commit: e5b4b8f74ae97147b52041ed4a8c1c9b03952a07 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Jul 21 09:00:57 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Jul 21 09:00:57 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e5b4b8f7
sci-biology/mira-4.9.5: fix missing AND in Makefile; install config files for staden and consed viewers/editors (maybe use config protect?) Package-Manager: portage-2.2.18 sci-biology/mira/ChangeLog | 5 +++++ .../mira-4.9.5-fix-miramer-symlink-error.patch | 22 ++++++++++++++++++++++ sci-biology/mira/mira-4.9.5.ebuild | 16 +++++++++++++++- 3 files changed, 42 insertions(+), 1 deletion(-) diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog index 8e61af5..68522a6 100644 --- a/sci-biology/mira/ChangeLog +++ b/sci-biology/mira/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.31 2015/04/07 14:33:30 jlec Exp $ + 21 Jul 2015; Martin Mokrejs <[email protected]> + +files/mira-4.9.5-fix-miramer-symlink-error.patch, mira-4.9.5.ebuild: + sci-biology/mira-4.9.5: fix missing AND in Makefile; install config files for + staden and consed viewers/editors (maybe use config protect?) + 08 Jun 2015; Justin Lecher <[email protected]> metadata.xml: sci-biology/mira: Updating remote-id in metadata.xml diff --git a/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch b/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch new file mode 100644 index 0000000..6bdda94 --- /dev/null +++ b/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch @@ -0,0 +1,22 @@ +--- mira-4.9.5/src/progs/Makefile.in.ori 2015-07-21 00:55:09.860884698 +0200 ++++ mira-4.9.5/src/progs/Makefile.in 2015-07-21 00:55:29.660884750 +0200 +@@ -717,7 +717,7 @@ + rm -f mirabait$(EXEEXT) && \ + $(LN_S) mira$(EXEEXT) mirabait$(EXEEXT) &&\ + rm -f miraconvert$(EXEEXT) && \ +- $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) \ ++ $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) && \ + rm -f miramer$(EXEEXT) && \ + $(LN_S) mira$(EXEEXT) miramer$(EXEEXT) + +--- mira-4.9.5/src/progs/Makefile.am.ori 2015-07-21 01:30:09.580890184 +0200 ++++ mira-4.9.5/src/progs/Makefile.am 2015-07-21 01:30:24.590890223 +0200 +@@ -51,7 +51,7 @@ + rm -f mirabait$(EXEEXT) && \ + $(LN_S) mira$(EXEEXT) mirabait$(EXEEXT) &&\ + rm -f miraconvert$(EXEEXT) && \ +- $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) \ ++ $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) && \ + rm -f miramer$(EXEEXT) && \ + $(LN_S) mira$(EXEEXT) miramer$(EXEEXT) + diff --git a/sci-biology/mira/mira-4.9.5.ebuild b/sci-biology/mira/mira-4.9.5.ebuild index e643b5b..ebd9e14 100644 --- a/sci-biology/mira/mira-4.9.5.ebuild +++ b/sci-biology/mira/mira-4.9.5.ebuild @@ -42,7 +42,8 @@ src_prepare() { find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die epatch \ "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \ - "${FILESDIR}"/${P}-cout.patch + "${FILESDIR}"/${P}-cout.patch \ + "${FILESDIR}"/${P}-fix-miramer-symlink-error.patch sed \ -e "s:-O[23]::g" \ @@ -71,6 +72,19 @@ src_install() { dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} + + # if sci-biology/staden is installed, ideally use configprotect? + if [ -e "${ED}"/usr/share/staden/etc/GTAGDB ]; then + if [ `grep -c HAF "${ED}"/usr/share/staden/etc/GTAGDB` -eq 0 ]; then + cat "${ED}"/usr/share/staden/etc/GTAGDB "${S}"/src/support/GTAGDB > "${WORKDIR}"/GTAGDB || die + insinto /usr/share/staden/etc/ + doins "${WORKDIR}"/GTAGDB + fi + fi + if [ -e "/etc/consedrc/" ]; then + insinto /etc/consedrc + doins "${S}"/src/support/consedtaglib.txt + fi } pkg_postinst() {
