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5 changed files with 1 additions and 109 deletions
1
.gitignore
vendored
1
.gitignore
vendored
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@ -1 +0,0 @@
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wise2.2.0.tar.gz
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1
dead.package
Normal file
1
dead.package
Normal file
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@ -0,0 +1 @@
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Orphaned by upstream; no longer needed in Fedora
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1
sources
1
sources
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0584240f77885e37528e99e64535ab60 wise2.2.0.tar.gz
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@ -1,10 +0,0 @@
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--- src/makefile.orig 2007-04-11 07:52:41.000000000 -0700
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+++ src/makefile 2007-04-11 07:53:04.000000000 -0700
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@@ -89,7 +89,6 @@
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bin :
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mkdir bin
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mv models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/genomewise ./bin
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- csh welcome.csh
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libs :
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(cd base ; make CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a )
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97
wise2.spec
97
wise2.spec
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@ -1,97 +0,0 @@
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Name: wise2
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Version: 2.2.0
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Release: 7%{?dist}
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Summary: Tools for comparison of biopolymers
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Group: Applications/Engineering
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## Everything is licensed under a BSD-style license except for
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## the HMMer2 libraries and models directory which are GPLv2+
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## see LICENSE files for details.
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License: BSD and GPLv2+
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URL: http://www.ebi.ac.uk/Wise2/
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Source0: ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/wise%{version}.tar.gz
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Patch0: wise2-build.patch
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BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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%description
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Wise2 is a package focused on comparisons of biopolymers, commonly DNA
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sequence and protein sequence. A strength of Wise2 is the
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comparison of DNA sequence at the level of its protein
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translation. This comparison allows the simultaneous prediction of
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gene structure with homology based alignment.
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%prep
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%setup -q -n wise%{version}
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## don't run "welcome.csh"
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%patch0 -p0
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## fix interpreter in examples
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sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' docs/gettex.pl
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## fix perms
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chmod -x test_data/rrm.HMM
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## pull out licenses
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for i in base dynlibsrc dyc
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do
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cp src/$i/LICENSE LICENSE.$i
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done
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cp src/models/GNULICENSE LICENSE.GPL
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%build
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cd src
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## removed "{?_smp_mflags}", does not support parallel build
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make CC=gcc CFLAGS="-c $RPM_OPT_FLAGS -D_POSIX_C_SOURCE=200112L" all
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%install
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rm -rf $RPM_BUILD_ROOT
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cd src/bin
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%{__mkdir_p} $RPM_BUILD_ROOT%{_bindir}
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for i in dba dnal estwise estwisedb genewise genewisedb genomewise psw pswdb
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do
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%{__install} $i $RPM_BUILD_ROOT/%{_bindir}
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done
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cd -
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# install architecture-independent data and config files
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%{__mkdir_p} $RPM_BUILD_ROOT%{_datadir}/wise2
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cd wisecfg
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%{__install} -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2
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# install scripts to automatically set the WISECONFIGDIR environment variable
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%{__mkdir_p} $RPM_BUILD_ROOT%{_sysconfdir}/profile.d
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echo "export WISECONFIGDIR=%{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.sh
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echo "setenv WISECONFIGDIR %{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.csh
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%clean
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rm -rf $RPM_BUILD_ROOT
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%files
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%defattr(-,root,root,-)
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%doc docs test_data
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%doc INSTALL LICENSE README LICENSE.base LICENSE.dynlibsrc LICENSE.dyc LICENSE.GPL
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%{_bindir}/*
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%{_datadir}/wise2
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%config(noreplace) %{_sysconfdir}/profile.d/*
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%changelog
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* Mon Jul 27 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-7
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild
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* Thu Jul 16 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 2.2.0-6
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- Add -D_POSIX_C_SOURCE=200112L to CFLAGS as a workaround to fix FTBFS (#511627)
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* Wed Feb 25 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-5
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild
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* Sat Feb 9 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 2.2.0-4
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- rebuilt for GCC 4.3 as requested by Fedora Release Engineering
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* Thu Aug 16 2007 Alex Lancaster <alexl@users.sourceforge.net> 2.2.0-3
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- Clarify license as BSD and GPLv2+
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* Mon Apr 12 2007 Alex Lancaster <alexl@users.sourceforge.net> 2.2.0-2
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- Pass $RPM_OPT_FLAGS to compiler as per suggestion from Ralf Corsepius.
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* Mon Apr 11 2007 Alex Lancaster <alexl@users.sourceforge.net> 2.2.0-1
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- Initial Fedora package.
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