From 28cd404904d116e61e95ddc28168f555e48df9e8 Mon Sep 17 00:00:00 2001 From: Warren Togami Date: Mon, 23 Apr 2007 16:50:47 +0000 Subject: [PATCH 1/5] Initialize branch FC-6 for wise2 --- branch | 1 + 1 file changed, 1 insertion(+) create mode 100644 branch diff --git a/branch b/branch new file mode 100644 index 0000000..d5b6362 --- /dev/null +++ b/branch @@ -0,0 +1 @@ +FC-6 From 5d7b12b2bc2d25b85fa23779dfd3426bdb314e88 Mon Sep 17 00:00:00 2001 From: alexlan Date: Tue, 24 Apr 2007 05:27:07 +0000 Subject: [PATCH 2/5] Initial FC-6 import. --- .cvsignore | 1 + sources | 1 + wise2-build.patch | 10 ++++++ wise2.spec | 79 +++++++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 91 insertions(+) create mode 100644 wise2-build.patch create mode 100644 wise2.spec diff --git a/.cvsignore b/.cvsignore index e69de29..ba20b1d 100644 --- a/.cvsignore +++ b/.cvsignore @@ -0,0 +1 @@ +wise2.2.0.tar.gz diff --git a/sources b/sources index e69de29..8d1f2c3 100644 --- a/sources +++ b/sources @@ -0,0 +1 @@ +0584240f77885e37528e99e64535ab60 wise2.2.0.tar.gz diff --git a/wise2-build.patch b/wise2-build.patch new file mode 100644 index 0000000..1965c5b --- /dev/null +++ b/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 ) diff --git a/wise2.spec b/wise2.spec new file mode 100644 index 0000000..812d6f0 --- /dev/null +++ b/wise2.spec @@ -0,0 +1,79 @@ +Name: wise2 +Version: 2.2.0 +Release: 2%{?dist} +Summary: Tools for comparison of biopolymers + +Group: Applications/Engineering +License: GPL +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 +* Mon Apr 12 2007 Alex Lancaster 2.2.0-2 +- Pass $RPM_OPT_FLAGS to compiler as per suggestion from Ralf Corsepius. + +* Mon Apr 11 2007 Alex Lancaster 2.2.0-1 +- Initial Fedora package. From 2183557d89b3c5d18b9c26277debfa16a85a3373 Mon Sep 17 00:00:00 2001 From: alexlan Date: Fri, 17 Aug 2007 05:53:01 +0000 Subject: [PATCH 3/5] - Clarify license as BSD and GPLv2+ --- wise2.spec | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/wise2.spec b/wise2.spec index 812d6f0..b4482cc 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,10 +1,13 @@ Name: wise2 Version: 2.2.0 -Release: 2%{?dist} +Release: 3%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering -License: GPL +## 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 @@ -72,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Thu Aug 16 2007 Alex Lancaster 2.2.0-3 +- Clarify license as BSD and GPLv2+ + * Mon Apr 12 2007 Alex Lancaster 2.2.0-2 - Pass $RPM_OPT_FLAGS to compiler as per suggestion from Ralf Corsepius. From 8d8c0e237560256a8d92eaf4b3682ae1596a80f8 Mon Sep 17 00:00:00 2001 From: Bill Nottingham Date: Thu, 26 Nov 2009 01:17:28 +0000 Subject: [PATCH 4/5] Fix typo that causes a failure to update the common directory. (releng #2781) --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 6b22444..7015d7e 100644 --- a/Makefile +++ b/Makefile @@ -4,7 +4,7 @@ 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 "$$d/Makefile.common" ; break ; fi ; done +for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$d/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done endef MAKEFILE_COMMON := $(shell $(find-makefile-common)) From c93dd1804b0b9768ecc1e75d1389cbd975eae207 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 29 Jul 2010 15:22:09 +0000 Subject: [PATCH 5/5] dist-git conversion --- .cvsignore => .gitignore | 0 Makefile | 21 --------------------- branch | 1 - 3 files changed, 22 deletions(-) rename .cvsignore => .gitignore (100%) delete mode 100644 Makefile delete mode 100644 branch diff --git a/.cvsignore b/.gitignore similarity index 100% rename from .cvsignore rename to .gitignore diff --git a/Makefile b/Makefile deleted file mode 100644 index 7015d7e..0000000 --- a/Makefile +++ /dev/null @@ -1,21 +0,0 @@ -# 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 $$d/Makefile.common ] ; then cd $$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) diff --git a/branch b/branch deleted file mode 100644 index d5b6362..0000000 --- a/branch +++ /dev/null @@ -1 +0,0 @@ -FC-6