File xtandem.spec of Package xtandem

# $Id$

#
# Copyright 2013 Archie L. Cobbs.
# 
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
# 
#     http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
# License for the specific language governing permissions and limitations
# under the License.
# 

%define         package_version         2017.02.01
%define         archive_version         17-02-01-4
Name:           xtandem
Version:        %{package_version}
Release:        0
Summary:        Tool for protein identification from mass spectra
License:        Artistic-2.0
Group:          Productivity/Scientific/Chemistry
URL:            https://www.thegpm.org/TANDEM/index.html
Source0:        ftp://ftp.thegpm.org/projects/tandem/source/tandem-linux-%{archive_version}.zip
Source1:        %{name}.1
Source2:        tandem2csv.xsl
Source3:        plibrary.pl
Source4:        xtandem2mgf.1
Patch0:         sample-files.patch
Patch1:         error-message.patch
Patch2:         decomp.patch
Patch3:         plibrary.patch
Patch4:         no-spectra-segfault.patch
Patch5:         rt-seconds.patch
Patch6:         Fix-build-with-GCC7.patch
BuildRequires:  dos2unix
BuildRequires:  gcc-c++
BuildRequires:  libexpat-devel
BuildRequires:  make
BuildRequires:  tar
BuildRequires:  unzip
BuildRequires:  zlib-devel

%description
X! Tandem open source is software that can match tandem mass spectra
with peptide sequences, in a process that has come to be known as protein
identification.

This software has a very simple, sophisticated application programming
interface (API): it simply takes an XML file of instructions on its
command line, and outputs the results into an XML file, which has been
specified in the input XML file. This format is used for all of the X!
series search engines, as well as the GPM and GPMDB.

Unlike some earlier generation search engines, all of the X! Series search
engines calculate statistical confidence (expectation values) for all of
the individual spectrum-to-sequence assignments. They also reassemble all
of the peptide assignments in a data set onto the known protein sequences
and assign the statistical confidence that this assembly and alignment
is non-random. Therefore, separate assembly and statistical analysis
software, e.g. PeptideProphet and ProteinProphet, do not need to be used.

%prep
%setup -q -n tandem-linux-%{archive_version}
cp %{SOURCE3} xtandem2mgf
find . -type f -not -name "*.exe" -not -name "*.zip" -exec dos2unix {} \;
%patch0 -p1
%patch1 -p1
%patch2 -p1
%patch3 -p1
%patch4 -p1
%patch5 -p1
%if 0%{?suse_version} >= 1500
%patch6 -p1
%endif

%build
( cd src && make -f Makefile_ubuntu %{?_smp_mflags} )

%install

# executables
install -d %{buildroot}%{_bindir}
install -m 755 bin/tandem.exe %{buildroot}%{_bindir}/%{name}
install -m 755 xtandem2mgf %{buildroot}%{_bindir}/

# man pages
install -d %{buildroot}%{_mandir}/man1
install -m 644 %{SOURCE1} %{buildroot}%{_mandir}/man1/%{name}.1
install -m 644 %{SOURCE4} %{buildroot}%{_mandir}/man1/xtandem2mgf.1

# sample files
install -d %{buildroot}%{_datadir}/%{name}
install -m 644 bin/*.xml %{buildroot}%{_datadir}/%{name}/
install -m 644 bin/*.mgf %{buildroot}%{_datadir}/%{name}/

# stylesheet files
install -d %{buildroot}%{_datadir}/%{name}/xsl/
install -m 644 bin/*.xsl bin/*.css %{buildroot}%{_datadir}/%{name}/xsl/
install -m 644 %{SOURCE2} %{buildroot}%{_datadir}/%{name}/xsl/

%files
%license LICENSE
%dir %{_datadir}/%{name}
%{_bindir}/*
%{_mandir}/man1/*
%{_datadir}/%{name}/*

%changelog