137 lines
3.7 KiB
RPMSpec
137 lines
3.7 KiB
RPMSpec
%define _lto_cflags %{nil}
|
|
|
|
Name: wise2
|
|
Version: 2.4.1
|
|
Release: %autorelease
|
|
Summary: Tools for comparison of bio-polymers
|
|
|
|
## 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-3-Clause AND GPL-2.0-or-later
|
|
URL: http://www.ebi.ac.uk/~birney/%{name}/
|
|
Source0: http://www.ebi.ac.uk/~birney/%{name}/wise%{version}.tar.gz
|
|
|
|
## Patches from Debian package. Thanks to Philipp Benner
|
|
Patch0: %{name}-build.patch
|
|
Patch1: %{name}-isnumber.patch
|
|
Patch2: %{name}-glib2.patch
|
|
Patch3: %{name}-getline.patch
|
|
Patch4: %{name}-ld--as-needed.patch
|
|
Patch5: %{name}-mayhem.patch
|
|
Patch6: %{name}-c99.patch
|
|
|
|
BuildRequires: make
|
|
BuildRequires: glib2-devel
|
|
BuildRequires: gcc
|
|
BuildRequires: perl
|
|
BuildRequires: strace
|
|
|
|
%description
|
|
Wise2 is a package focused on comparisons of bio-polymers, 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.
|
|
|
|
|
|
%package doc
|
|
Summary: Wise2 documentation
|
|
BuildArch: noarch
|
|
|
|
%description doc
|
|
Wise2, Wise2api and Dynamite documentation files.
|
|
|
|
|
|
%package examples
|
|
Summary: Wise2 examples
|
|
Requires: %{name}%{?_isa} = %{version}-%{release}
|
|
|
|
%description examples
|
|
Here are some examples that you might want to try out. The
|
|
Wise2 executables of course should be installed before.
|
|
|
|
%prep
|
|
%autosetup -p1 -n wise%{version}
|
|
|
|
# Remove spurious-executable-perm
|
|
chmod a-x src/external/mott/mott_api.c
|
|
chmod a-x src/external/mott/mott_api.h
|
|
chmod a-x src/external/mott/gaplib.c
|
|
chmod a-x src/external/mott/gapstat.h
|
|
|
|
## 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
|
|
## removed "{?_smp_mflags}", does not support parallel build
|
|
export LDFLAGS="%{__global_ldflags}"
|
|
make -C src CC=gcc \
|
|
CFLAGS=" -c %{build_cflags} -pthread -D_GNU_SOURCE %(pkg-config --cflags glib-2.0) -D_POSIX_C_SOURCE=200112L" all
|
|
|
|
%install
|
|
pushd src/bin
|
|
mkdir -p $RPM_BUILD_ROOT%{_bindir}
|
|
for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb
|
|
do
|
|
install -pm 755 $i $RPM_BUILD_ROOT%{_bindir}
|
|
done
|
|
popd
|
|
|
|
# install architecture-independent data and config files
|
|
mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2
|
|
pushd wisecfg
|
|
install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2
|
|
popd
|
|
|
|
# install architecture-independent files to run example tests
|
|
mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2/examples
|
|
pushd test_data
|
|
install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2/examples
|
|
popd
|
|
|
|
# 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/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.csh
|
|
|
|
%check
|
|
export WISECONFIGDIR=$PWD/wisecfg
|
|
make -C src test
|
|
|
|
%files
|
|
%doc README
|
|
%license LICENSE LICENSE.base LICENSE.dynlibsrc LICENSE.dyc LICENSE.GPL
|
|
%{_bindir}/genewisedb
|
|
%{_bindir}/estwisedb
|
|
%{_bindir}/genewise
|
|
%{_bindir}/estwise
|
|
%{_bindir}/scanwise
|
|
%{_bindir}/promoterwise
|
|
%{_bindir}/pswdb
|
|
%{_bindir}/dba
|
|
%{_bindir}/psw
|
|
%{_bindir}/scanwise_server
|
|
%{_bindir}/dnal
|
|
%{_datadir}/wise2/
|
|
%config(noreplace) %{_sysconfdir}/profile.d/*
|
|
|
|
%files doc
|
|
%license LICENSE
|
|
%doc docs
|
|
|
|
%files examples
|
|
%doc test_data/README
|
|
%{_datadir}/wise2/examples/
|
|
|
|
%changelog
|
|
%autochangelog
|