path: root/app-sci/staden/staden-1.4.1-r1.ebuild

# Copyright 1999-2004 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/app-sci/staden/staden-1.4.1-r1.ebuild,v 1.1 2004/09/15 19:09:27 ribosome Exp $

inherit eutils

DESCRIPTION="The Staden Package - Biological sequence handling and analysis"
HOMEPAGE="http://${PN}.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/${PN}-src-rel-${PV//./-}.tar.gz
	mirror://gentoo/${P}-missing-doc.tar.bz2"
LICENSE="${PN}"

SLOT="0"
KEYWORDS="~x86"
IUSE="emboss ifc"

DEPEND="${RDEPEND}
	dev-lang/perl
	media-gfx/imagemagick
	virtual/emacs
	virtual/tetex
	emboss? ( app-sci/emboss )
	ifc? ( dev-lang/ifc )"

RDEPEND="app-shells/ksh
	dev-lang/tcl
	dev-lang/tk
	=dev-tcltk/itcl-3.2*
	dev-tcltk/iwidgets
	media-libs/libpng
	virtual/x11"

S=${WORKDIR}/${PN}-src-rel-${PV//./-}

pkg_setup() {
	# Check for a Fortran compiler.
	if ! which ${F77:-g77} &> /dev/null; then
		echo
		eerror "The Fortran compiler \"${F77:-g77}\" could not be found on your system."
		if [ -z ${F77} ] || [ ${F77} = g77 ]; then
			eerror 'Please reinstall "sys-devel/gcc" with the "f77" "USE" flag enabled.'
		elif [ ${F77} = ifc ] && ! use ifc &> /dev/null; then
			eerror 'Please set the "ifc" "USE" flag if you want to use the Intel Fortran'
			eerror 'Compiler to build this package. This will ensure the "dev-lang/ifc"'
			eerror 'package gets installed on your system.'
		elif [ ${F77} = ifc ] && use ifc &> /dev/null; then
			eerror 'Please ensure "ifc" is in a directory referenced in "PATH".'
		else
			eerror 'Please make sure the variable ${F77} is set to the name of a valid'
			eerror 'Fortran compiler installed on your system. Make sure this executable'
			eerror 'is in a directory referenced by "PATH", and that the corresponding'
			eerror '"USE" flag is set if applicable (for example "ifc" if you use the'
			eerror 'Intel Fortran Compiler).'
		fi
		die "Fortran compiler not found."
	fi

	# Check for X authority if building the EMBOSS tcl/tk GUIs.
	if use "emboss" && [ -z ${XAUTHORITY} ]; then
		echo
		eerror 'The "XAUTHORITY" environment variable is not set on your system.'
		eerror 'Access to an X display is required to build the EMBOSS tcl/tk GUIs.'
		eerror 'Please either unset the "emboss" "USE" flag to install this package'
		eerror 'without building the EMBOSS GUIs (you will still be provided with a'
		eerror 'set of prebuilt GUIs) or configure access to an X display. You can'
		eerror 'transfer the X credentials of an ordinary user to the account you'
		eerror 'use to execute "emerge" with the "sux" command, which is part of the'
		eerror '"x11-misc/sux" package. See: "http://www.gentoo.org/doc/en/su-x.xml"'
		eerror 'for an introduction to installing and using "sux" on Gentoo.'
		die '"XAUTHORITY" not set.'
	fi
}

src_unpack() {
	unpack ${A}

	# Abandon hope, all ye who enter here.

	# 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.
	cd ${S}
	einfo "Patching Staden Package Makefiles:"
	epatch ${FILESDIR}/${P}-gap4.patch
	epatch ${FILESDIR}/${P}-mutscan.patch
	epatch ${FILESDIR}/${P}-prefinish.patch
	epatch ${FILESDIR}/${P}-tk_utils.patch
	epatch ${FILESDIR}/${P}-tracediff.patch
	echo

	# "getopt" is incorrectly included as an extern (for Win32 compatibility).
	einfo "Patching Staden Package code:"
	epatch ${FILESDIR}/${P}-getopt.patch
	echo

	# 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 \
		&& einfo "Successfully applied sed script to patch update-nodes." \
		|| eerror "Failed to apply sed script to patch update-nodes."

	# 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} \
			&& einfo "Successfully applied sed script to patch ${SCRIPT}." \
			|| eerror "Failed to apply sed script to patch ${SCRIPT}."
	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 \
		&& einfo "Successfully applied sed script to patch make.ps." \
		|| eerror "Failed to apply sed script to patch make.ps."

	# 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} \
			&& einfo "Successfully applied sed scripts to patch ${FILE}." \
			|| eerror "Failed to apply sed scripts to patch ${FILE}."
	done
	echo

	# "CFLAGS" and "FFLAGS" need to be set to the user's values in the build
	# system global Makefile.
	einfo "Applying user-defined compilation/linking flags:"
	cd ${S}/src/mk
	sed -i -e "s/COPT		= -O2 -g3 -DNDEBUG/COPT = ${CFLAGS:-"-O2 -g3 -DNDEBUG"}/" global.mk \
		&& einfo "Successfully applied sed script to set CFLAGS." \
		|| eerror "Failed to apply sed script to set CFLAGS."
	sed -i -e "s/FOPT		= -O2 -g3 -DNDEBUG/FOPT = ${FFLAGS:-"-O2 -g3 -DNDEBUG"}/" global.mk \
		&& einfo "Successfully applied sed script to set FFLAGS." \
		|| eerror "Failed to apply sed script to set FFLAGS."
}

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.

	# Compiles executables and libraries, builds documentation.
	make \
		STADENROOT="${S}" \
		SRCROOT="${S}/src" \
		MACHINE="linux" \
		JOB="all" \
		O="linux-binaries" \
		CC=${CC:-gcc} \
		CXX=${CXX:-g++} \
		F77=${F77:-g77} \
		|| die "Package compilation failed."

	# Moves executables in "${S}/linux-bin" and libraries to ${S}/lib.
	make \
		STADENROOT="${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 trashed "linux-binaries" file and replace it by a directory
	# containing the appropriate libraries.
	rm ${S}/lib/linux-binaries
	mkdir ${S}/lib/linux-binaries
	mv ${S}/src/lib/linux-binaries/* ${S}/lib/linux-binaries

	# Link "itcl" and "itk" libraries to the Staden libraries directories.
	ln -s /usr/lib/libitcl3.2.so ${S}/lib/itcl3.3/libitcl3.3.so
	ln -s /usr/lib/libitk3.2.so ${S}/lib/itk3.3/libitk3.3.so

	# Patched version of iwidgetsrc
	cp ${FILESDIR}/${P}-iwidgetsrc.new ${S}/tables/iwidgetsrc

	# Build tcl/tk GUIs for EMBOSS programs if requested.
	use "emboss" && STADENROOT="${S}" ${S}/linux-bin/create_emboss_files

	# 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.
	cp ${FILESDIR}/${P}-staden_help.new ${S}/linux-bin/staden_help
	chmod +x ${S}/linux-bin/staden_help

	# 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
	into /opt/${PN}
	mkdir -p ${D}/opt/${PN}
	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}/{ChangeLog,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 ${S}/doc/manual/*unix*.{gif,html,index}
	insinto /opt/${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 ${WORKDIR}/${P}-missing-doc/documentation.html
	insinto /opt/${PN}/doc/misc
	doins ${WORKDIR}/${P}-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.dvi manual.dvi
	newins ${S}/doc/manual/manual_unix.ps manual.ps
	newins ${S}/doc/manual/mini_unix.ps mini_manual.ps
	newins ${S}/doc/scripting_manual/scripting.dvi scripting_manual.dvi
	newins ${S}/doc/scripting_manual/scripting.ps scripting_manual.ps

	# A short course in printable format, along with example data
	mkdir -p ${D}/opt/${PN}/course
	mv ${S}/course/data ${D}/opt/${PN}/course
	insinto /opt/${PN}/course
	doins ${S}/course/README
	newins ${S}/course/unix_docs/course_unix.pdf course_project_management.pdf
	newins ${S}/course/unix_docs/course_unix.ps course_project_management.ps
	newins ${S}/course/mutation_texi/notes.ps course_mutation_detection.ps
}

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.'
	ewarn
	ewarn 'The default EMBOSS tcl/tk GUIs (which get installed if you did not'
	ewarn 'set the "emboss" "USE" flag) are way out of date, while the custom'
	ewarn 'GUIs (which are built if you set the "emboss" "USE" flag) do not'
	ewarn 'support many of the most recent EMBOSS/EMBASSY programs.'
	echo
}