diff options
Diffstat (limited to 'sci-biology/staden/staden-1.4.1-r7.ebuild')
| -rw-r--r-- | sci-biology/staden/staden-1.4.1-r7.ebuild | 297 |
1 files changed, 0 insertions, 297 deletions
diff --git a/sci-biology/staden/staden-1.4.1-r7.ebuild b/sci-biology/staden/staden-1.4.1-r7.ebuild deleted file mode 100644 index fd8140f8556f..000000000000 --- a/sci-biology/staden/staden-1.4.1-r7.ebuild +++ /dev/null @@ -1,297 +0,0 @@ -# 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-1.4.1-r7.ebuild,v 1.6 2005/03/08 18:32:21 vapier Exp $ - -inherit eutils toolchain-funcs - -DESCRIPTION="The Staden Package - Biological sequence handling and analysis" -HOMEPAGE="http://staden.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${PN}-src-rel-${PV//./-}.tar.gz - doc? ( mirror://sourceforge/${PN}/course-1.1.tar.gz ) - mirror://gentoo/${P}-missing-doc.tar.bz2" -LICENSE="staden" - -SLOT="0" -KEYWORDS="x86" -IUSE="doc" - -DEPEND="${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-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 "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. - cd ${S} - einfo "Patching Staden Package Makefiles:" - epatch ${FILESDIR}/${P}-top.patch - 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 - 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 - cd ${S}/src/mutlib - cd ${S} - echo - - einfo "Patching Staden Package code:" - - # "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 - 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 - - # 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} - 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 - - # 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 - echo - - # "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 -i -e "s/COPT = -O2 -g3 -DNDEBUG/COPT = ${CFLAGS:-"-O2 -g3 -DNDEBUG"} -fPIC/" global.mk - sed -i -e "s/FOPT = -O2 -g3 -DNDEBUG/FOPT = ${FFLAGS:-"-O2 -g3 -DNDEBUG"} -fPIC/" global.mk -} - -src_compile() { - # "MACHINE", "{STADEN,SRC}ROOT" and "JOB" are mandatory arguments to the - # Staden Package build process. "O" is redefined on the command line to - # avoid a conflict between Portage and the Staden Package build system, - # which both use this variable. (In Portage, its value is the directory - # containing the current ebuild, while in the Staden Package build system - # it is set to the directory containing the compiler object files.) - # Compiler program names also need to be specified to override the - # incorrect hardcoded ones. - - # Compile executables and libraries. - make \ - STADENROOT="${S}" \ - SRCROOT="${S}/src" \ - MACHINE="linux" \ - JOB="all" \ - O="linux-binaries" \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - F77=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=$(tc-getCXX) \ - F77=g77 \ - || die "Document compilation failed." - - # Moves executables in "${S}/linux-bin" and libraries to ${S}/lib. - 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 trashed "linux-binaries" file and replace it by a directory - # containing the appropriate libraries. Remove libread since an updated - # version is included in "sci-libs/io_lib". - rm ${S}/lib/linux-binaries - rm ${S}/src/lib/linux-binaries/libread.so - mkdir ${S}/lib/linux-binaries - cp ${S}/src/lib/linux-binaries/* ${S}/lib/linux-binaries - - # 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}/src/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}/{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 - 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 -} |