.cvsignore

@@ -0,0 +1 @@
+wise2.2.0.tar.gz

Makefile

@@ -0,0 +1,21 @@
+# Makefile for source rpm: wise2
+# $Id$
+NAME := wise2
+SPECFILE = $(firstword $(wildcard *.spec))
+
+define find-makefile-common
+for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done
+endef
+
+MAKEFILE_COMMON := $(shell $(find-makefile-common))
+
+ifeq ($(MAKEFILE_COMMON),)
+# attept a checkout
+define checkout-makefile-common
+test -f CVS/Root && { cvs -Q -d $$(cat CVS/Root) checkout common && echo "common/Makefile.common" ; } || { echo "ERROR: I can't figure out how to checkout the 'common' module." ; exit -1 ; } >&2
+endef
+
+MAKEFILE_COMMON := $(shell $(checkout-makefile-common))
+endif
+
+include $(MAKEFILE_COMMON)

dead.package

@@ -1 +0,0 @@
-Orphaned by upstream; no longer needed in Fedora

sources

@@ -0,0 +1 @@
+0584240f77885e37528e99e64535ab60  wise2.2.0.tar.gz

wise2-build.patch

@@ -0,0 +1,10 @@
+--- src/makefile.orig	2007-04-11 07:52:41.000000000 -0700
++++ src/makefile	2007-04-11 07:53:04.000000000 -0700
+@@ -89,7 +89,6 @@
+ bin : 
+ 	mkdir bin
+ 	mv models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/genomewise ./bin
+-	csh welcome.csh
+ 
+ libs : 
+ 	(cd base   ; make CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a )

wise2.spec

@@ -0,0 +1,91 @@
+Name:           wise2
+Version:        2.2.0
+Release:        5%{?dist}
+Summary:        Tools for comparison of biopolymers
+
+Group:          Applications/Engineering
+## Everything is licensed under a BSD-style license except for
+## the HMMer2 libraries and models directory which are GPLv2+
+## see LICENSE files for details. 
+License:        BSD and GPLv2+
+URL:            http://www.ebi.ac.uk/Wise2/
+Source0:        ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/wise%{version}.tar.gz
+Patch0:         wise2-build.patch
+BuildRoot:      %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+
+%description
+Wise2 is a package focused on comparisons of biopolymers, commonly DNA
+sequence and protein sequence.  A strength of Wise2 is the
+comparison of DNA sequence at the level of its protein
+translation. This comparison allows the simultaneous prediction of
+gene structure with homology based alignment.
+
+%prep
+%setup -q -n wise%{version}
+
+## don't run "welcome.csh"
+%patch0 -p0
+
+## fix interpreter in examples
+sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' docs/gettex.pl
+## fix perms 
+chmod -x test_data/rrm.HMM
+
+## pull out licenses
+for i in base dynlibsrc dyc
+do
+    cp src/$i/LICENSE LICENSE.$i
+done
+cp src/models/GNULICENSE LICENSE.GPL
+
+%build
+cd src
+## removed "{?_smp_mflags}", does not support parallel build
+make CC=gcc CFLAGS="-c $RPM_OPT_FLAGS" all
+
+%install
+rm -rf $RPM_BUILD_ROOT
+cd src/bin
+%{__mkdir_p} $RPM_BUILD_ROOT%{_bindir}
+for i in dba dnal estwise estwisedb genewise genewisedb genomewise psw pswdb
+do
+    %{__install} $i $RPM_BUILD_ROOT/%{_bindir} 
+done
+cd -
+# install architecture-independent data and config files
+%{__mkdir_p} $RPM_BUILD_ROOT%{_datadir}/wise2
+cd wisecfg
+%{__install} -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2
+
+# install scripts to automatically set the WISECONFIGDIR environment variable
+%{__mkdir_p} $RPM_BUILD_ROOT%{_sysconfdir}/profile.d
+echo "export WISECONFIGDIR=%{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.sh
+echo "setenv WISECONFIGDIR %{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.csh
+
+%clean
+rm -rf $RPM_BUILD_ROOT
+
+
+%files
+%defattr(-,root,root,-)
+%doc docs test_data
+%doc INSTALL LICENSE README LICENSE.base LICENSE.dynlibsrc LICENSE.dyc LICENSE.GPL
+%{_bindir}/*
+%{_datadir}/wise2
+%config(noreplace) %{_sysconfdir}/profile.d/*
+
+%changelog
+* Wed Feb 25 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.0-5
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild
+
+* Sat Feb  9 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 2.2.0-4
+- rebuilt for GCC 4.3 as requested by Fedora Release Engineering
+
+* Thu Aug 16 2007 Alex Lancaster <alexl@users.sourceforge.net> 2.2.0-3
+- Clarify license as BSD and GPLv2+
+
+* Mon Apr 12 2007 Alex Lancaster <alexl@users.sourceforge.net> 2.2.0-2
+- Pass $RPM_OPT_FLAGS to compiler as per suggestion from Ralf Corsepius.
+
+* Mon Apr 11 2007 Alex Lancaster <alexl@users.sourceforge.net> 2.2.0-1
+- Initial Fedora package.