diff options
Diffstat (limited to 'sci-chemistry/ccp4')
20 files changed, 822 insertions, 0 deletions
diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest new file mode 100644 index 0000000..67521db --- /dev/null +++ b/sci-chemistry/ccp4/Manifest @@ -0,0 +1,19 @@ +MD5 6297a21e1e45183fe8df70e18c8f2c2d ccp4-5.99.5.ebuild 12167 +MD5 b25f261958764a4ef684582b517d63c5 files/add-xdl-libdir.patch 1545 +MD5 5d4c15532a50ac2e00b68f9a57ce79f2 files/ccp4-5.99.5-install-libs-at-install-time.patch 890 +MD5 b7c4c90e38ef49651876128a209b4546 files/ccp4i-default-to-firefox.patch 717 +MD5 a9fd6533dc70e2c88e4623509e20c30b files/check-blas-lapack-pthread.patch 5335 +MD5 cee8a62b63386a13f4276cab7bf09260 files/clipper-find-mccp4-includes.patch 491 +MD5 fcf801c9c9f1cc7f35294ff95776ff5e files/create-mosflm-bindir.patch 438 +MD5 934ef33e2fc72b4c4ba6ec4fbc3d7122 files/digest-ccp4-5.99.5 129 +MD5 de25d6e610b32fbe607f62914e83a229 files/dont-build-pdb-extract.patch 914 +MD5 8638a4880d926711233e53382f35205a files/dont-build-rasmol.patch 725 +MD5 12cd3967d76e228401cfcd8d156e924d files/dont-chmod-python-binary.patch 606 +MD5 898701d32b28c3916d4374a6c58ef7b9 files/dont-make-dirs-in-configure.patch 2780 +MD5 5c89d8a6c5570d442a71a8c598a80f72 files/make-ipmosflm-dir.patch 375 +MD5 962cb5c0c55797f865254e4dc374183b files/make-mosflm-cbf-libdir.patch 415 +MD5 e38e0ef05c30c16148e8319e0bb0977d files/make-mosflm-index-libdir.patch 358 +MD5 703cb01ad626d4dbf4176a18ea5269a1 files/make-mosflm-libdir.patch 371 +MD5 88b9b19d31b2128746bb99fc27882357 files/make-phaser-bindir.patch 380 +MD5 e74f4860f9f1c929c3b4d4e06fba68e9 files/no-phaser-ld-assume-kernel.patch 581 +MD5 bcdb856dae7ea7b22d130474f6c17b7d files/pass-clipper-enablevals.patch 501 diff --git a/sci-chemistry/ccp4/ccp4-5.99.5.ebuild b/sci-chemistry/ccp4/ccp4-5.99.5.ebuild new file mode 100644 index 0000000..65fc05e --- /dev/null +++ b/sci-chemistry/ccp4/ccp4-5.99.5.ebuild @@ -0,0 +1,377 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +inherit fortran eutils gnuconfig + +FORTRAN="g77 ifc" + +DESCRIPTION="Protein X-ray crystallography toolkit" +HOMEPAGE="http://www.ccp4.ac.uk/" +SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/${PV}/packed/${PN}-core.tar.gz" +# ftp://ftp.ccp4.ac.uk/ccp4/${PV}/packed/phaser-cctbx.tar.gz" +# ftp://ftp.ccp4.ac.uk/ccp4/${PV}/prerelease/${P}_gfortran.tar.gz" +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~ppc ~x86" +IUSE="X" +# app-office/sc overlaps sc binary and man page +# We can't rename ours since the automated ccp4i interface expects it there, +# as do many scripts. app-office/sc can't rename its because that's the name +# of the package. +RDEPEND="X? ( + || ( + ( + x11-libs/libX11 + x11-libs/libXt + x11-libs/libXaw + ) + virtual/x11 + ) + ) + >=dev-lang/tcl-8.3 + >=dev-lang/tk-8.3 + >=dev-tcltk/blt-2.4 + virtual/lapack + virtual/blas + =sci-libs/fftw-2* + sci-chemistry/pdb-extract + sci-chemistry/rasmol + sci-libs/mccp4 + app-shells/tcsh + !app-office/sc" +DEPEND="${RDEPEND} + X? ( + || ( + ( + x11-misc/imake + x11-proto/inputproto + x11-proto/xextproto + ) + virtual/x11 + ) + )" + +src_unpack() { + unpack ${A} + +# These two only needed when attempting to install outside build dir via +# --bindir and --libdir instead of straight copying after build + # it attempts to install some libraries during the build +# epatch ${FILESDIR}/${P}-install-libs-at-install-time.patch + # hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view + # without this patch when --libdir is set + # Rotgen still needs more patching to find it +# epatch ${FILESDIR}/add-xdl-libdir.patch + + # it tries to create libdir, bindir etc on live system in configure + epatch ${FILESDIR}/dont-make-dirs-in-configure.patch + + # We already have sci-chemistry/rasmol + epatch ${FILESDIR}/dont-build-rasmol.patch + + # We already have sci-chemistry/pdb-extract +# Use configure option instead +# epatch ${FILESDIR}/dont-build-pdb-extract.patch + + epatch ${FILESDIR}/create-mosflm-bindir.patch + epatch ${FILESDIR}/make-mosflm-libdir.patch + epatch ${FILESDIR}/make-mosflm-index-libdir.patch + epatch ${FILESDIR}/make-mosflm-cbf-libdir.patch + epatch ${FILESDIR}/make-ipmosflm-dir.patch + +# Don't use these when we aren't building phaser +# epatch ${FILESDIR}/make-phaser-bindir.patch +# epatch ${FILESDIR}/no-phaser-ld-assume-kernel.patch +# # scons config.py tries to chmod python on live system +# epatch ${FILESDIR}/dont-chmod-python-binary.patch + + # Don't use this when we aren't building clipper + # For some reason clipper check for $enableval even when --enable is passed + epatch ${FILESDIR}/pass-clipper-enablevals.patch + epatch ${FILESDIR}/clipper-find-mccp4-includes.patch + + # Default to firefox browser, not 'netscape' + epatch ${FILESDIR}/ccp4i-default-to-firefox.patch + + # Also use -lpthread when linking blas and lapack + # We may need more fixing to use libcblas for the C files + epatch ${FILESDIR}/check-blas-lapack-pthread.patch + + gnuconfig_update +} + +src_compile() { + # GENTOO_OSNAME can be one of: + # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd + # linux_compaq_compilers linux_intel_compilers generic Darwin + # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers + if [[ "${FORTRANC}" = "ifc" ]]; then + if use ia64; then + GENTOO_OSNAME="ia64_linux_intel" + else + # Should be valid for x86, maybe amd64 + GENTOO_OSNAME="linux_intel_compilers" + fi + else + # Should be valid for x86 and amd64, at least + GENTOO_OSNAME="linux" + fi + + # Sets up env + ln -s \ + ccp4.setup-bash \ + ${S}/include/ccp4.setup + + # We agree to the license by emerging this, set in LICENSE + sed -i \ + -e "s~^\(^agreed=\).*~\1yes~g" \ + ${S}/configure + + # Fix up variables -- need to reset CCP4_MASTER at install-time + sed -i \ + -e "s~^\(setenv CCP4_MASTER.*\)/xtal~\1${WORKDIR}~g" \ + -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \ + ${S}/include/ccp4.setup* + + # Set up variables for build + source ${S}/include/ccp4.setup + + export CC=$(tc-getCC) + export CXX=$(tc-getCXX) + export COPTIM=${CFLAGS} + export CXXOPTIM=${CXXFLAGS} + # Default to -O2 if FFLAGS is unset + export FC=${FORTRANC} + export FOPTIM=${FFLAGS:- -O2} + + # Can't use econf, configure rejects unknown options like --prefix + ./configure \ + $(use_enable X x) \ + --with-shared-libs \ + --with-fftw=/usr \ + --with-warnings \ + --disable-pdb_extract \ + --disable-cctbx \ + --disable-phaser \ + ${GENTOO_OSNAME} || die "econf failed" + emake -j1 || die "emake failed" +} + +src_install() { +# Only needed when using --bindir and --libdir + # Needed to avoid errors. Originally tried to make lib and bin + # in configure script, now patched out by dont-make-dirs-in-configure.patch +# dodir /usr/include /usr/$(get_libdir) /usr/bin + + make install || die "install failed" + + # Fix env + sed -i \ + -e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \ + -e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \ + -e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \ + -e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/$(get_libdir)/ccp4/include~g" \ + -e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/$(get_libdir)/ccp4/data~g" \ + -e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \ + -e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \ + ${S}/include/ccp4.setup* + + # Get rid of S instances + # Also the main clipper library is built as libclipper-core, not libclipper + sed -i \ + -e "s:${S}:${ROOT}usr:g" \ + -e "s:lclipper :lclipper-core:g" \ + ${S}/bin/clipper-config +# sed -i \ +# -e "s:${S}:${ROOT}usr:g" \ +# ${S}/$(get_libdir)/cctbx/cctbx_build/setpaths* + + # Bins + EXEDESTTREE="/usr/bin" doexe ${S}/bin/* + + # Libs + for file in ${S}/lib/*; do + if [[ -d ${file} ]]; then + continue + elif [[ -x ${file} ]]; then + dolib.so ${file} + else + INSDESTTREE="/usr/$(get_libdir)" doins ${file} + fi + done + + # Fix libdir in all *.la files + sed -i \ + -e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \ + ${D}/usr/$(get_libdir)/*.la + + # Library symlinks + local LIBNAMES="libclipper-ccp4.so.0.0.0 + libclipper-cif.so.0.0.0 + libclipper-contrib.so.0.0.0 + libclipper-core.so.0.0.0 + libclipper-minimol.so.0.0.0 + libclipper-mmdbold.so.0.0.0 + libclipper-mmdb.so.0.0.0 + libclipper-mtz.so.1.0.0 + libclipper-phs.so.0.0.0 + libjwc_c.so.0.1.1 + libjwc_f.so.0.1.1 + libssm.so.0.0.0 + libxdl_viewextra.so.0.0.0 + libxdl_view.so.2.0.0" + + for LIBNAME in ${LIBNAMES}; do + library_dosym ${LIBNAME} + done + +# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so +# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0 +# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0.0 +# +# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so +# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0 +# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0.0 +# +# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so +# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0 +# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0.0 +# +# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so +# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0 +# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0.0 +# +# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so +# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0 +# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0.0 +# +# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so +# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0 +# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0.0 +# +# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so +# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0 +# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0.0 +# +# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so +# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1 +# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1.0 +# +# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so +# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0 +# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0.0 +# +# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so +# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0 +# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0.1 +# +# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so +# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0 +# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0.1 +# +# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so +# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0 +# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0.0 +# +# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so +# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0 +# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0.0 +# +# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so +# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2 +# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2.0 + + # Environment files, setup scripts, etc. + INSDESTTREE="/usr/$(get_libdir)/ccp4/include" doins ${S}/include/* + + # CCP4Interface - GUI + INSDESTTREE="/usr/$(get_libdir)/ccp4" doins -r ${S}/ccp4i + EXEDESTTREE="/usr/$(get_libdir)/ccp4/ccp4i/bin" doexe ${S}/ccp4i/bin/* + + # Data + INSDESTTREE="/usr/$(get_libdir)/ccp4" doins -r ${S}/lib/data + + # Include files + for i in ccp4 clipper mmdb ssm; do + INSDESTTREE="/usr/include" doins -r ${S}/include/${i} + done + + # Install docs and examples + + doman ${S}/man/cat1/* + + mv ${S}/manual/README ${S}/manual/README-manual + dodoc ${S}/manual/* + + dodoc ${S}/README ${S}/CHANGES + + dodoc ${S}/doc/* + rm ${D}/usr/share/doc/${PF}/GNUmakefile.gz + rm ${D}/usr/share/doc/${PF}/COPYING.gz + + dohtml -r ${S}/html/* + dodoc ${S}/examples/README + + for i in data rnase toxd; do + DOCDESTTREE="examples/${i}" dodoc ${S}/examples/${i}/* + done + + DOCDESTTREE="examples/tutorial" dohtml -r ${S}/examples/tutorial/html + DOCDESTTREE="examples/tutorial" dohtml examples/tutorial/tut.css + for i in data results; do + DOCDESTTREE="examples/tutorial/${i}" dodoc ${S}/examples/tutorial/${i}/* + done + + for i in non-runnable runnable; do + DOCDESTTREE="examples/unix/${i}" dodoc ${S}/examples/unix/${i} + done + + # Needed for ccp4i docs to work + dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples + dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/examples + + # Fix overlaps with other packages + rm ${D}/usr/share/man/man1/rasmol.1.gz +} + +pkg_postinst() { + einfo "The Web browser defaults to firefox. Change CCP4_BROWSER" + einfo "in /usr/$(get_libdir)/ccp4/include/ccp4.setup* to modify this." + + ewarn "Set your .bashrc or other shell login file to source" + ewarn "one of the ccp4.setup* files in ${ROOT}usr/$(get_libdir)/ccp4/include." + ewarn "CCP4 will not work without this." +} + +# Links libname.so, libname.so.major and libname.so.major.minor +# to libname.so.major.minor.micro +library_dosym() { + local LIBNAME LIBDIR SUFFIX CORE_LIBNAME LIB_MAJOR LIB_MINOR LIB_VERSIONS + + LIBNAME=${1} + LIBDIR=${2:-/usr/$(get_libdir)} + + # Tag / on the end of libdir if needed + if [[ ${LIBDIR:$((${#LIBDIR}-1)):1} != "/" ]]; then + LIBDIR="${LIBDIR}/" + fi + + if [[ "${LIBNAME}" != *.so.* ]]; then + msg="library_dosym() requires a shared, versioned library as an argument" + eerror "$msg" + die "$msg" + fi + + SUFFIX=${LIBNAME##*so.} + CORE_LIBNAME=${LIBNAME%.so.*} + CORE_LIBNAME="${CORE_LIBNAME}.so" + LIB_MAJOR=${SUFFIX%%.*} + LIB_MINOR=${SUFFIX#*.} + LIB_MINOR=${SUFFIX%%.*} + LIB_VERSIONS="${LIB_MAJOR} ${LIB_MAJOR}.${LIB_MINOR}" + for LIB_SUFFIX in .${LIB_MAJOR} .${LIB_MAJOR}.${LIB_MINOR} ""; do + einfo "Calling dosym ${LIBNAME} ${LIBDIR} ${CORE_LIBNAME} ${LIB_SUFFIX}" + dosym ${LIBNAME} ${LIBDIR}${CORE_LIBNAME}${LIB_SUFFIX} + done +} diff --git a/sci-chemistry/ccp4/files/add-xdl-libdir.patch b/sci-chemistry/ccp4/files/add-xdl-libdir.patch new file mode 100644 index 0000000..fbb5dad --- /dev/null +++ b/sci-chemistry/ccp4/files/add-xdl-libdir.patch @@ -0,0 +1,29 @@ +--- ccp4-5.99.5.orig/configure 2005-12-05 02:26:38.000000000 -0800 ++++ ccp4-5.99.5 /configure 2005-12-05 02:30:35.000000000 -0800 +@@ -1616,7 +1616,7 @@ + sftools_FLAGS='$XFFLAGS $FOPTIM' \ + lgglib_FLAGS='$XFFLAGS -O0' \ + arp_waters_FLAGS='$XFFLAGS $FOPTIM' "} +- XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -lxdl_view"} ++ XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -L${CCP4}/x-windows/xdl_view/src -lxdl_view"} + XWIN_LIB=${XWIN_LIB:-"-L/usr/X11R6/lib -lXt -lSM -lX11 -lICE"} + XTYPE=${XTYPE:-"LINUX"} + TIDY=${TIDY:-"rm -f sta*"} +@@ -1752,7 +1752,7 @@ + arp_waters_FLAGS='$XFFLAGS $FOPTIM -fforce-mem' \ + mlphare_FLAGS='$XFFLAGS $FOPTIM -fno-move-all-movables' \ + stereo_FLAGS='$XFFLAGS $FOPTIM -fno-move-all-movables' "} +- XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -lxdl_view"} ++ XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -L${CCP4}/x-windows/xdl_view/src -lxdl_view"} + XWIN_LIB=${XWIN_LIB:-"-L/usr/X11R6/lib -lXt -lSM -lX11 -lICE"} + XTYPE=${XTYPE:-"LINUX"} + CXX_LIBS=${CXX_LIBS:-"-lstdc++"} +@@ -1871,7 +1871,7 @@ + refmac5_FLAGS='$XFFLAGS $FOPTIM' \ + arp_waters_FLAGS='$XFFLAGS $FOPTIM'\ + distang_FLAGS='$XFFLAGS -O1' "} +- XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -lxdl_view"} ++ XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -L${CCP4}/x-windows/xdl_view/src -lxdl_view"} + XWIN_LIB=${XWIN_LIB:-"-L/usr/X11R6/lib -lXt -lSM -lX11 -lICE"} + XTYPE=${XTYPE:-"LINUX"} + if test "$shared_lib" = yes; then diff --git a/sci-chemistry/ccp4/files/ccp4-5.99.5-install-libs-at-install-time.patch b/sci-chemistry/ccp4/files/ccp4-5.99.5-install-libs-at-install-time.patch new file mode 100644 index 0000000..9170124 --- /dev/null +++ b/sci-chemistry/ccp4/files/ccp4-5.99.5-install-libs-at-install-time.patch @@ -0,0 +1,40 @@ +--- ccp4-5.99.5.orig/x-windows/Makefile.in 2005-12-05 01:30:59.000000000 -0800 ++++ ccp4-5.99.5.orig/x-windows/Makefile.in 2005-12-05 01:31:50.000000000 -0800 +@@ -42,8 +42,7 @@ + xdlview_dir = $(srcdir)/xdl_view/src + xdlview : + cd $(xdlview_dir) ; \ +- $(MAKE) $(MFLAGS) ; \ +- $(MAKE) install ++ $(MAKE) $(MFLAGS) + + # + # rotgen and libraries +@@ -56,15 +55,13 @@ + # + libjwc_c : + cd $(libjwc_c_dir) ; \ +- $(MAKE) $(MFLAGS) ; \ +- $(MAKE) install ++ $(MAKE) $(MFLAGS) + # + # libjwc_f + # + libjwc_f : + cd $(libjwc_f_dir) ; \ +- $(MAKE) $(MFLAGS) ; \ +- $(MAKE) install ++ $(MAKE) $(MFLAGS) + # + # rotgen + # +@@ -167,6 +164,9 @@ + $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) + cd $(rotgen_dir); $(MAKE) install + $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) ++ cd $(xdlview_dir); $(MAKE) install ++ cd $(libjwc_c_dir); $(MAKE) install ++ cd $(libjwc_f_dir); $(MAKE) install + # + # clean + # diff --git a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch new file mode 100644 index 0000000..106db89 --- /dev/null +++ b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch @@ -0,0 +1,13 @@ +--- ccp4-5.99.5.orig/ccp4i/etc/configure.def.dist 2006-01-06 17:54:17.000000000 -0800 ++++ ccp4-5.99.5/ccp4i/etc/configure.def.dist 2006-01-06 17:54:47.000000000 -0800 +@@ -54,8 +54,8 @@ + MESSAGE _text "" + BLT_LIBRARY _text "" + MENU_LENGTH _positiveint 25 +-HYPERTEXT_VIEWER _text netscape +-START_NETSCAPE _text netscape ++HYPERTEXT_VIEWER _text firefox ++START_NETSCAPE _text firefox + O_MAPMAN _text mapman + MAPMAN_MAXSIZE _positiveint 4194304 + QUANTA_MBKALL _text mbkall diff --git a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch new file mode 100644 index 0000000..02a2aa6 --- /dev/null +++ b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch @@ -0,0 +1,103 @@ +--- ccp4-5.99.5.orig/configure 2006-01-17 00:35:36.000000000 -0800 ++++ ccp4-5.99.5/configure 2006-01-17 10:44:39.000000000 -0800 +@@ -2410,12 +2410,12 @@ + end + EOF + #firslty test without -lblas +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lpthread" + echo $test_compile + if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then + # Compilation was okay +- echo "... only -llapack needed" +- XLAPACK_LIB="-llapack" ++ echo "... only -llapack -lpthread needed" ++ XLAPACK_LIB="-llapack -lpthread" + # Set the next two variables so that configure + # doesn't try to build netlib libraries + LAPACKLIB="lapack" +@@ -2424,12 +2424,12 @@ + tryblas= + else + echo "more than just -llapack needed...." +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas -lpthread" + echo $test_compile + if { (eval $test_compile ) 2>&1; } && test -s testlink ; then + # Compilation was okay +- echo "...-llapack and -lblas were needed" +- XLAPACK_LIB="-llapack -lblas" ++ echo "...-llapack, -lpthread and -lblas were needed" ++ XLAPACK_LIB="-llapack -lpthread -lblas" + # Set the next two variables so that configure + # doesn't try to build netlib libraries + LAPACKLIB="lapack blas" +@@ -2720,8 +2720,8 @@ + STOP + END + EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" + echo $test_compile + if { (eval $test_compile ) 2>&1; } && test -s testlink ; then + have_lapack=yes +@@ -2738,7 +2738,7 @@ + LAPACKDIR="$testdir" + echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" + # +- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" ++ XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB -lpthread" + # + # Test to see if we need BLAS too + # Do this by trying to compile a test program +@@ -2750,8 +2750,8 @@ + if test -f testlsame ; then + rm -f testsame testlsame.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then + have_blas=yes +@@ -2830,8 +2830,8 @@ + STOP + END + EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlink ; then + have_blas=yes +@@ -3033,7 +3033,7 @@ + if test -f testlsame ; then + rm -f testsame testlsame.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then + echo "Found LSAME in lib$BLASLIB" +@@ -3046,7 +3046,7 @@ + if test -f testxerbla ; then + rm -f testxerbla testxerbla.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testxerbla ; then + # Found lsame +@@ -3080,7 +3080,7 @@ + cd ../.. + # + lapackdir=lib/lapack +- XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB" ++ XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB -lpthread" + # netlib lapack is in fortran, so we may need the fortran libraries when + # we are linking using the C or C++ compilers + case $system in diff --git a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch new file mode 100644 index 0000000..3bf5a06 --- /dev/null +++ b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5/lib/clipper/configure.orig 2006-01-07 16:54:13.000000000 -0800 ++++ ccp4-5.99.5/lib/clipper/configure 2006-01-07 16:54:31.000000000 -0800 +@@ -21751,7 +21751,7 @@ + + if test "x$mccp4_prefix" != x; then + # ie. mccp4=thing was given (thing is what we're checking for) +- ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include" ++ ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include -I$mccp4_prefix/include/mccp4" + ac_MCCP4_LDOPTS="-L$mccp4_prefix/lib -lmccp4" + else + # treat as standard lib/include diff --git a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch new file mode 100644 index 0000000..34d6197 --- /dev/null +++ b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Makefile.in 2006-01-06 12:31:02.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Makefile.in 2006-01-06 12:31:30.000000000 -0800 +@@ -158,6 +158,7 @@ + install_obj = ipdisp.exe hklview xdldataman xdlmapman \ + rotgen ipmosflm + install: all ++ mkdir -p $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/ipdisp.exe $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/ipdisp/ipdisp $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir) diff --git a/sci-chemistry/ccp4/files/digest-ccp4-5.99.5 b/sci-chemistry/ccp4/files/digest-ccp4-5.99.5 new file mode 100644 index 0000000..f00d379 --- /dev/null +++ b/sci-chemistry/ccp4/files/digest-ccp4-5.99.5 @@ -0,0 +1,2 @@ +MD5 1dc37afc2597bceaabd971ba20d86ac3 ccp4-core.tar.gz 59156210 +MD5 ac745815cdff2c4c719e9171f029b3ba phaser-cctbx.tar.gz 17821731 diff --git a/sci-chemistry/ccp4/files/dont-build-pdb-extract.patch b/sci-chemistry/ccp4/files/dont-build-pdb-extract.patch new file mode 100644 index 0000000..721b235 --- /dev/null +++ b/sci-chemistry/ccp4/files/dont-build-pdb-extract.patch @@ -0,0 +1,21 @@ +--- ccp4-5.99.5.orig/src/Makefile.in 2006-01-05 22:52:56.000000000 -0800 ++++ ccp4-5.99.5/src/Makefile.in 2006-01-05 22:55:58.000000000 -0800 +@@ -57,7 +57,7 @@ + + PDB_EXTRACT_TARGETS = pdb_extract extract pdb_extract_sf + +-all : $(CTARGETS) $(CXXTARGETS) $(FTARGETS) $(OTHERS) $(PDB_EXTRACT_SUITE) ccp4mapwish phaser ++all : $(CTARGETS) $(CXXTARGETS) $(FTARGETS) $(OTHERS) ccp4mapwish phaser + + .PHONY : all install instsome clean realclean distclean + +@@ -67,9 +67,6 @@ + -for i in $(CTARGETS) $(CXXTARGETS) $(FTARGETS) $(OTHERS) $(JAVATARGETS); do \ + test -s $$i && $(INSTALL_PROGRAM) `pwd`/$$i $(bindir)/$$i || true ;\ + done +- for i in $(PDB_EXTRACT_TARGETS); do \ +- test -s harvest_app_/pdb_extract/bin/$$i && $(INSTALL_PROGRAM) harvest_app_/pdb_extract/bin/$$i $(bindir)/$$i || true ;\ +- done + if test -f ccp4mapwish_/Makefile; then \ + cd ccp4mapwish_; $(MAKE) -i $(MFLAGS) $@; \ + else true; fi diff --git a/sci-chemistry/ccp4/files/dont-build-rasmol.patch b/sci-chemistry/ccp4/files/dont-build-rasmol.patch new file mode 100644 index 0000000..8da54fd --- /dev/null +++ b/sci-chemistry/ccp4/files/dont-build-rasmol.patch @@ -0,0 +1,19 @@ +--- ccp4-5.99.5.orig/x-windows/Makefile.in 2005-12-05 03:06:57.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Makefile.in 2005-12-05 03:07:23.000000000 -0800 +@@ -35,7 +35,7 @@ + # + # all + # +-all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy rasmol2 ipmosflm ++all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy ipmosflm + # + # xdl_view + # +@@ -161,7 +161,6 @@ + $(INSTALL_PROGRAM) $(srcdir)/xdldataman $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/xdlmapman $(bindir) + cd $(srcdir)/XCCPJIFFY ; $(MAKE) install +- $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) + cd $(rotgen_dir); $(MAKE) install + $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) + cd $(xdlview_dir); $(MAKE) install diff --git a/sci-chemistry/ccp4/files/dont-chmod-python-binary.patch b/sci-chemistry/ccp4/files/dont-chmod-python-binary.patch new file mode 100644 index 0000000..21f3053 --- /dev/null +++ b/sci-chemistry/ccp4/files/dont-chmod-python-binary.patch @@ -0,0 +1,14 @@ +--- ccp4-5.99.5.orig/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py 2006-01-06 21:48:09.000000000 -0800 ++++ ccp4-5.99.5/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py 2006-01-06 21:46:24.000000000 -0800 +@@ -756,8 +756,9 @@ + else: + action = self.write_bin_sh_dispatcher + ext = "" +- try: os.chmod(source_file, 0755) +- except OSError: pass ++ if source_file != self.python_exe: ++ try: os.chmod(source_file, 0755) ++ except OSError: pass + target_file_ext = target_file + ext + remove_or_rename(target_file_ext) + try: action(source_file, target_file_ext) diff --git a/sci-chemistry/ccp4/files/dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/dont-make-dirs-in-configure.patch new file mode 100644 index 0000000..24504d9 --- /dev/null +++ b/sci-chemistry/ccp4/files/dont-make-dirs-in-configure.patch @@ -0,0 +1,87 @@ +--- ccp4-5.99.5.orig/configure 2005-12-05 02:03:51.000000000 -0800 ++++ ccp4-5.99.5/configure 2005-12-05 02:03:54.000000000 -0800 +@@ -604,45 +604,45 @@ + # echo "! Beware -- the $system installation isn't properly tested." ; } + syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' + +-if test -z "$onlylibs" ; then +- for i in CCP4_SCR BINSORT_SCR; do +- if ( eval test -d \$$i || eval mkdir \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the value of $i." +- badvar=1 +- fi +- done +- +- for i in libdir bindir; do +- if ( eval test -d \$$i || eval mkdir \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the argument of --$i." +- badvar=1 +- fi +- done +- +- for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do +- if test -d $i || mkdir $i; then : +- else +- eval echo "! No directory $i and can\'t create it." +- badvar=1 +- fi +- done +-else +- # Kludge to fool the "Makefile" target in the top-level CCP4 +- # Makefile into not trying to remake src/Makefile.in +- for i in $srcdir/src $srcdir/lib/src ; do +- if test -d $i || mkdir $i; then +- if ! test -f $i/Makefile.in ; then +- echo +- echo "onlylibs: making dummy file $i/Makefile.in" +- touch $i/Makefile.in +- fi +- fi +- done +-fi ++#if test -z "$onlylibs" ; then ++# for i in CCP4_SCR BINSORT_SCR; do ++# if ( eval test -d \$$i || eval mkdir \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the value of $i." ++# badvar=1 ++# fi ++# done ++# ++# for i in libdir bindir; do ++# if ( eval test -d \$$i || eval mkdir \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the argument of --$i." ++# badvar=1 ++# fi ++# done ++# ++# for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do ++# if test -d $i || mkdir $i; then : ++# else ++# eval echo "! No directory $i and can\'t create it." ++# badvar=1 ++# fi ++# done ++#else ++# # Kludge to fool the "Makefile" target in the top-level CCP4 ++# # Makefile into not trying to remake src/Makefile.in ++# for i in $srcdir/src $srcdir/lib/src ; do ++# if test -d $i || mkdir $i; then ++# if ! test -f $i/Makefile.in ; then ++# echo ++# echo "onlylibs: making dummy file $i/Makefile.in" ++# touch $i/Makefile.in ++# fi ++# fi ++# done ++#fi + + ### sanity checks + diff --git a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch new file mode 100644 index 0000000..7813141 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:12.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:41.000000000 -0800 +@@ -37,6 +37,7 @@ + ${F77} ${FFLAGS} -o $@ $< + + ipmosflm: ${OBJS} ++ mkdir -p ${DPSBIN} + ${FLINK} ${FFLAGS} ${OBJS} ${LOCALLIBS} ${LIBS} \ + -o ${DPSBIN}/ipmosflm ${LDFLAGS} + diff --git a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch new file mode 100644 index 0000000..ae4b763 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:42:19.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:43:35.000000000 -0800 +@@ -132,7 +132,7 @@ + # + # CBF library + # +-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) ++$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB) + $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) + $(AR) cr $@ *.o + $(RANLIB) $@ diff --git a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch new file mode 100644 index 0000000..97607b6 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:09.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:30.000000000 -0800 +@@ -76,6 +76,7 @@ + + # local version of libdps_index.a + ${LIB}/dps_index.a: ${IOBJS} ${HOBJS} ++ mkdir -p ${LIB} + ar ru ${LIB}/dps_index.a ${IOBJS} ${HOBJS} + + ${LIB}/libpeak.a: diff --git a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch new file mode 100644 index 0000000..eac1b9f --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:48:47.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:49:02.000000000 -0800 +@@ -42,6 +42,7 @@ + $(LOCALLIBS) $(LIBS) + + index: $(IOBJS) ++ mkdir -p $(LIBDIR) + ${AR} $(AR_FLAGS) $(LIBDIR)/libdps_index.a $(IOBJS) + chmod 644 $(LIBDIR)/libdps_index.a + diff --git a/sci-chemistry/ccp4/files/make-phaser-bindir.patch b/sci-chemistry/ccp4/files/make-phaser-bindir.patch new file mode 100644 index 0000000..cdf1460 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-phaser-bindir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/src/phaser/ccp4_build 2006-01-06 15:56:22.000000000 -0800 ++++ ccp4-5.99.5/src/phaser/ccp4_build 2006-01-06 15:55:49.000000000 -0800 +@@ -65,6 +65,7 @@ + ./install $phaseropts --static_libraries --component="phaser" --target="exe/phaser" + + # Install in CCP4 bindir ++mkdir -p $bindir + cp phaser-$PHASER_VERSION/build/$PHASER_MTYPE/exe/phaser $bindir + + echo " " diff --git a/sci-chemistry/ccp4/files/no-phaser-ld-assume-kernel.patch b/sci-chemistry/ccp4/files/no-phaser-ld-assume-kernel.patch new file mode 100644 index 0000000..8011c3f --- /dev/null +++ b/sci-chemistry/ccp4/files/no-phaser-ld-assume-kernel.patch @@ -0,0 +1,15 @@ +--- ccp4-5.99.5.orig/src/phaser/conf/configure-options 2006-01-06 11:27:28.000000000 -0800 ++++ ccp4-5.99.5/src/phaser/conf/configure-options 2006-01-06 11:26:29.000000000 -0800 +@@ -33,9 +33,9 @@ + set font_dirs = '' + set strip_command = 'strip' + set wxpython_env = '' +- if ( "$PHASER_MTYPE" == "intel-linux" ) then +- setenv LD_ASSUME_KERNEL 2.4.1 +- endif ++# if ( "$PHASER_MTYPE" == "intel-linux" ) then ++# setenv LD_ASSUME_KERNEL 2.4.1 ++# endif + else if ( "$PHASER_MTYPE" == "alpha-tru64" ) then + set python_configure = '--with-cxx=cxx' + set libpng_arch = 'dec' diff --git a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch new file mode 100644 index 0000000..3e1a8b0 --- /dev/null +++ b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5.orig/configure 2006-01-06 11:45:43.000000000 -0800 ++++ ccp4-5.99.5/configure 2006-01-06 11:46:53.000000000 -0800 +@@ -3210,7 +3210,7 @@ + #ccp4 setup + xopts="${xopts} --with-ccp4=${srcdir}" + #interface setup +- xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol" ++ xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-mmdbold --enable-mtz --with-mccp4=/usr" + echo + echo "********* CLIPPER CONFIGURATION ***********" + echo |