sci-biology/ncbi-blast+: new package, ebuild derived from ncbi-tools++-12.0.0.ebuild with a Debian patch

6 files changed, 1043 insertions, 0 deletions

diff --git a/sci-biology/ncbi-blast+/ChangeLog b/sci-biology/ncbi-blast+/ChangeLog
new file mode 100644
index 000000000..819f1f40c
--- /dev/null
+++ b/sci-biology/ncbi-blast+/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/ncbi-blast+
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ncbi-blast+-2.2.30 (14 Jan 2015)
+
+  14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +ncbi-blast+-2.2.30.ebuild, +files/disable-testsuite-compilation.txt,
+  +files/fix_lib_deps.patch, +metadata.xml:
+  ebuild derived from ncbi-tools++-12.0.0.ebuild with a Debian patch
+
diff --git a/sci-biology/ncbi-blast+/Manifest b/sci-biology/ncbi-blast+/Manifest
new file mode 100644
index 000000000..9fbe3ef98
--- /dev/null
+++ b/sci-biology/ncbi-blast+/Manifest
@@ -0,0 +1 @@
+DIST ncbi-blast-2.2.30+-src.tar.gz 18985378 SHA256 26f72d51c81b9497f33b7274109565c36692572faef4d72377f79b7e59910e40 SHA512 501727486aaa384ee5c40368332243ec2e19f22ab88f50c9396b4d33738bde4dbb5d3a1025ae599c1b5f4b4dd3d065ba4d0eb30305f42bfc781c95bbc4140a17 WHIRLPOOL 64f63fdf1502f3d069ffa645b378fb50469d689b70eefbbc85e04bbe4ae896d1e4dfc860a81e2d7c27bc9484eb6a9651ac02ee1d712b9a511d33a9be241154e9
diff --git a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt
new file mode 100644
index 000000000..aeaf75e45
--- /dev/null
+++ b/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt
@@ -0,0 +1,3 @@
+.*
+-.*/test
+-.*/unit_test
diff --git a/sci-biology/ncbi-blast+/files/fix_lib_deps.patch b/sci-biology/ncbi-blast+/files/fix_lib_deps.patch
new file mode 100644
index 000000000..13dffeee7
--- /dev/null
+++ b/sci-biology/ncbi-blast+/files/fix_lib_deps.patch
@@ -0,0 +1,668 @@
+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
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/ncbi-blast+/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
new file mode 100644
index 000000000..6b95dc413
--- /dev/null
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -0,0 +1,351 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils flag-o-matic multilib toolchain-funcs
+
+MY_PV="2.2.30"
+MY_P="ncbi-blast-${PV}+-src"
+# workdir/ncbi-blast-2.2.30+-src
+# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
+
+DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+SRC_URI="
+	ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${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 fastcgi fltk freetype gif
+	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+	sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+#KEYWORDS=""
+
+# sys-libs/db should be compiled with USE=cxx
+DEPEND="
+	!sci-biology/ncbi-tools++
+	!sci-biology/sra_sdk
+	berkdb? ( sys-libs/db:4.3[cxx] )
+	boost? ( dev-libs/boost )
+	curl? ( net-misc/curl )
+	sqlite? ( dev-db/sqlite )
+	sqlite3? ( dev-db/sqlite:3 )
+	mysql? ( virtual/mysql )
+	fltk? ( x11-libs/fltk )
+	opengl? ( virtual/opengl media-libs/glew )
+	mesa? ( media-libs/mesa[osmesa] )
+	glut? ( media-libs/freeglut )
+	freetype? ( media-libs/freetype )
+	fastcgi? ( www-apache/mod_fastcgi )
+	gnutls? ( net-libs/gnutls )
+	python? ( dev-lang/python )
+	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? ( virtual/jpeg )
+	png? ( media-libs/libpng )
+	tiff? ( media-libs/tiff )
+	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 ${PATCHES[@]}
+
+	# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
+	epatch "${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
+}
+
+# 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")
+	$(use_with fastcgi fastcgi "${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")
+#	$(use_with X x) # there is no --with-x option
+	)
+
+	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
+	use test ||	myconf+=( --with-projects="${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/'
+}