# 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.ebuild,v 1.8 2005/05/09 21:22:05 ribosome Exp $ inherit eutils toolchain-funcs TCLV=8.4.6 TKV=8.4.6 DESCRIPTION="The Staden Package - Biological sequence handling and analysis" 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/${PN}/course-1.1.tar.gz )" LICENSE="${PN}" SLOT="0" KEYWORDS="x86" IUSE="doc" DEPEND="${RDEPEND} dev-lang/perl media-gfx/imagemagick virtual/emacs virtual/tetex" RDEPEND="app-shells/ksh dev-lang/tcl dev-lang/tk sci-libs/io_lib =dev-tcltk/itcl-3.2* dev-tcltk/iwidgets media-libs/libpng virtual/x11" S=${WORKDIR}/${PN}-src-${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 "fortran" "USE" flag enabled.' 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 included in "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 } src_unpack() { unpack ${A} # 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). mv ${WORKDIR}/tcl${TCLV} ${S}/src mv ${WORKDIR}/tk${TKV} ${S}/src 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 }