diff options
author | Justin Lecher <jlec@gentoo.org> | 2011-03-04 17:02:15 +0000 |
---|---|---|
committer | Justin Lecher <jlec@gentoo.org> | 2011-03-04 17:02:15 +0000 |
commit | dafe1f72650973093cf13698620dcd342f864864 (patch) | |
tree | a81fc03023ac2ad32656e43020ad1721df842a5e /sci-chemistry/ccp4-apps/files | |
parent | Maintenance. EAPI=3. Depend on x11-libs/gtk+:2 (diff) | |
download | gentoo-2-dafe1f72650973093cf13698620dcd342f864864.tar.gz gentoo-2-dafe1f72650973093cf13698620dcd342f864864.tar.bz2 gentoo-2-dafe1f72650973093cf13698620dcd342f864864.zip |
Streamline configure
(Portage version: 2.2.0_alpha26/cvs/Linux x86_64)
Diffstat (limited to 'sci-chemistry/ccp4-apps/files')
6 files changed, 60 insertions, 488 deletions
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-mmdbold-ggc-4.3.patch b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-mmdbold-ggc-4.3.patch deleted file mode 100644 index 66186609a668..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-mmdbold-ggc-4.3.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- ccp4-6.0.99e.orig/lib/clipper/clipper/mmdbold/clipper_mmdb.cpp 2008-07-31 13:23:13.000000000 -0700 -+++ ccp4-6.0.99e/lib/clipper/clipper/mmdbold/clipper_mmdb.cpp 2008-07-31 13:47:35.000000000 -0700 -@@ -43,7 +43,7 @@ - - #include <set> - #include <algorithm> -- -+#include <string.h> - - namespace clipper { - ---- ccp4-6.0.99e.orig/lib/clipper/clipper/mmdbold/clipper_mmdb_wrapper.cpp.orig 2008-07-31 13:49:53.000000000 -0700 -+++ ccp4-6.0.99e/lib/clipper/clipper/mmdbold/clipper_mmdb_wrapper.cpp 2008-07-31 13:50:25.000000000 -0700 -@@ -40,7 +40,7 @@ - //L MA 02111-1307 USA - - #include "clipper_mmdb_wrapper.h" -- -+#include <string.h> - - namespace clipper { - diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-fix-setup-bash-incompatibility.patch b/sci-chemistry/ccp4-apps/files/6.1.3-fix-setup-bash-incompatibility.patch deleted file mode 100644 index d98f54cdb3c1..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-fix-setup-bash-incompatibility.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ccp4-6.0.99e.orig/include/ccp4.setup-bash 2008-07-31 10:37:22.000000000 -0700 -+++ ccp4-6.0.99e/include/ccp4.setup-bash 2008-07-31 12:47:14.000000000 -0700 -@@ -181,7 +181,7 @@ - - #Python path for the subprocess fixed module - --if ($ccp4_first_in_path) then -+if [ $ccp4_first_in_path -eq 1 ]; then - setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} - else - setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch new file mode 100644 index 000000000000..a5144cfa5d33 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch @@ -0,0 +1,60 @@ +diff --git a/src/Makefile.in b/src/Makefile.in +index 70781f3..b2dcc25 100755 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -760,7 +760,7 @@ chainsawobjs = chainsaw.o + pdbcur : $(pdbcurobjs) + @$(SETFLAGS) ; rm -f pdbcur; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o pdbcur $(pdbcurobjs) $(LDCXXFLAGS) + ncont : $(ncontobjs) +- @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) ++ @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) -lmmdb + coord_format : $(coord_formatobjs) + @$(SETFLAGS) xxx=1 ; \ + rm -f coord_format; \ +diff --git a/src/rapper/LOOP/Makefile.am b/src/rapper/LOOP/Makefile.am +index 85f212e..2608c6d 100755 +--- a/src/rapper/LOOP/Makefile.am ++++ b/src/rapper/LOOP/Makefile.am +@@ -15,12 +15,12 @@ params.cpp typed_value.cpp misc.cpp residue.cpp atom.cpp psa.cpp edm_sidechains. + hash_table.cpp surface.cpp parse.cpp band.cpp edensity.cpp read_map.cpp iterator.cpp \ + residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp + +-rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la ++rapper_LDADD = @GC_LIBS@ @LIBXML_LIBS@ + + pkgdatadir = $(datadir)/rapper + dist_pkgdata_DATA = params.xml + +-INCLUDES = -I. -I../gc7.0/include -I../libxml2/include ++INCLUDES = -I. @LIBXML_CFLAGS@ @GC_CFLAGS@ + #SUBDIRS = \ + #@PYTHON_USE_TRUE@ python + +diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am +index e78b10d..486b931 100755 +--- a/src/rapper/Makefile.am ++++ b/src/rapper/Makefile.am +@@ -1,3 +1,3 @@ +-SUBDIRS = libxml2 gc7.0 LOOP data ++SUBDIRS = LOOP data + + EXTRA_DIST = +diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac +index 5e4ef69..268a579 100755 +--- a/src/rapper/configure.ac ++++ b/src/rapper/configure.ac +@@ -48,6 +48,13 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno) + + AC_SUBST(rapper_LDFLAGS) + +-AC_CONFIG_SUBDIRS([gc7.0 libxml2]) ++PKG_CHECK_MODULES([LIBXML],[libxml-2.0]) ++AC_SUBST([LIBXML_CFLAGS]) ++AC_SUBST([LIBXML_LIBS]) ++ ++PKG_CHECK_MODULES([GC],[bdw-gc]) ++AC_SUBST([GC_CFLAGS]) ++AC_SUBST([GC_LIBS]) ++ + #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile) + AC_OUTPUT(Makefile LOOP/Makefile data/Makefile) diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper.patch b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper.patch deleted file mode 100644 index a71c1354436c..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper.patch +++ /dev/null @@ -1,77 +0,0 @@ ---- src/rapper/LOOP/Makefile.in 2008-05-29 16:39:40.000000000 +0200 -+++ src/rapper/LOOP/Makefile.in.new 2009-03-12 20:40:03.157602172 +0100 -@@ -111,9 +111,9 @@ - pyexecdir = @pyexecdir@ - pythondir = @pythondir@ - rapper_LDFLAGS = @rapper_LDFLAGS@ --bin_PROGRAMS = rapper -+bin_PROGRAMS = rappermc - --rapper_SOURCES = \ -+rappermc_SOURCES = \ - kip.h aaconv.cpp atomconv.cpp kip_snake.cpp \ - kip_pdb.cpp measure.cpp lib_frags.cpp ran2.cpp \ - heap.cpp queue.cpp 3Dgeom.cpp space_grid.cpp list.cpp search_residue.cpp bitfield.cpp \ -@@ -129,7 +129,7 @@ - residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp - - --rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la -+rappermc_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la - dist_pkgdata_DATA = params.xml - - INCLUDES = -I. -I../gc7.0/include -I../libxml2/include -@@ -139,7 +139,7 @@ - bin_PROGRAMS = rapper$(EXEEXT) - PROGRAMS = $(bin_PROGRAMS) - --am_rapper_OBJECTS = aaconv.$(OBJEXT) atomconv.$(OBJEXT) \ -+am_rappermc_OBJECTS = aaconv.$(OBJEXT) atomconv.$(OBJEXT) \ - kip_snake.$(OBJEXT) kip_pdb.$(OBJEXT) measure.$(OBJEXT) \ - lib_frags.$(OBJEXT) ran2.$(OBJEXT) heap.$(OBJEXT) \ - queue.$(OBJEXT) 3Dgeom.$(OBJEXT) space_grid.$(OBJEXT) \ -@@ -164,8 +164,8 @@ - iterator.$(OBJEXT) residue_range.$(OBJEXT) \ - pop_search_frags.$(OBJEXT) saxs.$(OBJEXT) lib_choral.$(OBJEXT) \ - pdf.$(OBJEXT) WeightedDistribMean.$(OBJEXT) --rapper_OBJECTS = $(am_rapper_OBJECTS) --rapper_DEPENDENCIES = ../gc7.0/libgc.la ../libxml2/libxml2.la -+rappermc_OBJECTS = $(am_rapper_OBJECTS) -+rappermc_DEPENDENCIES = ../gc7.0/libgc.la ../libxml2/libxml2.la - - DEFS = @DEFS@ - DEFAULT_INCLUDES = -I. -I$(srcdir) -@@ -233,11 +233,11 @@ - CCLD = $(CC) - LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ - $(AM_LDFLAGS) $(LDFLAGS) -o $@ --DIST_SOURCES = $(rapper_SOURCES) -+DIST_SOURCES = $(rappermc_SOURCES) - DATA = $(dist_pkgdata_DATA) - - DIST_COMMON = $(dist_pkgdata_DATA) Makefile.am Makefile.in --SOURCES = $(rapper_SOURCES) -+SOURCES = $(rappermc_SOURCES) - - all: all-am - ---- src/rapper/LOOP/Makefile.am 2008-01-24 15:08:17.000000000 +0100 -+++ src/rapper/LOOP/Makefile.am.new 2009-03-12 23:01:56.697533874 +0100 -@@ -1,6 +1,6 @@ --bin_PROGRAMS = rapper -+bin_PROGRAMS = rappermc - --rapper_SOURCES = \ -+rappermc_SOURCES = \ - kip.h aaconv.cpp atomconv.cpp kip_snake.cpp \ - kip_pdb.cpp measure.cpp lib_frags.cpp ran2.cpp \ - heap.cpp queue.cpp 3Dgeom.cpp space_grid.cpp list.cpp search_residue.cpp bitfield.cpp \ -@@ -15,7 +15,7 @@ - hash_table.cpp surface.cpp parse.cpp band.cpp edensity.cpp read_map.cpp iterator.cpp \ - residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp - --rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la -+rappermc_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la - - pkgdatadir = $(datadir)/rapper - dist_pkgdata_DATA = params.xml diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-rename-truncate.patch b/sci-chemistry/ccp4-apps/files/6.1.3-rename-truncate.patch deleted file mode 100644 index 43bfcf7c7a0e..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-rename-truncate.patch +++ /dev/null @@ -1,42 +0,0 @@ -coreutils now installs a binary called truncate. - ---- src/Makefile.in.orig 2009-03-02 23:25:45.000000000 -0800 -+++ src/Makefile.in 2009-03-02 23:25:53.000000000 -0800 -@@ -41,7 +41,7 @@ - professs r500 rantan rebatch reindex revise rfcorr rotamer rotmat \ - rstats rwcontents sapi scaleit scalepack2mtz seqwt sfall sigmaa sortmtz sortwater \ - stgrid stnet surface tffc tracer \ --truncate unique vecref vectors volume watertidy watncs watpeak \ -+ftruncate unique vecref vectors volume watertidy watncs watpeak \ - wilson $(CIFTARGETS) - - BALBESTARGETS = search_DB get_structure_DB f2cif check_file_DB check_cell_sg \ -@@ -982,7 +982,7 @@ - surface: $(srcdir)/surface.f - tffc: $(srcdir)/tffc.f - tracer: $(srcdir)/tracer.f --truncate: $(srcdir)/truncate.f -+ftruncate: $(srcdir)/truncate.f - unique: $(srcdir)/unique.f - vecref: $(srcdir)/vecref.f - vectors: $(srcdir)/vectors.f ---- examples/unix/runnable/truncate.exam.orig 2009-03-02 23:35:04.000000000 -0800 -+++ examples/unix/runnable/truncate.exam 2009-03-02 23:35:11.000000000 -0800 -@@ -15,7 +15,7 @@ - exit 1 - fi - # --truncate hklin $CCP4_SCR/aucn_mrg.mtz \ -+ftruncate hklin $CCP4_SCR/aucn_mrg.mtz \ - hklout $CCP4_SCR/aucn_trn.mtz <<EOF-trunc - title DMSO red aucn2 Data - mosflm - truncate yes -@@ -28,7 +28,7 @@ - # do this if you already have Fs but want to look at the - # output graphs of TRUNCATE - --truncate hklin $CEXAM/rnase/rnase18.mtz <<EOF -+ftruncate hklin $CEXAM/rnase/rnase18.mtz <<EOF - title Analysis of rnase data - labin F=FNAT SIGF=SIGFNAT - nresidue 192 diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-setup.patch b/sci-chemistry/ccp4-apps/files/6.1.3-setup.patch deleted file mode 100644 index c85c688debe4..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-setup.patch +++ /dev/null @@ -1,336 +0,0 @@ -diff --git a/include/ccp4.setup-bash b/include/ccp4.setup-bash -index 9848101..d76fe3b 100755 ---- a/include/ccp4.setup-bash -+++ b/include/ccp4.setup-bash -@@ -37,8 +37,8 @@ fi - # This is usually the directory in which you ran the tar command to unpack the - # code, and is assumed to be shared between machines at a multi-machine site. - --setenv CCP4_MASTER /xtal --setenv CCP4 $CCP4_MASTER/ccp4-6.1.2 -+setenv CCP4_MASTER /usr -+setenv CCP4 $CCP4_MASTER - - # Check for existence of CCP4_MASTER - if (! test -d $CCP4_MASTER) ; then -@@ -54,7 +54,7 @@ fi - # files. A dedicated scratch filesystem is probably better than (/usr)/tmp - # BINSORT_SCR: a scratch directory for binsort's use; normally same as CCP4_SCR - --setenv CCP4_SCR /tmp/$USER -+setenv CCP4_SCR /tmp/$USER - # check to see if this exists and if not try to make it - test -d $CCP4_SCR || mkdir $CCP4_SCR - test -d $CCP4_SCR || \ -@@ -70,7 +70,7 @@ setenv CCP4I_TOP ${CCP4}/ccp4i - # For 'standard' installations this is /usr/local/bin - # but note the SGI distributed version of Tcl/Tk is not - # appropriate version --setenv CCP4I_TCLTK /usr/local/bin -+setenv CCP4I_TCLTK /usr/bin - # CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help - setenv CCP4I_HELP ${CCP4I_TOP}/help - -@@ -128,7 +128,7 @@ setenv GFORTRAN_UNBUFFERED_ALL Y - # # for multiple systems - # foo) - setenv CBIN $CCP4/bin -- setenv CLIB $CCP4/lib -+ setenv CLIB $CCP4/GENTOOLIBDIR - - setenv CCP4_BROWSER firefox - -@@ -188,9 +188,9 @@ fi - #Python path for the subprocess fixed module - - if [ $ccp4_first_in_path -eq 1 ]; then -- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} -+ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} - else -- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python -+ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python - fi - - ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### -@@ -292,14 +292,12 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg - - ### dbCCP4i database handler setup ### - --setenv DBCCP4I_TOP ${CCP4}/share/dbccp4i -+setenv DBCCP4I_TOP ${CCP4}/share/ccp4/dbccp4i - - ### IMOSFLM environment is now defined here - - setenv MOSFLM_EXEC ${CBIN}/ipmosflm - setenv MOSFLM_WISH ${CCP4I_TCLTK}/wish --setenv IMOSFLM_VERSION "1.0.0" -- - - ### MMCIFDIC is now defined here. cif_mmdic.lib is a binary file === - # so on multiple installs it need to be unique and not in $CLIBD -@@ -309,21 +307,13 @@ setenv MMCIFDIC $CLIB/cif_mmdic.lib - ### MOLREPLIB Point to the location of the files bs-zeros.dat ps.resource symlib.blc - # They are distributed with CCP4 in $CLIBD. This env must have the trailing \ or / - --setenv MOLREPLIB $CCP4/lib/data/monomers/ -+setenv MOLREPLIB $CCP4/share/ccp4/data/monomers/ - - ### CRANK points to location of Crank automation suite within ccp4i - --setenv CRANK $CCP4/ccp4i/crank -+setenv CRANK $CCP4I_TOP/bin/crank - setenv CCP4_CRANK 1 - --### XIA2 setup --# XIAROOT directory (default is under the share folder) -- --if test -e $CCP4/share/XIAROOT/setup.sh --then --. $CCP4/share/XIAROOT/setup.sh --fi -- - # Note: The PATH is updated with the xia2 Applications directory in the - # construct below. - -@@ -339,7 +329,7 @@ fi - # They are distributed with CCP4 in $CLIBD/monomers. This env must have - # the trailing \ or / - --setenv CLIBD_MON $CCP4/lib/data/monomers/ -+setenv CLIBD_MON $CCP4/share/ccp4/data/monomers/ - - ### PUBLIC_FONT84, CCP4_HELPDIR, HELPDIR, MOSHELPFILE ### - # (essential for the relevant programs) -@@ -347,10 +337,10 @@ setenv PUBLIC_FONT84 $CLIB/font84.dat # plot84 fonts [used by plot84lib] - - # location of VMS-style help files required for mosflm [used by hlplib, chelp, - # chlp, (ip)mosflm]: --setenv CCP4_HELPDIR $CCP4/help/ # NB trailing / -+setenv CCP4_HELPDIR $CCP4I_TOP/help/ # NB trailing / - - # Rasmol path. Needed for prog. to find rasmol.hlp --setenv RASMOLPATH $CCP4/x-windows/RasMol/src -+setenv RASMOLPATH $CCP4/GENTOOLIBDIR/rasmol - - # CCP4 executables and scripts live in $CBIN and $CETC respectively; put them - # on the path in an appropriate order for scripts to be used as wrappers for -@@ -373,32 +363,14 @@ done - - # Optional (useful) additional environment variables - setenv CCP4 $CCP4 -- setenv CDOC $CCP4/doc -- setenv CHTML $CCP4/html -- setenv CETC $CCP4/etc -- setenv CEXAM $CCP4/examples -+ setenv CDOC $DBCCP4I_TOP/doc -+ setenv CHTML $CCP4I_TOP/html -+ setenv CETC $CCP4I_TOP/etc -+ setenv CEXAM $CLIB/ccp4/examples - setenv CINCL $CCP4/include -- setenv CLIBD $CCP4/lib/data -- setenv CLIBS $CCP4/lib/src -- setenv CPROG $CCP4/src -+ setenv CLIBD $CCP4/share/ccp4/data - - if [ "`basename $SHELL`" != "ksh" ]; then --# useful aliases, at least for developers -- alias ccp4 'pushd $CCP4>/dev/null' -- alias xtal 'pushd $CCP4_MASTER>/dev/null' -- alias cbin 'pushd $CBIN>/dev/null' -- alias cetc 'pushd $CETC>/dev/null' -- alias cprog 'pushd $CPROG>/dev/null' -- alias cincl 'pushd $CINCL>/dev/null' -- alias clib 'pushd $CLIB>/dev/null' -- alias clibd 'pushd $CLIBD>/dev/null' -- alias clibs 'pushd $CLIBS>/dev/null' -- alias cbin 'pushd $CBIN>/dev/null' -- alias cexam 'pushd $CEXAM>/dev/null' -- alias cdoc 'pushd $CDOC>/dev/null' -- alias chtml 'pushd $CHTML>/dev/null' -- alias ccp4help '$CCP4_BROWSER $CHTML/INDEX.html \&' -- - ### laue, lget, linkimages ### - - ### only if we have the Laue software suite... -@@ -430,23 +402,6 @@ if [ "`basename $SHELL`" != "ksh" ]; then - alias lbin 'pushd $CBIN>/dev/null' - - fi -- -+else - unset alias # clean up - fi # ksh test -- --# Set-up cctbx environment --test -r $CCP4/lib/cctbx/cctbx_build/setpaths.sh && . $CCP4/lib/cctbx/cctbx_build/setpaths.sh -- --# Set-up phaser environment --if ( test -d $CCP4/src/phaser) ; then -- phaser_mtype=`$CCP4/src/phaser/bin/machine_type` -- phaser_version=`grep PHASER_VERSION $CCP4/src/phaser/conf/version.sh | awk '{print $3}'` -- phaser_setup_file="${CCP4}/src/phaser/phaser-${phaser_version}/build/${phaser_mtype}/setpaths.sh" -- test -r $phaser_setup_file && . $phaser_setup_file --fi -- --#BALBES root configuration --if ( test -d $CCP4/share/balbes/BALBES_0.0.1) --then -- setenv BALBES_ROOT $CCP4/share/balbes/BALBES_0.0.1 --fi -diff --git a/include/ccp4.setup-csh b/include/ccp4.setup-csh -index 42f0820..ed3c671 100755 ---- a/include/ccp4.setup-csh -+++ b/include/ccp4.setup-csh -@@ -24,8 +24,8 @@ - # This is usually the directory in which you ran the tar command to unpack the - # code, and is assumed to be shared between machines at a multi-machine site. - --setenv CCP4_MASTER /xtal --setenv CCP4 $CCP4_MASTER/ccp4-6.1.2 -+setenv CCP4_MASTER /usr -+setenv CCP4 $CCP4_MASTER - - # Check for existence of CCP4_MASTER - if (! -e $CCP4_MASTER) then -@@ -57,7 +57,7 @@ setenv CCP4I_TOP ${CCP4}/ccp4i - # For 'standard' installations this is /usr/local/bin - # but note the SGI distributed version of Tcl/Tk is not - # appropriate version --setenv CCP4I_TCLTK /usr/local/bin -+setenv CCP4I_TCLTK /usr/bin - # CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help - setenv CCP4I_HELP ${CCP4I_TOP}/help - -@@ -115,7 +115,7 @@ setenv GFORTRAN_UNBUFFERED_ALL Y - # # for multiple systems - # case 'foo': - setenv CBIN $CCP4/bin -- setenv CLIB $CCP4/lib -+ setenv CLIB $CCP4/GENTOOLIBDIR - - setenv CCP4_BROWSER firefox - -@@ -180,9 +180,9 @@ endif - #Python path for the subprocess fixed module - if (${?PYTHONPATH}) then - if ($ccp4_first_in_path) then -- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} -+ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} - else -- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python -+ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python - endif - else - setenv PYTHONPATH ${CCP4}/share/python -@@ -284,13 +284,12 @@ if (-e $CCP4/include/ccp4.msg) cat $CCP4/include/ccp4.msg - - ### dbCCP4i database handler setup ### - --setenv DBCCP4I_TOP ${CCP4}/share/dbccp4i -+setenv DBCCP4I_TOP ${CCP4}/share/ccp4/dbccp4i - - ### IMOSFLM environment is now defined here - - setenv MOSFLM_EXEC ${CBIN}/ipmosflm - setenv MOSFLM_WISH ${CCP4I_TCLTK}/wish --setenv IMOSFLM_VERSION "1.0.0" - - ### MMCIFDIC is now defined here. cif_mmdic.lib is a binary file === - # so on multiple installs it need to be unique and not in $CLIBD -@@ -300,20 +299,13 @@ setenv MMCIFDIC $CLIB/cif_mmdic.lib - ### MOLREPLIB Point to the location of the files bs-zeros.dat ps.resource symlib.blc - # They are distributed with CCP4 in $CLIBD. This env must have the trailing \ or / - --setenv MOLREPLIB $CCP4/lib/data/monomers/ -+setenv MOLREPLIB $CCP4/share/ccp4/data/monomers/ - - ### CRANK points to location of Crank automation suite within ccp4i - --setenv CRANK $CCP4/ccp4i/crank -+setenv CRANK $CCP4I_TOP/bin/crank - setenv CCP4_CRANK 1 - --### XIA2 setup --# XIAROOT directory (default is under the share folder) -- --if (-e $CCP4/share/XIAROOT/setup.csh) then -- source $CCP4/share/XIAROOT/setup.csh --endif -- - # Note: The PATH is updated with the xia2 Applications directory in the - # construct below. - -@@ -328,7 +320,7 @@ endif - # They are distributed with CCP4 in $CLIBD/monomers. This env must have - # the trailing \ or / - --setenv CLIBD_MON $CCP4/lib/data/monomers/ -+setenv CLIBD_MON $CCP4/share/ccp4/data/monomers/ - - ### PUBLIC_FONT84, CCP4_HELPDIR, HELPDIR, MOSHELPFILE ### - # (essential for the relevant programs) -@@ -339,7 +331,7 @@ setenv PUBLIC_FONT84 $CLIB/font84.dat # plot84 fonts [used by plot84lib] - setenv CCP4_HELPDIR $CCP4/help/ # NB trailing / - - # Rasmol path. Needed for prog. to find rasmol.hlp --setenv RASMOLPATH $CCP4/x-windows/RasMol/src -+setenv RASMOLPATH $CCP4/GENTOOLIBDIR/rasmol - - # CCP4 executables and scripts live in $CBIN and $CETC respectively; put them - # on the path in an appropriate order for scripts to be used as wrappers for -@@ -366,30 +358,12 @@ end - - # Optional (useful) additional environment variables - setenv CCP4 $CCP4 -- setenv CDOC $CCP4/doc -- setenv CHTML $CCP4/html -- setenv CETC $CCP4/etc -- setenv CEXAM $CCP4/examples -+ setenv CDOC $DBCCP4I_TOP/doc -+ setenv CHTML $CCP4I_TOP/html -+ setenv CETC $CCP4I_TOP/etc -+ setenv CEXAM $CLIB/ccp4/examples - setenv CINCL $CCP4/include -- setenv CLIBD $CCP4/lib/data -- setenv CLIBS $CCP4/lib/src -- setenv CPROG $CCP4/src -- --# useful aliases, at least for developers -- alias ccp4 'pushd $CCP4>/dev/null' -- alias xtal 'pushd $CCP4_MASTER>/dev/null' -- alias cbin 'pushd $CBIN>/dev/null' -- alias cetc 'pushd $CETC>/dev/null' -- alias cprog 'pushd $CPROG>/dev/null' -- alias cincl 'pushd $CINCL>/dev/null' -- alias clib 'pushd $CLIB>/dev/null' -- alias clibd 'pushd $CLIBD>/dev/null' -- alias clibs 'pushd $CLIBS>/dev/null' -- alias cbin 'pushd $CBIN>/dev/null' -- alias cexam 'pushd $CEXAM>/dev/null' -- alias cdoc 'pushd $CDOC>/dev/null' -- alias chtml 'pushd $CHTML>/dev/null' -- alias ccp4help '$CCP4_BROWSER $CHTML/INDEX.html &' -+ setenv CLIBD $CCP4/share/ccp4/data - - ### laue, lget, linkimages ### - -@@ -421,19 +395,3 @@ end - # - - endif -- --# Set-up cctbx environment --if (-e $CCP4/lib/cctbx/cctbx_build/setpaths.csh) source $CCP4/lib/cctbx/cctbx_build/setpaths.csh -- --# Set-up phaser environment --if (-d $CCP4/src/phaser) then -- set phaser_mtype = `$CCP4/src/phaser/bin/machine_type` -- set phaser_version = `grep PHASER_VERSION $CCP4/src/phaser/conf/version.csh | awk '{print $3}'` -- set phaser_setup_file = "${CCP4}/src/phaser/phaser-${phaser_version}/build/${phaser_mtype}/setpaths.csh" -- if (-e $phaser_setup_file) source $phaser_setup_file --endif -- --#BALBES root configuration --if ( -d $CCP4/share/balbes/BALBES_0.0.1) then -- setenv BALBES_ROOT $CCP4/share/balbes/BALBES_0.0.1 --endif |