--- /dev/null
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/staden-1.5.3-r1.ebuild,v 1.1 2005/11/13 05:38:39 ribosome Exp $
+
+inherit eutils toolchain-funcs fortran
+
+TCLV="8.4.6"
+TKV="8.4.6"
+
+DESCRIPTION="The Staden Package - Biological sequence handling and analysis"
+LICENSE="${PN}"
+HOMEPAGE="http://staden.sourceforge.net"
+SRC_URI="mirror://sourceforge/${PN}/${PN}-src-${PV//./-}.tar.gz
+ mirror://gentoo/${PN}-1.4.1-missing-doc.tar.bz2
+ mirror://sourceforge/tcl/tcl${TCLV}-src.tar.gz
+ mirror://sourceforge/tcl/tk${TKV}-src.tar.gz
+ doc? ( mirror://sourceforge/${PN}/course-1.1.tar.gz )"
+
+SLOT="0"
+IUSE="doc"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="app-shells/ksh
+ dev-lang/tcl
+ dev-lang/tk
+ sci-libs/io_lib
+ =dev-tcltk/itcl-3.2*
+ dev-tcltk/iwidgets
+ media-libs/libpng
+ virtual/x11"
+
+DEPEND="${RDEPEND}
+ dev-lang/perl
+ media-gfx/imagemagick
+ virtual/emacs
+ virtual/tetex"
+
+S="${WORKDIR}/${PN}-src-${PV//./-}"
+
+src_unpack() {
+ unpack ${A}
+ mv "${WORKDIR}"/tcl${TCLV} "${S}"/src
+ mv "${WORKDIR}"/tk${TKV} "${S}"/src
+
+ # The following Makefiles are more or less broken. Libraries are missing,
+ # or their directories are not included, or the variables are not set
+ # correctly and must be replaced by hardcoded library names. The
+ # top-level Makefile is also changed to avoid compiling documentation
+ # (which is provided prebuilt because of numerous compilation/dead links
+ # problems).
+ cd "${S}"
+ epatch "${FILESDIR}"/${P}-top.patch
+ epatch "${FILESDIR}"/${P}-text_utils.patch
+ epatch "${FILESDIR}"/${P}-tk_utils.patch
+ epatch "${FILESDIR}"/${P}-prefinish.patch
+ epatch "${FILESDIR}"/${P}-tracediff.patch
+ epatch "${FILESDIR}"/${P}-mutscan.patch
+ epatch "${FILESDIR}"/${P}-mutlib-gcc-3.4.patch
+ cd "${S}"/src/mk
+ # Remove the "-fpic" flag. This will be replaced by "-fPIC".
+ sed -i -e 's/SHLIB_CFLAGS = -fpic/SHLIB_CFLAGS = /' linux.mk || die
+ cd "${S}"
+
+ # "getopt" is incorrectly included as an extern (for Win32 compatibility).
+ epatch "${FILESDIR}"/${P}-getopt.patch
+
+ # The original iwidgetsrc crashes...
+ einfo 'Replacing broken iwidgetsrc'
+ cp "${FILESDIR}"/${P}-iwidgetsrc.new "${S}"/tables/iwidgetsrc
+
+ # Netscape is not a good default browser (security masked in Portage).
+ # Use documentation.html rather than staden_home.html as the top-level
+ # hypertext documentation file.
+ einfo 'Replacing old staden_help script.'
+ cp "${FILESDIR}"/${P}-staden_help.new "${S}"/src/scripts/staden_help
+ chmod +x "${S}"/src/scripts/staden_help
+
+ # The documentation building process is broken on Gentoo, mainly because
+ # incorrect program locations are assumed.
+ einfo "Patching Staden Package documentation build system."
+
+ # Documentation build process cannot find "update-nodes.el".
+ cd "${S}"/doc/manual/tools
+ sed -i -e 's%emacs -batch $1 -l ${DOCDIR:-.}/tools/update-nodes.el%emacs -batch $1 -l ${DOCDIR:-..}/manual/tools/update-nodes.el%' update-nodes || die
+
+ # Perl scripts search for "pearl" in "/usr/local".
+ for SCRIPT in *.pl texi2html; do
+ sed -i -e 's%/usr/local/bin/perl%/usr/bin/perl%' ${SCRIPT} || die
+ done
+
+ # The "convert" tool from Imagemagick is searched for in "/usr/X11R6".
+ sed -i -e 's%/usr/X11R6/bin/convert%/usr/bin/convert%' make_ps | die
+
+ # Solves issues with images in the exercise* texi files.
+ cd "${S}"/course/texi
+ for FILE in exercise*.texi; do
+ sed -i -e 's/,,8in}/,,8in,,eps}/' ${FILE}
+ sed -i -e 's/,6in}/,6in,,,eps}/' ${FILE}
+ done
+
+ # "CFLAGS" and "FFLAGS" need to be set to the user's values in the build
+ # system global Makefile. We also want only "-fPIC" shared libraries.
+ einfo "Applying user-defined compilation/linking flags:"
+ cd "${S}"/src/mk
+ sed -e "s/COPT = -O2 -g3 -DNDEBUG/COPT = ${CFLAGS:-"-O2 -g3 -DNDEBUG"} -fPIC/" \
+ -e "s/FOPT = -O2 -g3 -DNDEBUG/FOPT = ${FFLAGS:-"-O2 -g3 -DNDEBUG"} -fPIC/" \
+ -i global.mk || die
+}
+
+src_compile() {
+ # "MACHINE", "{STADEN,SRC}ROOT" and "JOB" are mandatory arguments to the
+ # Staden Package build process. "O" is redefined on the command line to
+ # avoid a conflict between Portage and the Staden Package build system,
+ # which both use this variable. (In Portage, its value is the directory
+ # containing the current ebuild, while in the Staden Package build system
+ # it is set to the directory containing the compiler object files.)
+ # Compiler program names also need to be specified to override the
+ # incorrect hardcoded ones.
+
+ # Compile executables and libraries.
+ make \
+ STADENROOT="${S}" \
+ SRCROOT="${S}/src" \
+ MACHINE="linux" \
+ JOB="all" \
+ O="linux-binaries" \
+ CC=$(tc-getCC) \
+ CXX=$(tc-getCXX) \
+ F77=${F77:-g77} \
+ || die "Package compilation failed."
+
+ # Build documentation.
+ cd "${S}"/doc
+ make \
+ STADENROOT="${S}" \
+ SRCROOT="${S}/src" \
+ MACHINE="linux" \
+ JOB="all" \
+ O="linux-binaries" \
+ CC=$(tc-getCC) \
+ CXX=$(tc-getCXX) \
+ F77=${F77:-g77} \
+ || die "Package compilation failed."
+
+
+ # The install process will copy the libraries in ${S}/lib/linux-binaries,
+ # but this directory is in fact a symlink to the source directory.
+ rm "${S}"/lib/linux-binaries
+ mkdir "${S}"/lib/linux-binaries
+
+ # Moves executables in "${S}/linux-bin" and libraries to
+ # ${S}/lib/linux-binaries.
+ cd "${S}"
+ make \
+ STADENROOT="${S}" \
+ SRCROOT="${S}/src" \
+ MACHINE="linux" \
+ JOB="all" \
+ O="linux-binaries" \
+ install || die "Package pre-installation failed."
+
+ # Remove Makefiles from directories which will be manually installed.
+ rm "${S}"/lib/Makefile
+ rm "${S}"/demo/Makefile
+ rm "${S}"/tables/Makefile
+ rm "${S}"/userdata/Makefile
+
+ #Remove libread since an updated version is included in "sci-libs/io_lib".
+ rm "${S}"/lib/linux-binaries/libread.so
+ # Delete the binaries already included in "sci-libs/io_lib".
+ for FILE in convert_trace \
+ extract_seq \
+ get_comment \
+ index_tar \
+ makeSCF \
+ scf_{dump,info,update} \
+ trace_dump; do
+ rm "${S}"/linux-bin/${FILE}
+ done
+
+ # These won't be found if they are not symlinked in the lib dir.
+ ln -s /usr/$(get_libdir)/libitcl3.2.so "${S}"/lib/itcl3.3/libitcl3.3.so
+ ln -s /usr/$(get_libdir)/libitk3.2.so "${S}"/lib/itk3.3/libitk3.3.so
+
+ # Remove the (broken) prebuilt EMBOSS tcl/tk GUIs.
+ rm "${S}"/tables/emboss_menu
+ rm -r "${S}"/lib/spin2_emboss/acdtcl
+ rm -r "${S}"/lib/spin_emboss/acdtcl
+
+ # Patch hypertext documentation.
+ cd "${S}"/doc/manual
+ for FILE in *.html; do
+ sed -i -e 's%<a href="../staden_home.html"><img src="i/nav_home.gif" alt="home"></a>%%' ${FILE}
+ done
+ cd "${S}"/doc/scripting_manual
+ for FILE in *.html; do
+ sed -i -e 's%<a href="../staden_home.html"><img src="i/nav_home.gif" alt="home"></a>%%' ${FILE}
+ done
+}
+
+src_install() {
+ # Executables and libraries
+ mkdir -p "${D}"/opt/${PN}
+
+ for FILE in "${S}"/lib/linux-binaries/*; do
+ dolib ${FILE}
+ done
+
+ mv "${S}"/linux-bin "${D}"/opt/${PN}/linux-bin
+ mv "${S}"/lib "${D}"/opt/${PN}/lib
+
+ # Shared files
+ mv "${S}"/demo "${D}"/opt/${PN}
+ mv "${S}"/tables "${D}"/opt/${PN}
+ mv "${S}"/userdata "${D}"/opt/${PN}
+
+ # "env" file for setting paths to Staden Package root, libraries, tables...
+ insinto /etc/env.d
+ newins "${FILESDIR}"/${P}-env 27${PN}
+
+ # Basic documentation
+ insinto /opt/${PN}/doc
+ doins "${S}"/doc/Acknowledgements
+ newins "${S}"/doc/emboss.txt README.emboss
+
+ # Man pages
+ doman "${S}"/doc/manual/man/man*/*.*
+
+ # Hypertext documentation
+ insinto /opt/${PN}/doc/manual
+ doins "${S}"/doc/manual/*unix*.{png,html,index}
+ insinto /opt/${PN}/doc/scripting_manual
+ doins "${S}"/doc/scripting_manual/*.html
+ insinto /opt/${PN}/doc/manual/i
+ doins "${S}"/doc/manual/i/*
+ insinto /opt/${PN}/doc/scripting_manual/i
+ doins "${S}"/doc/scripting_manual/i/*
+
+ # Missing hypertext documentation
+ insinto /opt/${PN}/doc
+ doins "${WORKDIR}"/${PN}-1.4.1-missing-doc/documentation.html
+ insinto /opt/${PN}/doc/misc
+ doins "${WORKDIR}"/${PN}-1.4.1-missing-doc/misc/*
+ insinto /opt/${PN}/doc/misc/i
+ doins "${S}"/doc/manual/i/*
+
+ # Printable manuals and articles
+ insinto /opt/${PN}/doc
+ newins "${S}"/doc/gkb547_gml.pdf Staden1998.pdf
+ newins "${S}"/doc/manual/manual_unix.pdf manual.pdf
+ newins "${S}"/doc/manual/mini_unix.pdf mini_manual.pdf
+ newins "${S}"/doc/scripting_manual/scripting.pdf scripting_manual.pdf
+
+ # A short course in printable format, along with example data
+ if use doc; then
+ mkdir -p "${D}"/opt/${PN}/course
+ mv "${WORKDIR}"/course-1.1/data "${D}"/opt/${PN}/course/data
+ insinto /opt/${PN}/course
+ doins "${WORKDIR}"/course-1.1/README
+ newins "${WORKDIR}"/course-1.1/unix_docs/mutation_talk.ppt course_mutation_detection_diapos.pdf
+ newins "${WORKDIR}"/course-1.1/unix_docs/course_unix.pdf course_project_management.pdf
+ newins "${WORKDIR}"/course-1.1/unix_docs/mutation_notes.pdf course_mutation_detection.pdf
+ fi
+}
+
+pkg_postinst() {
+ echo
+ ewarn 'Known issues:'
+ ewarn
+ ewarn 'The help browser integrated in the GUI applications reports missing'
+ ewarn 'files when following hyperlinks on the main documentation page. This'
+ ewarn 'seems to be a problem in the Staden Package help browser. You might'
+ ewarn 'want to use your favorite browser instead of the integrated one to'
+ ewarn 'read the documentation.'
+ ewarn
+ ewarn 'The GUI programs may crash when bringing up the font selection'
+ ewarn 'dialog. This problem is related to the presence of certain'
+ ewarn 'fonts in "FontPath". If you experience this problem, try using'
+ ewarn '"strace" to identify the problematic font(s) and either uninstall'
+ ewarn 'them or remove the directory they are in from "FontPath" by'
+ ewarn 'editing your X server configuration file.'
+ echo
+}
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