fix pyrogen

3 files changed, 118 insertions, 38 deletions

diff --git a/PKGBUILD b/PKGBUILD
index 0feba02ee127..65d7cd345f5d 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -6,9 +6,12 @@ pkgdesc="Crystallographic Object-Oriented Toolkit for model building, completion
 arch=('i686' 'x86_64')
 url="http://lmb.bioch.ox.ac.uk/coot/"
 license=('GPL')
+replaces=('coot-data')
 depends=('guile1.8' 'guile1.8-lib' 'guile1.8-gtk' 'guile1.8-gui' 'gtkglext' 'libccp4' 'clipper' 'goocanvas1' 'gsl' 'libgnomecanvas' 'imlib' 'swig'
-         'freeglut' 'libgl' 'gtk2' 'cairo' 'libssm>=1.4' 'zlib' 'curl' 'python2' 'pygtk' 'gtkglarea' 'which' 'bc' 'sqlite' 'rdkit' 'mmdb2>=2.0.12-4')
-source=(http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/$pkgname-$pkgver.tar.gz
+         'freeglut' 'libgl' 'gtk2' 'cairo' 'libssm>=1.4.0-2' 'zlib' 'curl' 'python2' 'pygtk' 'gtkglarea' 'which' 'bc' 'sqlite' 'rdkit-python2' 'mmdb2>=2.0.12-4')
+source=(http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/$pkgname/source/releases/$pkgname-$pkgver.tar.gz
+        https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/$pkgname/dependencies/refmac-monomer-library.tar.gz
+        https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/$pkgname/dependencies/reference-structures.tar.gz
         coot-configure.ac.patch
         coot-makefile.patch
         coot-guile.patch
@@ -18,15 +21,13 @@ source=(http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/$pkg
         coot-lbg.patch
         coot-python.patch
         coot-lidia.patch
+        coot-pyrogen.patch
+        coot.in
         )
-#	coot-configure.in.patch
-#	coot-user-manual.texi.patch
-#	coot-makefile.patch
-#        coot-guile.patch
-#        coot-python.patch
-#        coot-icons.patch
-#        coot-lidia.patch)
+
 sha256sums=('df31ab66d7c3de6524fefcafaab6acc11e4525b930fed3b929ed773ae1776aa7'
+            '03562eec612103a48bd114cfe0d171943e88f94b84610d16d542cda138e5f36b'
+            '44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a'
             '2babfbc3cb798868d9e22f19ee49d12981fac35e3dfba2d8f7318716f59f673c'
             '9ad5a56116748ab5b1f77b2a4b2e3df47847ff881579105dff6589ed60ac8eb4'
             'c15e844536f512c2d5524391dbc046a889a0d5f8c23336b854508e453e226911'
@@ -35,7 +36,9 @@ sha256sums=('df31ab66d7c3de6524fefcafaab6acc11e4525b930fed3b929ed773ae1776aa7'
             '8b1c499ce5d506419ca72f999b6a0332a2edcc30e3128b1eb0bd3d399d0d80a6'
             '423a50d27639376c52e6987877acea908d854decb48c7c2452f7f5ecb92b60e9'
             'f4747e1fc7a3387f42b6c40358f999404761a0282ee6be3c621091d9d5d88099'
-            'dd2eb7c66ff2fa6f68a9d1e834e1911d2a1669a76ed29b5dbd6863619edcba18')
+            'dd2eb7c66ff2fa6f68a9d1e834e1911d2a1669a76ed29b5dbd6863619edcba18'
+            '987e41d1b8adf87c2b66e75c07ac85810381354b3b78cb708ebadd8bbada8251'
+            '681606cc5e1cb832235f568a59df6738461afa8270a25c468b92920ef269a250')
 
 build() {
 
@@ -50,16 +53,19 @@ build() {
   patch -Np0 -i "$srcdir/coot-lbg.patch"
   patch -Np0 -i "$srcdir/coot-python.patch"
   patch -Np0 -i "$srcdir/coot-lidia.patch"
+  patch -Np0 -i "$srcdir/coot-pyrogen.patch"
 
 
   iconv -f iso8859-1 -t utf-8 README > README.conv && mv -f README.conv README
 
+  cp $srcdir/coot.in src/
+
   aclocal -I macros
   libtoolize --automake --copy
   autoconf
   automake --copy --add-missing --gnu
 
-  # Work around coot's code not beeing completely standart compliant
+  # Work around coot's code not beeing completely standard compliant
   CXXFLAGS="${CXXFLAGS} -fpermissive"
 
   ./configure --prefix=/usr \
@@ -74,36 +80,27 @@ build() {
               --with-enhanced-ligand-tools RDKIT_LIBS="-lRDKitMolDraw2D -lRDKitForceFieldHelpers -lRDKitDescriptors -lRDKitForceField -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDistGeomHelpers -lRDKitDistGeometry -lRDKitAlignment -lRDKitEigenSolvers -lRDKitDepictor -lRDKitMolChemicalFeatures -lRDKitFileParsers  -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7" RDKIT_CXXFLAGS="-I/usr/include/rdkit"
 
   make
-
-#  patch -Np0 -i "$srcdir/coot-configure.in.patch"
-
-# patch -Np0 -i "$srcdir/coot-user-manual.texi.patch"
-# patch -Np0 -i "$srcdir/coot-guile.patch"
-# patch -Np0 -i "$srcdir/coot-python.patch"
-# patch -Np0 -i "$srcdir/coot-icons.patch"
-# patch -Np0 -i "$srcdir/coot-lidia.patch"
-
-#  iconv -f iso8859-1 -t utf-8 README > README.conv && mv -f README.conv README
-#
-#  aclocal -I macros
-#  libtoolize --automake --copy
-#  autoconf
-#  automake --copy --add-missing --gnu
-#
-#  CXXFLAGS="${CXXFLAGS} -fpermissive"
-#  CFLAGS="${CFLAGS} -fpermissive"
-#
-#  ./configure --prefix=/usr \
-#              --includedir=/usr/include/coot \
-#              --with-guile \
-#              --with-python \
-#              --with-pygtk \
-#              --disable-static
-#
-#  make
 }
 
 package() {
   cd "$srcdir/$pkgname-$pkgver"
   make DESTDIR="$pkgdir/" install
+  sed -i 's|COOT_PYTHON_DIR=|COOT_PYTHON_DIR=/usr/lib/python2.7/site-packages/coot|' src/$pkgname
+  sed -i 's|COOT_REFMAC_LIB_DIR=|COOT_REFMAC_LIB_DIR=/usr/share/coot/lib/|' src/$pkgname
+  install -p -m 755 src/$pkgname $pkgdir/usr/bin
+
+  # remove shebang from python scripts
+  for lib in $(find $pkgdir/usr/lib/python2.7/site-packages/$pkgname/ -name "*.py"); do
+    sed '/\/usr\/bin\/env/d' $lib > $lib.new &&
+    touch -r $lib $lib.new &&
+    mv $lib.new $lib
+  done
+
+  chmod 644 $pkgdir/usr/lib/python2.7/site-packages/$pkgname/$pkgname.py
+
+  install -d $pkgdir/usr/share/$pkgname/reference-structures
+  install -Dm644 $srcdir/reference-structures/*.pdb $pkgdir/usr/share/$pkgname/reference-structures/
+
+  install -d $pkgdir/usr/share/$pkgname/lib/data/monomers
+  cp -r $srcdir/monomers/* $pkgdir/usr/share/$pkgname/lib/data/monomers/
 }
diff --git a/coot-pyrogen.patch b/coot-pyrogen.patch
new file mode 100644
index 000000000000..c1bafb95685a
--- /dev/null
+++ b/coot-pyrogen.patch
@@ -0,0 +1,22 @@
+--- pyrogen/pyrogen.in.old	2016-06-29 05:00:18.000000000 +0200
++++ pyrogen/pyrogen.in	2017-06-15 22:11:34.872817885 +0200
+@@ -7,11 +7,11 @@
+ 
+ systype=$(uname)
+ 
+-if [ $systype = Darwin ] ; then 
++if [ $systype = Darwin ] ; then
+    prfx=$(dirname "$current_exe_dir")
+    if [ -z "$DYLD_FALLBACK_LIBRARY_PATH" ] ;  then
+ 	DYLD_FALLBACK_LIBRARY_PATH=$prfx/lib
+-   else 
++   else
+ 	DYLD_FALLBACK_LIBRARY_PATH=$prfx/lib:${DYLD_FALLBACK_LIBRARY_PATH}
+    fi
+    export DYLD_FALLBACK_LIBRARY_PATH
+@@ -22,4 +22,4 @@
+ 
+ export PATH=$prfx/bin:$PATH
+ 
+-python -m pyrogen $*
++python2 -m pyrogen $*
diff --git a/coot.in b/coot.in
new file mode 100644
index 000000000000..0bef02913191
--- /dev/null
+++ b/coot.in
@@ -0,0 +1,61 @@
+#!/bin/sh
+# -*-shell-script-*-
+# coot wrapper script 
+# Copyright 2004, 2005, 2006, 2007 University of York
+# written by Paul Emsley
+
+COOT_PREFIX="/usr"
+current_exe_dir="/usr/libexec"
+
+coot_real=$current_exe_dir/coot-bin
+# echo coot-real is at $coot_real
+
+# ----------------------------------------------------------------------------
+# ----------------------------------------------------------------------------
+# If the COOT_PREFIX is correct, then these should not need modification
+# i.e.  nothing below here need be changed.
+# ----------------------------------------------------------------------------
+# ----------------------------------------------------------------------------
+# 
+prefix=$COOT_PREFIX
+
+SYMINFO=$COOT_PREFIX/share/coot/syminfo.lib
+COOT_SCHEME_DIR=$COOT_PREFIX/share/coot/scheme
+COOT_STANDARD_RESIDUES=$COOT_PREFIX/share/coot/standard-residues.pdb
+COOT_PIXMAPS_DIR=$COOT_PREFIX/share/coot/pixmaps
+COOT_DATA_DIR=$COOT_PREFIX/share/coot
+COOT_RESOURCES_FILE=$COOT_PREFIX/share/coot/cootrc
+COOT_REF_STRUCTS=$COOT_PREFIX/share/coot/reference-structures
+COOT_PYTHON_DIR=
+COOT_REFMAC_LIB_DIR=
+
+PYTHONPATH=${PYTHONPATH:+"${PYTHONPATH}:"}$COOT_PYTHON_DIR
+
+GUILE_WARN_DEPRECATED=no
+
+if [ -n "$LOCAL_GUILE_LOAD_PATH_EXTRAS" ] ; then 
+    GUILE_LOAD_PATH=${LOCAL_GUILE_LOAD_PATH_EXTRAS}:$GUILE_LOAD_PATH
+    export GUILE_LOAD_PATH
+fi
+
+# echo GUILE_LOAD_PATH is now $GUILE_LOAD_PATH
+
+export SYMINFO
+export COOT_PREFIX
+export COOT_STANDARD_RESIDUES
+export COOT_REFMAC_LIB_DIR
+export COOT_PYTHON_DIR
+export PYTHONPATH
+export COOT_SCHEME_DIR
+export COOT_REF_STRUCTS
+export COOT_RESOURCES_FILE
+export COOT_PIXMAPS_DIR
+export COOT_DATA_DIR
+
+echo $coot_real $*
+$coot_real $*
+status=$?
+
+if [ $status != 0 ] ; then
+    /usr/bin/guile1.8 -s $COOT_PREFIX/share/coot/scheme/coot-crash-catcher.scm $coot_real
+fi