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File ncbi.spec of Package ncbi
# # spec file for package ncbi # # Copyright (c) 2012 SUSE LINUX Products GmbH, Nuernberg, Germany. # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed # upon. The license for this file, and modifications and additions to the # file, is the same license as for the pristine package itself (unless the # license for the pristine package is not an Open Source License, in which # case the license is the MIT License). An "Open Source License" is a # license that conforms to the Open Source Definition (Version 1.9) # published by the Open Source Initiative. # Please submit bugfixes or comments via http://bugs.opensuse.org/ # Name: ncbi Summary: NCBI Software Development Toolkit License: SUSE-Public-Domain Group: Productivity/Scientific/Other Version: 6.1 Release: 0 BuildRequires: fdupes BuildRequires: gcc BuildRequires: openmotif-devel BuildRequires: tcsh %if 0%{?suse_version} > 1140 BuildRequires: libjpeg-devel BuildRequires: pkgconfig(libpng) BuildRequires: pkgconfig(xmuu) BuildRequires: pkgconfig(xp) %endif Source: %{name}.tar.gz Patch0: ncbi-6.1-link-to-shared-motif.patch Patch1: ncbi-6.1-optflags.patch Patch2: ncbi-6.1-strncat-overflow.patch Patch3: ncbi-6.1-math-meaning.patch Patch4: ncbi-6.1-null-pointer.patch Patch5: ncbi-6.1-no-return.patch Patch6: ncbi-6.1-sequence-point.patch BuildRoot: %{_tmppath}/%{name}-%{version}-build Url: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbi.tar.gz %define wwwblastdir /var/lib/wwwblast %description The NCBI Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI. %package blast Summary: Basic Local Alignment and Search Tool Group: Productivity/Scientific/Other Requires: ncbi-data %description blast The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. %package tools Summary: Utilities from the NCBI toolkit Group: Productivity/Scientific/Other Requires: ncbi-data %description tools This packages includes the binaries excluding the blast programs. Also contains documentation and man pages. %package wwwblast Summary: Web-interface to the NCBI BLAST set of programs Group: Productivity/Scientific/Other Requires: apache2 Url: http://www.ncbi.nlm.nih.gov/BLAST/ %description wwwblast The wwwblast package contains a suite of standalone programs that perform various similarity searches using the BLAST heuristic algorithm. Similar to the NCBI BLAST server http://www.ncbi.nlm.nih.gov/blast/. wwwblast provides a graphic user interface (GUI) through the use of web forms. Individual program takes the user inputs from the web form and returns the search result to a browser window. There are different web forms for different BLAST programs. %package data Summary: NCBI toolkit data files Group: Productivity/Scientific/Other %description data Data files used by programs in the NCBI toolkit. %package devel Summary: NCBI toolkit header files needed for development Group: Development/Libraries/C and C++ %description devel This package contains the header files required for development of software using the NCBI toolkit. %prep %setup -q -c %{name} %patch0 %patch1 %patch2 %patch3 %patch4 %patch5 %patch6 # fix __DATE and __TIME this causes the package to rebuild when not needed BUILDTIME=$(LC_ALL=C date -ur %{_sourcedir}/%{name}.changes +'%H:%M') BUILDDATE=$(LC_ALL=C date -ur %{_sourcedir}/%{name}.changes +'%b %d %Y') sed -i "s/__TIME__/\"$BUILDTIME\"/" $(grep -rl '__TIME__' ncbi) sed -i "s/__DATE__/\"$BUILDDATE\"/" $(grep -rl '__DATE__' ncbi) sed -i 's/datetime/\dati/g' $(grep -rl 'datetime' ncbi) #remove executable permissions chmod -x ncbi/doc/blast/web_blast.pl chmod -x ncbi/doc/fwd_check.sh chmod -x ncbi/doc/fa2htgs/updateHtgsDoc #remove zero-length files cd ncbi/network/wwwblast rm wwwblast.log psiblast.log rpsblast.log sed -i 's:/usr/local/bin/perl:/usr/bin/perl:' config_setup.pl %build export CFLAGS="$RPM_OPT_FLAGS" ./ncbi/make/makedis.csh %install #install wwwblast *.cgi and *.REAL binaries mkdir -p %{buildroot}/%{wwwblastdir} cd ncbi install -m 755 bin/*.REAL %{buildroot}/%{wwwblastdir}/ install -m 755 bin/*.cgi %{buildroot}/%{wwwblastdir}/ rm -rf bin/*.REAL rm -rf bin/*.cgi #all other binaries mkdir -p %{buildroot}/%{_bindir} install -m 755 bin/* %{buildroot}/%{_bindir}/ #rename rpsblast as rpsblast-legacy (avoid conflict with blast+) mv %{buildroot}/%{_bindir}/rpsblast %{buildroot}/%{_bindir}/rpsblast-legacy #devel files mkdir -p %{buildroot}/%{_includedir}/ncbi cd include for m in `find . -type d`; do install -d -m 755 $m %{buildroot}/%{_includedir}/ncbi/$m done for n in `find . -type f`; do install -m 644 $n %{buildroot}/%{_includedir}/ncbi/$n done cd .. #documentation mkdir -p %{buildroot}/%{_mandir}/man1 install -m 644 doc/man/*.1 %{buildroot}/%{_mandir}/man1/ rm -rf doc/man mkdir -p %{buildroot}/%{_docdir}/ncbi-blast install -m 644 doc/blast/* %{buildroot}/%{_docdir}/ncbi-blast/ rm -rf doc/blast #data files mkdir -p %{buildroot}/%{_datadir}/ncbi/data install -m 644 data/* %{buildroot}/%{_datadir}/ncbi/data #wwwblast cd network/wwwblast for j in `find . -type d`; do install -d -m 755 %{buildroot}/%{wwwblastdir}/$j done mkdir -p %{buildroot}/%{wwwblastdir}/TmpGifs for k in `find . -type f`; do install -m 644 $k %{buildroot}/%{wwwblastdir}/$k; done cd %{buildroot}/%{wwwblastdir}/ for m in `find . -name '*.cgi'`; do chmod 755 $m; done chmod 755 %{buildroot}/%{wwwblastdir}/db/CDD/rpsfdb.csh chmod 755 %{buildroot}/%{wwwblastdir}/db/CDD/make_cdd.csh chmod 755 %{buildroot}/%{wwwblastdir}/config_setup.pl mkdir -p %{buildroot}/%{_sysconfdir}/apache2/conf.d cat << __EOF__ >> %{buildroot}/%{_sysconfdir}/apache2/conf.d/wwwblast.conf Alias /blast "/var/lib/wwwblast/" <Directory "/var/lib/wwwblast"> Options ExecCGI AllowOverride None AddHandler cgi-script .cgi .REAL Order allow,deny Allow from all </Directory> __EOF__ # create a dummy target for /etc/alternatives/rpsblast (avoid conflict with blast+) mkdir -p %{buildroot}%{_sysconfdir}/alternatives ln -s -f %{_sysconfdir}/alternatives/rpsblast %{buildroot}%{_bindir}/rpsblast %fdupes -s %{buildroot} %post blast update-alternatives --install \ %{_bindir}/rpsblast rpsblast %{_bindir}/rpsblast-legacy 15 %postun blast if [ ! -f %{_bindir}/rpsblast-legacy ] ; then update-alternatives --remove rpsblast %{_bindir}/rpsblast-legacy fi %clean %files blast %defattr(-,root,root) %{_bindir}/bl2seq %{_bindir}/blastall %{_bindir}/blastclust %{_bindir}/blastpgp %{_bindir}/copymat %{_bindir}/fastacmd %{_bindir}/formatdb %{_bindir}/formatrpsdb %{_bindir}/impala %{_bindir}/makemat %{_bindir}/megablast %{_bindir}/rpsblast %{_bindir}/rpsblast-legacy %{_bindir}/seedtop %{_docdir}/ncbi-blast %ghost %_sysconfdir/alternatives/rpsblast %files tools %defattr(-,root,root) %exclude %{_bindir}/bl2seq %exclude %{_bindir}/blastall %exclude %{_bindir}/blastclust %exclude %{_bindir}/blastpgp %exclude %{_bindir}/copymat %exclude %{_bindir}/fastacmd %exclude %{_bindir}/formatdb %exclude %{_bindir}/formatrpsdb %exclude %{_bindir}/impala %exclude %{_bindir}/makemat %exclude %{_bindir}/megablast %exclude %{_bindir}/rpsblast %exclude %{_bindir}/rpsblast-legacy %exclude %{_bindir}/seedtop %{_bindir}/* %{_mandir}/man1/* %doc ncbi/doc/* %files wwwblast %defattr(-,wwwrun,www) %dir %attr(-,root,root) /etc/apache2 %dir %attr(-,root,root) /etc/apache2/conf.d %config(noreplace) %attr(-,root,root) %{_sysconfdir}/apache2/conf.d/wwwblast.conf %dir /var/lib/wwwblast %config(noreplace) /var/lib/wwwblast/*.rc %exclude /var/lib/wwwblast/Src /var/lib/wwwblast/* %files data %defattr(-,root,root) %{_datadir}/ncbi %files devel %defattr(-,root,root) %{_includedir}/ncbi %changelog
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