%global debug_package %{nil}


Name:           trans-proteomic-pipeline
Version:        6.0.0
Release:        1%{?dist}
Summary:        The Trans-Proteomic Pipeline (TPP) includes all of the steps of the ISB MS/MS analysis pipeline.

License:        GPLv2.1
URL:            http://tools.proteomecenter.org/software.php
#Source0: 	TPP_6.0.0-src.tgz

Source0:	https://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v6.0%20%28OmegaBlock%29%20rev%200/TPP_6.0.0-src.tgz

BuildRequires:	g++ libstdc++-static glibc-static findutils patch subversion swig expat gnuplot bzip2 bzip2-devel unzip 
BuildRequires:	zlib-devel perl-XML-Parser perl-ExtUtils-MakeMaker
BuildRequires:	boost-devel boost-system boost-program-options boost-filesystem boost-iostreams boost-regex boost-thread boost-chrono boost-serialization

# Fedora gsl is 2.6, however tpp expects 1.14

%description
  	
PROTEOMICS TOOLS


The Trans-Proteomic Pipeline (TPP) includes all of the steps of the ISB MS/MS analysis pipeline, after the database search.

%prep
ls
echo "=========="
%setup -n release_6-0-0
ls


%build

# installer_linux wants me to `cd $(SRC_DIR)/src`, however, libcommon failed due to
# make: *** No rule to make target '/dev/shm/src/release_6-0-0/build/linux-x86_64-rc28/artifacts/TPPVersionInfo.o', needed by '/dev/shm/src/release_6-0-0/build/linux-x86_64-rc28/lib/libtpp.a'.  Stop.




#It even succeeded without sed. Then why not compile all dependencies?
sed -i 's/boost comet d3 expat fann gsl gzstream/boost comet expat fann gsl gzstream/' extern/Makefile


make  all


# make: *** No rule to make target '/src/release_6-0-0/build/linux-x86_64-rc28/html/', needed by 'd3'.  Stop.
# EXTERN_ALL ?= boost comet d3 expat fann gsl gzstream
# EXTERN_ALL ?= comet expat fann gzstream 
# Also avoid remaking boost

# -j8 seems causing errors

#%make_build

# make install
# install the files to /usr/local/tpp so it's easier to locate them
# no permission on copr

%install
echo "============= install bin =========="

# Binary
mkdir -p %{buildroot}%{_bindir}
install -m 755 build/linux-x86_64-rc28/bin/spectrast %{buildroot}%{_bindir}
#install -m 444 installer_win32/license.txt 



# in /usr/local/tpp/bin we hve
# [root@defe2c215412 bin]# ls
# ASAPRatioPeptideParser       RefreshParser              fileDownloader.pl
# ASAPRatioProteinRatioParser  RespectParser              fixPepXMLScan
# ASAPRatioPvalueParser        SPACEPro                   get_prots.pl
# CombineOut                   SSRCalc3.par               hardklor
# CompactParser                SSRCalc3.pl                idconvert
# DIALib-QC_RPlot.pl           Sequest2XML                indexmzXML
# DatabaseParser               Sqt2XML                    mergeCharges.pl
# DidIScanThat                 StPeter                    msconvert
# DiscoFilter                  StPeter2Matrix             novor2xml.pl
# EnzymeDigestionParser        Tandem2XML                 out2summary
# InterProphetParser           XPressPeptideParser        pepExtract
# InteractParser               XPressProteinRatioParser   pep_dbcount
# Kojak                        add_mz                     plotspectrast
# Lib2HTML                     assess_swathlib.pl         promast.pl
# LibraPeptideParser           batchcoverage              ptm2plot.pl
# LibraProteinRatioParser      calculate_pi               qtofpeakpicker
# Mascot2XML                   checkdb                    quiddist.pl
# Mayu.pl                      clips.pl                   readmzXML
# MikesMagicalMzMLShrinker     clustalo                   renamedat.pl
# MzXML2Search                 clustalo-README.txt        replaceall.pl
# Out2XML                      comet                      runMzIndex.pl
# PTMProphetParser             comparePeps_Categories.pl  spectrast
# PeptideMapper                compareProts.pl            subsetdb
# PeptideProphetParser         compareProts_ClusterHM.pl  tandem
# ProphetModels.pl             compute_p                  test_tpi.pl
# ProtProphModels.pl           createChargeFile.pl        tpp2mzid
# ProteinProphet               crypt                      tpp_hostname
# Q3ProteinRatioParser         decoyFASTA                 tpp_models.pl
# QuanticParser                decoyFastaGenerator.pl     tpptray.bat
# QuanticProteinParser         digestdb                   translateDNA2AA-FASTA
# RTCalc                       dta2mzxml                  updatepaths.pl
# RTCatalogParser              exporTPP.pl                xinteract

# rpmbuild -bs ~/rpmbuild/SPECS/trans-proteomic-pipeline.spec  && mock --enable-plugin=tmpfs --enable-plugin=yum_cache  ~/rpmbuild/SRPMS/trans-proteomic-pipeline-6.0.0-1.fc35.src.rpm

%clean
rm -rf %{buildroot}


%files
%{_bindir}/spectrast
%license installer_win32/license.txt 


%changelog

* Wed Sep 01 2021 Zhenbo Li <lizhenbo@yahoo.com> - 6.0.0-1
- Initial version of the package