add-riscv-support.patch

@@ -1,19 +0,0 @@
-Author: misaka00251 <liuxin@iscas.ac.cn>
-Date:   Wed Sep 21 11:15:51 2022 +0800
-
-	Fix support for RISC-V.
-
-diff --git a/c++/src/build-system/config.guess b/c++/src/build-system/config.guess
-index f475ceb..57481db 100755
---- a/c++/src/build-system/config.guess
-+++ b/c++/src/build-system/config.guess
-@@ -979,6 +979,9 @@ EOF
-     ppc:Linux:*:*)
- 	echo powerpc-unknown-linux-gnu
- 	exit ;;
-+	riscv32:Linux:*:* | riscv32be:Linux:*:* | riscv64:Linux:*:* | riscv64be:Linux:*:*)
-+	echo ${UNAME_MACHINE}-unknown-linux-gnu
-+	exit ;;
-     s390:Linux:*:* | s390x:Linux:*:*)
- 	echo ${UNAME_MACHINE}-ibm-linux
- 	exit ;;

disable-a-dependency-module-that-is-not-actually-use.patch

@@ -1,53 +0,0 @@
-From b84f84f9bd7b418dff6e47bdf6b3008a5ab74cf0 Mon Sep 17 00:00:00 2001
-From: herengui <herengui@kylinsec.com.cn>
-Date: Tue, 3 Dec 2024 15:16:53 +0000
-Subject: [PATCH] disable a dependency module that is not actually used
-
-Signed-off-by: herengui <herengui@kylinsec.com.cn>
----
- c++/src/objects/CMakeLists.txt   | 1 -
- c++/src/objects/Makefile.in      | 2 +-
- c++/src/objects/Makefile.sources | 2 +-
- 3 files changed, 2 insertions(+), 3 deletions(-)
-
-diff --git a/c++/src/objects/CMakeLists.txt b/c++/src/objects/CMakeLists.txt
-index 42c240b..b37ec99 100644
---- a/c++/src/objects/CMakeLists.txt
-+++ b/c++/src/objects/CMakeLists.txt
-@@ -37,7 +37,6 @@ NCBI_add_subdirectory(
-   pcassay
-   pcassay2
-   pcsubstance
--  proj
-   pub
-   pubmed
-   remap
-diff --git a/c++/src/objects/Makefile.in b/c++/src/objects/Makefile.in
-index 6f4ea42..c9c507b 100644
---- a/c++/src/objects/Makefile.in
-+++ b/c++/src/objects/Makefile.in
-@@ -6,7 +6,7 @@
- USR_PROJ = sources
- 
- SUB_PROJ = general biblio medline pub seqcode seq seqset submit \
--           seqedit seqsplit id1 id2 entrez2 pubmed medlars mla proj \
-+           seqedit seqsplit id1 id2 entrez2 pubmed medlars mla \
-            scoremat blast blastdb blastxml blastxml2 mmdb cn3d cdd ncbimime \
-            pcsubstance pcassay pcassay2 gbseq insdseq tinyseq biotree entrezgene \
-            omssa remap seqtest taxon1 taxon3 gbproj trackmgr valerr valid \
-diff --git a/c++/src/objects/Makefile.sources b/c++/src/objects/Makefile.sources
-index cad3b3b..8c53cfe 100644
---- a/c++/src/objects/Makefile.sources
-+++ b/c++/src/objects/Makefile.sources
-@@ -13,7 +13,7 @@ include $(builddir)/Makefile.mk
- MODULES = omssa access biblio blast blastdb blastxml blastxml2 cdd cn3d docsum biotree \
-           entrez2 entrezgene featdef gbseq general id1 id2 insdseq \
-           macro medlars medline mim mla mmdb1 mmdb2 mmdb3 ncbimime objprt \
--          proj pub pubmed scoremat seq seqalign seqblock seqcode \
-+          pub pubmed scoremat seq seqalign seqblock seqcode \
-           seqfeat seqloc seqsplit seqres seqset submit taxon1 taxon3 tinyseq \
-           pcsubstance pcassay remap homologene seqedit seqtable seqtest \
-           trackmgr gbproj valerr valid genesbyloc
--- 
-2.43.0
-

ncbi-blast.spec

@@ -1,15 +1,11 @@
 Name:                ncbi-blast
-Version:             2.14.0
+Version:             2.12.0
-Release:             3
+Release:             2
 Summary:             NCBI BLAST finds regions of similarity between biological sequences.
 License:             Public Domain
 URL:                 https://blast.ncbi.nlm.nih.gov/Blast.cgi
-Source0:             https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-%{version}+-src.tar.gz
+Source0:             https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-src.tar.gz
-%ifarch riscv64
+BuildRequires:       lmdb lmdb-devel gcc-c++ make
-Patch0:              add-riscv-support.patch
-%endif
-Patch1:              disable-a-dependency-module-that-is-not-actually-use.patch
-BuildRequires:       gcc-c++ make cpio zlib-devel lmdb-devel bzip2-devel
 %description
 The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of
 local similarity between sequences. The program compares nucleotide or
@@ -20,53 +16,33 @@ members of gene families.
 
 %prep
 %autosetup -n %{name}-%{version}+-src -p1
-%ifarch loongarch64
-%_update_config_guess
-%_update_config_sub
-%endif
 
 %build
 cd c++
 export CFLAGS="%{build_cflags}"
 export CXXFLAGS="%{build_cxxflags}"
 export LDFLAGS="%{build_ldflags}"
-./configure  --prefix=/usr --with-dll --with-mt --with-bz2
+./configure
 cd ReleaseMT/build
 sed -i "s/-fPIC/-fPIC -g/g" Makefile.mk
 %make_build all_r
 
 %install
-cd c++
+install -d %{buildroot}%{_bindir}
-install -d -m 0755 %{buildroot}%{_bindir}
+install -d %{buildroot}%{_includedir}/ncbi-blast
-install -d -m 0755 %{buildroot}%{_includedir}/ncbi-tools++
+install -d %{buildroot}%{_libdir}/ncbi-blast
-install -d -m 0755 %{buildroot}%{_libdir}/
+rm -rf c++/ReleaseMT/bin/windowmasker_2.2.22_adapter.py
-rm -rf ReleaseMT/bin/windowmasker_2.2.22_adapter.py
+install -m 0755 c++/ReleaseMT/bin/* %{buildroot}%{_bindir}/
-install -m 0755 ReleaseMT/bin/* %{buildroot}%{_bindir}/
+cp -r c++/ReleaseMT/inc/* %{buildroot}%{_includedir}/ncbi-blast
-cp -r ReleaseMT/inc/* %{buildroot}%{_includedir}/ncbi-tools++
+cp c++/ReleaseMT/lib/* %{buildroot}%{_libdir}/ncbi-blast/
-cp -r ReleaseMT/lib/* %{buildroot}%{_libdir}/
 
 %files
 %defattr(-,root,root)
 %_bindir/*
-%{_includedir}/ncbi-tools++/*
+%{_includedir}/ncbi-blast/*
-%{_libdir}/*
+%{_libdir}/ncbi-blast/*
 
 %changelog
-* Tue Dec 03 2024 herengui <herengui@kylinsec.com.cn> - 2.14.0-3
-- Resolving ncbi-blast conflicts with bzip2 and proj
-
-* Tue Apr 2 2024 zhangxianting <zhangxianting@uniontech.com> - 2.14.0-2
-- not need requires package
-
-* Fri Jul 2 2023 guoyizhang <kuoi@bioarchlinux.org> - 2.14.0-1
-- update to 2.14.0
-
-* Wed May 31 2023 huajingyun <huajingyun@loongson.cn> - 2.12.0-4
-- update config.guess and config.sub for loongarch64
-
-* Thu Nov 24 2022 misaka00251 <liuxin@iscas.ac.cn> - 2.12.0-3
-- Add riscv support
-
 * Tue Feb 15 2022 herengui <herengui@uniontech.com> - 2.12.0-2
 - add missing buildrquires.
 

ncbi-blast.yaml

@@ -1,4 +0,0 @@
-version_control: github
-src_repo: ncbi-blast/ncbi-blast
-tag_prefix: ^
-separator: .