC = read_util format_guess_ex \

-       message_listener line_error

- 

- 

--DLL_LIB = creaders

-+DLL_LIB = submit seqset seq pub general xser creaders sequtil xutil xncbi

- 

- 

- 

---- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib

-+++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib

-@@ -12,7 +12,7 @@ mask_writer_seqloc \

- mask_writer_blastdb_maskinfo

- 

- ASN_DEP = seqset

--DLL_LIB = seqdb blastdb

-+DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi

- 

- WATCHERS = morgulis camacho

- 

---- a/c++/src/objtools/simple/Makefile.xobjsimple.lib

-+++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib

-@@ -7,6 +7,8 @@ WATCHERS =  jcherry

- 

- ASN_DEP = seqset

- 

-+DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi

-+

- LIB = xobjsimple

- SRC = simple_om

- 

---- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib

-+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib

-@@ -24,6 +24,8 @@ seqdbobj

- 

- LIB = seqdb

- 

-+DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi

-+

- CFLAGS   = $(FAST_CFLAGS)

- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)

- CXXFLAGS = $(FAST_CXXFLAGS)

---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib

-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib

-@@ -7,6 +7,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_

- 

- ASN_DEP = blastdb seqset

- 

-+DLL_LIB = seqdb xobjmgr seqset seq xncbi

-+

- WATCHERS = camacho

- 

- 

---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib

-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib

-@@ -5,6 +5,8 @@ SRC = bdbloader_rmt remote_blastdb_adapt

- 

- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)

- 

-+DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi

-+

- ASN_DEP = blastdb xnetblast

- 

- WATCHERS = camacho

---- a/c++/src/algo/blast/api/Makefile.xblast.lib

-+++ b/c++/src/algo/blast/api/Makefile.xblast.lib

-@@ -74,14 +74,15 @@ cdd_pssm_input \

- deltablast_options \

- deltablast

- 

--SRC  = $(SRC_C:%=.core_%) $(SRC_CXX)

-+SRC  = $(SRC_CXX) # $(SRC_C:%=.core_%)

- 

- LIB = xblast

- 

- DLL_LIB = xalgoblastdbindex composition_adjustment xalgowinmask \

- 	xalgodustmask seqmasks_io seqdb $(OBJREAD_LIBS) xobjutil \

- 	blastdb xnetblastcli xnetblast scoremat xconnect tables \

--	$(SOBJMGR_LIBS)

-+        $(SOBJMGR_LIBS) blast seqdb seqset seq general \

-+        xser xconnect sequtil tables xutil xncbi

- 

- CFLAGS   = $(FAST_CFLAGS) 

- CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)

---- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib

-+++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib

-@@ -24,7 +24,9 @@ SRC  = $(SRC_CXX)

- 

- LIB = blastinput

- 

--DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil

-+    DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \

-+              $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \

-+              scoremat seqset seq xser xutil xncbi

- 

- # should be redundant, given the above :-/

- ASN_DEP = seqset xnetblast

---- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib

-+++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib

-@@ -8,6 +8,8 @@ LIB = xalgodustmask

- 

- SRC = symdust

- 

-+DLL_LIB = xobjmgr seq xncbi

-+

- CXXFLAGS = $(FAST_CXXFLAGS)

- LDFLAGS  = $(FAST_LDFLAGS)

- 

---- a/c++/src/connect/Makefile.xconnect.lib

-+++ b/c++/src/connect/Makefile.xconnect.lib

-@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM)

- LIB  = xconnect

- PROJ_TAG = core

- 

-+DLL_LIB = xncbi

-+

- LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)

- 

- WATCHERS = lavr

---- a/c++/src/connect/ext/Makefile.xconnext.lib

-+++ b/c++/src/connect/ext/Makefile.xconnext.lib

-@@ -6,6 +6,8 @@ SRC      = $(SRC_C) ncbi_dblb_svcmapper

- 

- LIB      = xconnext

- 

-+DLL_LIB = xconnect xncbi

-+

- WATCHERS = lavr

- 

- 

---- a/c++/src/objects/blast/Makefile.blast.lib

-+++ b/c++/src/objects/blast/Makefile.blast.lib

-@@ -1,6 +1,8 @@

- LIB = xnetblast

- SRC = blast__ blast___ names

- 

-+DLL_LIB = scoremat seqset seq xser xncbi

-+

- WATCHERS = camacho

- 

- 

---- a/c++/src/objects/blastxml/Makefile.blastxml.lib

-+++ b/c++/src/objects/blastxml/Makefile.blastxml.lib

-@@ -1,6 +1,8 @@

- LIB = blastxml

- SRC = blastxml__ blastxml___

- 

-+DLL_LIB = xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     xser

---- a/c++/src/objects/scoremat/Makefile.scoremat.lib

-+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib

-@@ -1,6 +1,8 @@

- LIB = scoremat

- SRC = scoremat__ scoremat___

- 

-+DLL_LIB = seqset seq general xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     seqset

---- a/c++/src/objects/seqedit/Makefile.seqedit.lib

-+++ b/c++/src/objects/seqedit/Makefile.seqedit.lib

-@@ -1,6 +1,7 @@

- LIB = seqedit

- SRC = seqedit__ seqedit___

-- 

-+

-+DLL_LIB = seqset seq general xser xncbi

- 

- 

- USES_LIBRARIES =  \

---- a/c++/src/objects/submit/Makefile.submit.lib

-+++ b/c++/src/objects/submit/Makefile.submit.lib

-@@ -1,6 +1,8 @@

- LIB = submit

- SRC = submit__ submit___

- 

-+DLL_LIB = seqset seq biblio general xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     seqset

---- a/c++/src/objmgr/util/Makefile.util.lib

-+++ b/c++/src/objmgr/util/Makefile.util.lib

-@@ -8,6 +8,8 @@ ASN_DEP = submit

- SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci

- LIB = xobjutil

- 

-+DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi

-+

- WATCHERS = ucko vasilche kornbluh

- 

- 

---- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib

-+++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib

-@@ -11,6 +11,7 @@ SRC = seq_writer blastdb_dataextract bla

- 

- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)

- 

-+DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi

- 

- ###  EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST

- # CFLAGS   = $(FAST_CFLAGS)

---- a/c++/src/objtools/blast/services/Makefile.blast_services.lib

-+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib

-@@ -8,6 +8,8 @@ SRC = blast_services

- 

- LIB = blast_services

- 

-+DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi

-+

- CFLAGS   = $(FAST_CFLAGS)

- CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS)

- CXXFLAGS = $(FAST_CXXFLAGS)

---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib

-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib

-@@ -12,6 +12,9 @@ LIB_OR_DLL = both

- # Dependencies for shared library

- DLL_LIB = ncbi_xreader$(DLL)

- 

-+DLL_DLIB = ncbi_xreader_cache ncbi_xreader_id1 ncbi_xreader_id2 \

-+           id2 id1 ncbi_xreader xobjmgr seq xutil xncbi

-+

- WATCHERS = vasilche

- 

- 

---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib

-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib

-@@ -15,6 +15,9 @@ LIB_OR_DLL = both

- DLL_LIB = 

- DLL_DLIB = $(GENBANK_READER_LDEP)

- 

-+DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \

-+           xser xconnect xcompress xutil xncbi

-+

- WATCHERS = vasilche

- 

- 

---- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib

-+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib

-@@ -12,6 +12,8 @@ LIB_OR_DLL = both

- # Dependencies for shared library

- DLL_LIB = ncbi_xreader$(DLL)

- 

-+DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi

-+

- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)

- 

- WATCHERS = vasilche

---- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib

-+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib

-@@ -12,6 +12,8 @@ LIB_OR_DLL = both

- # Dependencies for shared library

- DLL_LIB = xconnect ncbi_xreader$(DLL)

- 

-+DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi

-+

- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)

- 

- WATCHERS = vasilche

---- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib

-+++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib

-@@ -12,7 +12,10 @@ LIB_OR_DLL = both

- CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)

- 

- # Dependencies for shared library (disabled due to problems on Darwin)

--# DLL_LIB = xconnect ncbi_xreader$(DLL)

-+DLL_LIB = xconnect ncbi_xreader$(DLL)

-+

-+DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi

-+

- 

- WATCHERS = vasilche

- 

---- a/c++/src/util/compress/api/Makefile.compress.lib

-+++ b/c++/src/util/compress/api/Makefile.compress.lib

-@@ -7,7 +7,7 @@ LIB = xcompress

- 

- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)

- 

--DLL_LIB =  $(BZ2_LIB)  $(Z_LIB)  $(LZO_LIB)

-+DLL_LIB =  $(BZ2_LIB)  $(Z_LIB)  $(LZO_LIB) xutil xncbi

- LIBS    =  $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS)

- 

- WATCHERS = ivanov

---- a/c++/src/util/sequtil/Makefile.sequtil.lib

-+++ b/c++/src/util/sequtil/Makefile.sequtil.lib

-@@ -3,6 +3,8 @@

- LIB = sequtil

- SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared

- 

-+DLL_LIB = xncbi

-+

- WATCHERS = shomrat

- 

- 

---- a/c++/src/corelib/Makefile.test_boost.lib

-+++ b/c++/src/corelib/Makefile.test_boost.lib

-@@ -3,6 +3,8 @@

- SRC = test_boost teamcity_messages

- LIB = test_boost

- 

-+DLL_LIB = xncbi

-+

- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)

- 

- REQUIRES = Boost.Test.Included

---- a/c++/src/corelib/Makefile.test_mt.lib

-+++ b/c++/src/corelib/Makefile.test_mt.lib

-@@ -3,6 +3,8 @@

- SRC = test_mt

- LIB    = test_mt

- 

-+DLL_LIB = xncbi

-+

- # REQUIRES = MT

- 

- USE_PCH = no

---- a/c++/src/objects/biblio/Makefile.biblio.lib

-+++ b/c++/src/objects/biblio/Makefile.biblio.lib

-@@ -1,6 +1,8 @@

- LIB = biblio

- SRC = biblio__ biblio___ citation_base

- 

-+DLL_LIB = general xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     general

---- a/c++/src/objects/blastdb/Makefile.blastdb.lib

-+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib

-@@ -1,5 +1,7 @@

- # $Id: Makefile.blastdb.lib 427424 2014-02-20 13:38:50Z gouriano $

- 

-+

-+DLL_LIB = seq xser xncbi

- LIB = blastdb

- SRC = blastdb__ blastdb___

- 

---- a/c++/src/objects/general/Makefile.general.lib

-+++ b/c++/src/objects/general/Makefile.general.lib

-@@ -1,6 +1,8 @@

- LIB = general

- SRC = general__ general___ uoconv

- 

-+DLL_LIB = xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     xser

---- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib

-+++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib

-@@ -3,6 +3,8 @@

- LIB = genome_collection

- SRC = genome_collection__ genome_collection___

- 

-+DLL_LIB = seq general xser xncbi

-+

- WATCHERS = dicuccio

- 

- 

---- a/c++/src/objects/id1/Makefile.id1.lib

-+++ b/c++/src/objects/id1/Makefile.id1.lib

-@@ -3,6 +3,8 @@ ASN_DEP = seq

- LIB = id1

- SRC = id1__ id1___

- 

-+DLL_LIB = seqset seq xser xncbi

-+

- WATCHERS = vasilche

- 

- 

---- a/c++/src/objects/id2/Makefile.id2.lib

-+++ b/c++/src/objects/id2/Makefile.id2.lib

-@@ -1,6 +1,8 @@

- LIB = id2

- SRC = id2__ id2___

- 

-+DLL_LIB = seqsplit seq xser xncbi

-+

- WATCHERS = vasilche

- 

- 

---- a/c++/src/objects/medline/Makefile.medline.lib

-+++ b/c++/src/objects/medline/Makefile.medline.lib

-@@ -1,6 +1,8 @@

- LIB = medline

- SRC = medline__ medline___

- 

-+DLL_LIB = biblio general xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     biblio

---- a/c++/src/objects/pub/Makefile.pub.lib

-+++ b/c++/src/objects/pub/Makefile.pub.lib

-@@ -1,6 +1,8 @@

- LIB = pub

- SRC = pub__ pub___

- 

-+DLL_LIB = medline biblio xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     medline

---- a/c++/src/objects/seq/Makefile.seq.lib

-+++ b/c++/src/objects/seq/Makefile.seq.lib

-@@ -12,6 +12,8 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport

-       seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \

-       seq_loc_from_string seq_loc_reverse_complementer

- 

-+DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi

-+

- WATCHERS = vasilche grichenk

- 

- 

---- a/c++/src/objects/seqcode/Makefile.seqcode.lib

-+++ b/c++/src/objects/seqcode/Makefile.seqcode.lib

-@@ -1,6 +1,8 @@

- LIB = seqcode

- SRC = seqcode__ seqcode___

- 

-+DLL_LIB = xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     xser

---- a/c++/src/objects/seqset/Makefile.seqset.lib

-+++ b/c++/src/objects/seqset/Makefile.seqset.lib

-@@ -1,6 +1,8 @@

- LIB = seqset

- SRC = seqset__ seqset___ gb_release_file

- 

-+DLL_LIB = seq general xser xncbi

-+

- 

- USES_LIBRARIES =  \

-     $(SEQ_LIBS) pub

---- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib

-+++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib

-@@ -1,6 +1,8 @@

- LIB = seqsplit

- SRC = seqsplit__ seqsplit___

- 

-+DLL_LIB = seqset seq xser xncbi

-+

- WATCHERS = vasilche

- 

- 

---- a/c++/src/serial/Makefile.serial.lib

-+++ b/c++/src/serial/Makefile.serial.lib

-@@ -18,6 +18,8 @@ SRC = \

- 

- LIB    = xser

- 

-+DLL_LIB = xutil xncbi

-+

- WATCHERS = gouriano

- 

- 

---- a/c++/src/util/Makefile.util.lib

-+++ b/c++/src/util/Makefile.util.lib

-@@ -12,6 +12,7 @@ SRC = random_gen utf8 checksum bytesrc s

- LIB = xutil

- PROJ_TAG = core

- 

-+DLL_LIB = xncbi

- LIBS = $(ORIG_LIBS)

- 

- WATCHERS = vakatov kornbluh

---- a/c++/src/util/xregexp/Makefile.xregexp.lib

-+++ b/c++/src/util/xregexp/Makefile.xregexp.lib

-@@ -6,7 +6,7 @@ LIB = xregexp

- 

- CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)

- 

--DLL_LIB = $(PCRE_LIB)

-+DLL_LIB = $(PCRE_LIB) xncbi

- LIBS    = $(PCRE_LIBS)

- 

- WATCHERS = ivanov

---- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib

-+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib

-@@ -8,6 +8,8 @@ LIB = xalgosegmask

- 

- SRC = segmask

- 

-+DLL_LIB = blast xobjmgr xncbi

-+

- CXXFLAGS = $(FAST_CXXFLAGS)

- LDFLAGS  = $(FAST_LDFLAGS)

- 

---- a/c++/src/objmgr/split/Makefile.id2_split.lib

-+++ b/c++/src/objmgr/split/Makefile.id2_split.lib

-@@ -17,7 +17,7 @@ LIB = id2_split

- 

- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)

- 

--DLL_LIB = $(SOBJMGR_LIBS)

-+DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi

- 

- WATCHERS = vasilche

- 

---- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib

-+++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib

-@@ -8,6 +8,9 @@ SRC = writedb writedb_impl writedb_volum

- 

- LIB = writedb

- 

-+DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \

-+          xser sequtil xutil xncbi

-+

- CFLAGS   = $(FAST_CFLAGS)

- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)

- CXXFLAGS = $(FAST_CXXFLAGS)

---- a/c++/src/algo/blast/Makefile.blast_macros.mk

-+++ b/c++/src/algo/blast/Makefile.blast_macros.mk

-@@ -18,7 +18,7 @@ BLAST_INPUT_LIBS = blastinput \

- BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)

- 

- # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS

--BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \

-+BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \

- 		xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \

- 		$(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables xalnmgr

- # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)

---- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app

-+++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app

-@@ -2,7 +2,7 @@ APP = makembindex

- SRC = main mkindex_app

- 

- LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \

--      $(OBJREAD_LIBS) xobjutil tables connect $(SOBJMGR_LIBS)

-+      $(OBJREAD_LIBS) xobjutil tables xconnect $(SOBJMGR_LIBS)

- LIB = $(LIB_:%=%$(STATIC))

- 

- CXXFLAGS = $(FAST_CXXFLAGS)

---- a/c++/src/build-system/library_relations.txt

-+++ b/c++/src/build-system/library_relations.txt

-@@ -1189,7 +1189,7 @@ xasmcompare needs $(SEQ_LIBS)

- xasmcompare needs pub

- xasn needs xhtml

- xasn needs3party $(NCBI_C_ncbi)

--xblast includes blast

-+xblast needs blast

- xblast needs xalgoblastdbindex

- xblast needs xalgodustmask

- xblast needs xalgowinmask

diff --git a/sci-biology/ncbi-blast+/metadata.xml b/sci-biology/ncbi-blast+/metadata.xml
deleted file mode 100644
index 93556eaa7..000000000
--- a/sci-biology/ncbi-blast+/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="boost">Undocumented USE</flag>
-		<flag name="cppunit">Undocumented USE</flag>
-		<flag name="freetype">Undocumented USE</flag>
-		<flag name="mesa">Undocumented USE</flag>
-		<flag name="muparser">Undocumented USE</flag>
-		<flag name="sablotron">Undocumented USE</flag>
-		<flag name="xerces">Undocumented USE</flag>
-		<flag name="xalan">Undocumented USE</flag>
-		<flag name="xslt">Undocumented USE</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
deleted file mode 100644
index 527acfadf..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ /dev/null
@@ -1,360 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit python-single-r1 toolchain-funcs
-
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="!test? ( test )"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
-	<sys-devel/gcc-10:=
-	!sci-biology/ncbi-tools++
-	berkdb? ( sys-libs/db:=[cxx(-)] )
-	boost? ( dev-libs/boost )
-	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	python? ( ${PYTHON_DEPS} )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( dev-libs/libxslt )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( media-libs/libjpeg-turbo:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
-	app-arch/bzip2
-	dev-libs/libpcre
-	dev-db/lmdb"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-#	filter-ldflags -Wl,--as-needed
-#	append-ldflags -Wl,--no-undefined
-#	sed -i -e 's/-print-file-name=libstdc++.a//' \
-#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-#		src/build-system/configure || die
-#	epatch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-##	local PATCHES=(
-##		"${FILESDIR}"/${P}-conf-opts.patch
-##		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups.patch
-##		"${FILESDIR}"/${P}-more-patches.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-##		"${FILESDIR}"/${P}-configure.patch
-##		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-##		"${FILESDIR}"/${P}-fix-install.patch
-##		)
-		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-##	epatch ${PATCHES[@]}
-
-	# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
-	# the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
-	# it is still present, plus in a few places was something else patched
-	# staying without any patches for now and lets see is it works on Gentoo
-	# epatch "${FILESDIR}"/fix_lib_deps.patch
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-##	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-	default
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	$(use_with debug)
-	$(use_with debug max-debug)
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-	#
-	# GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302
-	# $(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-#	$(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	$(use_with python python "${EPREFIX}/usr")
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	# prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution
-	--without-vdb
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?"
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
-	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
-	doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
-	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
deleted file mode 100644
index e90652f38..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ /dev/null
@@ -1,350 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="!test? ( test )"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
-	<sys-devel/gcc-10:=
-	!sci-biology/ncbi-tools++
-	berkdb? ( sys-libs/db:=[cxx(-)] )
-	boost? ( dev-libs/boost )
-	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( dev-libs/libxslt )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( media-libs/libjpeg-turbo:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
-	app-arch/bzip2
-	dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-PATCHES=(
-	"${FILESDIR}"/"${P}"__fix_lib_deps.patch
-)
-
-src_prepare() {
-#	filter-ldflags -Wl,--as-needed
-#	append-ldflags -Wl,--no-undefined
-#	sed -i -e 's/-print-file-name=libstdc++.a//' \
-#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-#		src/build-system/configure || die
-#	epatch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-##	local PATCHES=(
-##		"${FILESDIR}"/${P}-conf-opts.patch
-##		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups.patch
-##		"${FILESDIR}"/${P}-more-patches.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-##		"${FILESDIR}"/${P}-configure.patch
-##		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-##		"${FILESDIR}"/${P}-fix-install.patch
-##		)
-		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-##	epatch ${PATCHES[@]}
-
-	# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-##	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-	default
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	$(use_with debug)
-	$(use_with debug max-debug)
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-	$(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-#	$(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	# is python2
-	--without-python
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported"
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
-	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
-	doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
-	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
deleted file mode 100644
index ddeeac07d..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ /dev/null
@@ -1,350 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/t"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="!test? ( test )"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
-	<sys-devel/gcc-10:=
-	!sci-biology/ncbi-tools++
-	berkdb? ( sys-libs/db:=[cxx(-)] )
-	boost? ( dev-libs/boost )
-	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( dev-libs/libxslt )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( media-libs/libjpeg-turbo:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
-	app-arch/bzip2
-	dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-#	filter-ldflags -Wl,--as-needed
-#	append-ldflags -Wl,--no-undefined
-#	sed -i -e 's/-print-file-name=libstdc++.a//' \
-#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-#		src/build-system/configure || die
-#	epatch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-##	local PATCHES=(
-##		"${FILESDIR}"/${P}-conf-opts.patch
-##		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups.patch
-##		"${FILESDIR}"/${P}-more-patches.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-##		"${FILESDIR}"/${P}-configure.patch
-##		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-##		"${FILESDIR}"/${P}-fix-install.patch
-##		)
-		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-##	epatch ${PATCHES[@]}
-
-	# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
-	# the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
-	# it is still present, plus in a few places was something else patched
-	# staying without any patches for now and lets see is it works on Gentoo
-	# epatch "${FILESDIR}"/fix_lib_deps.patch
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-##	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-	default
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	$(use_with debug)
-	$(use_with debug max-debug)
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-	$(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-#	$(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	# is python2
-	--without-python
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported"
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
-	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
-	doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
-	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
deleted file mode 100644
index 976ea3804..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ /dev/null
@@ -1,355 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="!test? ( test )"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
-	<sys-devel/gcc-10:=
-	!sci-biology/ncbi-tools++
-	berkdb? ( sys-libs/db:=[cxx(-)] )
-	boost? ( dev-libs/boost )
-	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( dev-libs/libxslt )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( media-libs/libjpeg-turbo:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
-	app-arch/bzip2
-	dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-#	filter-ldflags -Wl,--as-needed
-#	append-ldflags -Wl,--no-undefined
-#	sed -i -e 's/-print-file-name=libstdc++.a//' \
-#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-#		src/build-system/configure || die
-#	epatch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-##	local PATCHES=(
-##		"${FILESDIR}"/${P}-conf-opts.patch
-##		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups.patch
-##		"${FILESDIR}"/${P}-more-patches.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-##		"${FILESDIR}"/${P}-configure.patch
-##		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-##		"${FILESDIR}"/${P}-fix-install.patch
-##		)
-		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-##	epatch ${PATCHES[@]}
-
-	# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
-	# the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
-	# it is still present, plus in a few places was something else patched
-	# staying without any patches for now and lets see is it works on Gentoo
-	# epatch "${FILESDIR}"/fix_lib_deps.patch
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-##	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-	default
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	$(use_with debug)
-	$(use_with debug max-debug)
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-	#
-	# GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302
-	# $(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-#	$(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	# is python2
-	--without-python
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	# prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution
-	--without-vdb
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
-	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
-	doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
-	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
deleted file mode 100644
index 527acfadf..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ /dev/null
@@ -1,360 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit python-single-r1 toolchain-funcs
-
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="!test? ( test )"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
-	<sys-devel/gcc-10:=
-	!sci-biology/ncbi-tools++
-	berkdb? ( sys-libs/db:=[cxx(-)] )
-	boost? ( dev-libs/boost )
-	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	python? ( ${PYTHON_DEPS} )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( dev-libs/libxslt )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( media-libs/libjpeg-turbo:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
-	app-arch/bzip2
-	dev-libs/libpcre
-	dev-db/lmdb"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-#	filter-ldflags -Wl,--as-needed
-#	append-ldflags -Wl,--no-undefined
-#	sed -i -e 's/-print-file-name=libstdc++.a//' \
-#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-#		src/build-system/configure || die
-#	epatch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-##	local PATCHES=(
-##		"${FILESDIR}"/${P}-conf-opts.patch
-##		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups.patch
-##		"${FILESDIR}"/${P}-more-patches.patch
-##		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-##		"${FILESDIR}"/${P}-configure.patch
-##		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-##		"${FILESDIR}"/${P}-fix-install.patch
-##		)
-		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-##	epatch ${PATCHES[@]}
-
-	# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
-	# the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
-	# it is still present, plus in a few places was something else patched
-	# staying without any patches for now and lets see is it works on Gentoo
-	# epatch "${FILESDIR}"/fix_lib_deps.patch
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-##	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-	default
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	$(use_with debug)
-	$(use_with debug max-debug)
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-	#
-	# GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302
-	# $(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-#	$(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	$(use_with python python "${EPREFIX}/usr")
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	# prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution
-	--without-vdb
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?"
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
-	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
-	doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
-	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}