Archie Cobbs
992971e53f
One package less failing in science. OBS-URL: https://build.opensuse.org/request/show/726471 OBS-URL: https://build.opensuse.org/package/show/science/xtandem?expand=0&rev=18
114 lines
3.7 KiB
RPMSpec
114 lines
3.7 KiB
RPMSpec
# $Id$
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#
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# Copyright 2013 Archie L. Cobbs.
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#
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# Licensed under the Apache License, Version 2.0 (the "License"); you may
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# not use this file except in compliance with the License. You may obtain
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# a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
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# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
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# License for the specific language governing permissions and limitations
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# under the License.
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#
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%define package_version 2017.02.01
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%define archive_version 17-02-01-4
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Name: xtandem
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Version: %{package_version}
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Release: 0
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Summary: Tool for protein identification from mass spectra
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License: Artistic-2.0
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Group: Productivity/Scientific/Chemistry
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URL: https://www.thegpm.org/TANDEM/index.html
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Source0: ftp://ftp.thegpm.org/projects/tandem/source/tandem-linux-%{archive_version}.zip
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Source1: %{name}.1
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Source2: tandem2csv.xsl
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Source3: plibrary.pl
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Source4: xtandem2mgf.1
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Patch0: sample-files.patch
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Patch1: error-message.patch
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Patch2: decomp.patch
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Patch3: plibrary.patch
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Patch4: no-spectra-segfault.patch
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Patch5: rt-seconds.patch
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Patch6: Fix-build-with-GCC7.patch
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BuildRequires: dos2unix
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BuildRequires: gcc-c++
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BuildRequires: libexpat-devel
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BuildRequires: make
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BuildRequires: tar
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BuildRequires: unzip
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BuildRequires: zlib-devel
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%description
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X! Tandem open source is software that can match tandem mass spectra
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with peptide sequences, in a process that has come to be known as protein
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identification.
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This software has a very simple, sophisticated application programming
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interface (API): it simply takes an XML file of instructions on its
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command line, and outputs the results into an XML file, which has been
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specified in the input XML file. This format is used for all of the X!
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series search engines, as well as the GPM and GPMDB.
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Unlike some earlier generation search engines, all of the X! Series search
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engines calculate statistical confidence (expectation values) for all of
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the individual spectrum-to-sequence assignments. They also reassemble all
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of the peptide assignments in a data set onto the known protein sequences
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and assign the statistical confidence that this assembly and alignment
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is non-random. Therefore, separate assembly and statistical analysis
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software, e.g. PeptideProphet and ProteinProphet, do not need to be used.
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%prep
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%setup -q -n tandem-linux-%{archive_version}
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cp %{SOURCE3} xtandem2mgf
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find . -type f -not -name "*.exe" -not -name "*.zip" -exec dos2unix {} \;
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%patch0 -p1
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%patch1 -p1
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%patch2 -p1
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%patch3 -p1
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%patch4 -p1
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%patch5 -p1
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%if 0%{?suse_version} >= 1500
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%patch6 -p1
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%endif
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%build
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( cd src && make -f Makefile_ubuntu %{?_smp_mflags} )
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%install
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# executables
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install -d %{buildroot}%{_bindir}
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install -m 755 bin/tandem.exe %{buildroot}%{_bindir}/%{name}
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install -m 755 xtandem2mgf %{buildroot}%{_bindir}/
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# man pages
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install -d %{buildroot}%{_mandir}/man1
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install -m 644 %{SOURCE1} %{buildroot}%{_mandir}/man1/%{name}.1
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install -m 644 %{SOURCE4} %{buildroot}%{_mandir}/man1/xtandem2mgf.1
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# sample files
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install -d %{buildroot}%{_datadir}/%{name}
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install -m 644 bin/*.xml %{buildroot}%{_datadir}/%{name}/
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install -m 644 bin/*.mgf %{buildroot}%{_datadir}/%{name}/
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# stylesheet files
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install -d %{buildroot}%{_datadir}/%{name}/xsl/
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install -m 644 bin/*.xsl bin/*.css %{buildroot}%{_datadir}/%{name}/xsl/
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install -m 644 %{SOURCE2} %{buildroot}%{_datadir}/%{name}/xsl/
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%files
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%license LICENSE
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%dir %{_datadir}/%{name}
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%{_bindir}/*
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%{_mandir}/man1/*
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%{_datadir}/%{name}/*
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%changelog
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