| 1 |
dberkholz 08/08/04 00:11:55 |
| 2 |
|
| 3 |
Added: 7.0.1-source-ccp4-if-needed.patch 7.0.1-setup.patch |
| 4 |
Log: |
| 5 |
(#212054) New package: ARP/wARP is a software for improvement and interpretation of crystallographic electron density maps. |
| 6 |
(Portage version: 2.2_rc5/cvs/Linux 2.6.26 x86_64) |
| 7 |
|
| 8 |
Revision Changes Path |
| 9 |
1.1 sci-chemistry/arp-warp-bin/files/7.0.1-source-ccp4-if-needed.patch |
| 10 |
|
| 11 |
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/arp-warp-bin/files/7.0.1-source-ccp4-if-needed.patch?rev=1.1&view=markup |
| 12 |
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/arp-warp-bin/files/7.0.1-source-ccp4-if-needed.patch?rev=1.1&content-type=text/plain |
| 13 |
|
| 14 |
Index: 7.0.1-source-ccp4-if-needed.patch |
| 15 |
=================================================================== |
| 16 |
--- share.orig/arpwarp_setup_base.bash 2008-08-03 16:50:03.000000000 -0700 |
| 17 |
+++ share/arpwarp_setup_base.bash 2008-08-03 16:51:20.000000000 -0700 |
| 18 |
@@ -23,11 +23,14 @@ |
| 19 |
# |
| 20 |
# Checks for CBIN variable |
| 21 |
if [ "$CBIN" = "" ]; then |
| 22 |
- echo |
| 23 |
- echo "Cannot setup ARP/wARP" |
| 24 |
- echo 'Variable $CBIN is not defined' |
| 25 |
- echo "Please install CCP4 first" |
| 26 |
- testccp='1' |
| 27 |
+ source /etc/profile.d/ccp4.setup.sh |
| 28 |
+ if [ "$CBIN" = "" ]; then |
| 29 |
+ echo |
| 30 |
+ echo "Cannot setup ARP/wARP" |
| 31 |
+ echo 'Variable $CBIN is not defined' |
| 32 |
+ echo "Please install CCP4 first" |
| 33 |
+ testccp='1' |
| 34 |
+ fi |
| 35 |
fi |
| 36 |
if [ "$testccp" = '0' ]; then |
| 37 |
if [ ! -d $CBIN ]; then |
| 38 |
--- share.orig/arpwarp_setup_base.csh 2008-08-03 16:50:06.000000000 -0700 |
| 39 |
+++ share/arpwarp_setup_base.csh 2008-08-03 16:52:03.000000000 -0700 |
| 40 |
@@ -22,11 +22,14 @@ |
| 41 |
# Settings for python |
| 42 |
# Checks for CBIN variable |
| 43 |
if ( ! $?CBIN ) then |
| 44 |
- echo |
| 45 |
- echo 'Cannot setup ARP/wARP' |
| 46 |
- echo 'Variable $CBIN is not defined' |
| 47 |
- echo 'Please install CCP4 first' |
| 48 |
- goto errorsetup |
| 49 |
+ source /etc/profile.d/ccp4.setup.sh |
| 50 |
+ if ( ! $?CBIN ) then |
| 51 |
+ echo |
| 52 |
+ echo 'Cannot setup ARP/wARP' |
| 53 |
+ echo 'Variable $CBIN is not defined' |
| 54 |
+ echo 'Please install CCP4 first' |
| 55 |
+ goto errorsetup |
| 56 |
+ endif |
| 57 |
endif |
| 58 |
if ( ! -d $CBIN ) then |
| 59 |
echo |
| 60 |
|
| 61 |
|
| 62 |
|
| 63 |
1.1 sci-chemistry/arp-warp-bin/files/7.0.1-setup.patch |
| 64 |
|
| 65 |
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/arp-warp-bin/files/7.0.1-setup.patch?rev=1.1&view=markup |
| 66 |
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/arp-warp-bin/files/7.0.1-setup.patch?rev=1.1&content-type=text/plain |
| 67 |
|
| 68 |
Index: 7.0.1-setup.patch |
| 69 |
=================================================================== |
| 70 |
diff -Nu -Nu -uarN arp_warp_7.0.1.orig/share/arpwarp_setup_base.bash arp_warp_7.0.1/share/arpwarp_setup_base.bash |
| 71 |
--- arp_warp_7.0.1.orig/share/arpwarp_setup_base.bash 2007-10-21 21:46:13.000000000 +0200 |
| 72 |
+++ arp_warp_7.0.1/share/arpwarp_setup_base.bash 2008-04-06 13:33:05.000000000 +0200 |
| 73 |
@@ -13,10 +13,10 @@ |
| 74 |
identifier=${nameprocessor}'-'${namesystem} |
| 75 |
fi |
| 76 |
# |
| 77 |
-arpwarphome="$1X" |
| 78 |
+arpwarphome="/opt/arp-warp-bin" |
| 79 |
# |
| 80 |
export warpbin=${arpwarphome}/bin/bin-${identifier} |
| 81 |
-export warpdoc=${arpwarphome}/manual |
| 82 |
+export warpdoc=/usr/share/doc/arp-warp-bin-7.0.1/html/ |
| 83 |
export PATH=${warpbin}:${PATH} |
| 84 |
# |
| 85 |
testccp='0' |
| 86 |
@@ -49,7 +49,7 @@ |
| 87 |
fi |
| 88 |
|
| 89 |
## 2. Complement by other potential places for python : |
| 90 |
- search_list="${search_list} /usr/local/bin/python /usr/bin/python" |
| 91 |
+ search_list="${search_list} /usr/bin/python" |
| 92 |
flex_wARP_python="/dev/null" |
| 93 |
|
| 94 |
## 3. Pick up the first one of the list which seems reasonable : |
| 95 |
@@ -73,30 +73,6 @@ |
| 96 |
export flex_wARP_bin=${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2} |
| 97 |
break |
| 98 |
fi |
| 99 |
-# 3.c Otherwise, we should be able to create the byte-code using the python. |
| 100 |
- /bin/mkdir -p ${arpwarphome}/byte-code/python-${pythonvrs1}.${pythonvrs2} 1> /dev/null 2>&1 |
| 101 |
- if [ 0 != $? ] ; then |
| 102 |
- /bin/mkdir -p ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2} 1> /dev/null 2>&1 |
| 103 |
- export flex_wARP_bin=${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2} |
| 104 |
- else |
| 105 |
- export flex_wARP_bin=${arpwarphome}/byte-code/python-${pythonvrs1}.${pythonvrs2} |
| 106 |
- fi |
| 107 |
- pushd ${flex_wARP_bin} 1> /dev/null 2>&1 |
| 108 |
- if [ 0 != $? ] ; then |
| 109 |
- export flex_wARP_bin=${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2} |
| 110 |
- /bin/mkdir -p ${flex_wARP_bin} 1> /dev/null 2>&1 |
| 111 |
- pushd ${flex_wARP_bin} 1> /dev/null 2>&1 |
| 112 |
- fi |
| 113 |
- /bin/cp -p ${arpwarphome}/flex-wARP-src/*.py . |
| 114 |
- ${python_to_test} ./compile.py |
| 115 |
- /bin/rm -f *.py |
| 116 |
- popd 1> /dev/null 2>&1 |
| 117 |
- if [ -e ${flex_wARP_bin}/CPyWARP.pyc ] ; then |
| 118 |
- export flex_wARP_python=${python_to_test} |
| 119 |
- echo "Created a new set of flex-wARP byte code in the directory :" |
| 120 |
- echo " '${flex_wARP_bin}'" |
| 121 |
- break |
| 122 |
- fi |
| 123 |
done |
| 124 |
## 4. If nothing is available, print out a message. |
| 125 |
if [ "/dev/null" != ${flex_wARP_python} ] ; then |
| 126 |
@@ -107,6 +83,7 @@ |
| 127 |
echo "WARNING while setting up ARP/wARP" |
| 128 |
echo "No valid 'python' command was found" |
| 129 |
echo "flex-warp ('ARP/wARP Expert System' in the GUI) will not be available." |
| 130 |
+ echo "Did you upgrade your python? Reemerge ArpWarp!" |
| 131 |
echo |
| 132 |
export flex_wARP_warpbin="Unavailable" |
| 133 |
export flex_wARP_cbin="Unavailable" |
| 134 |
@@ -115,17 +92,3 @@ |
| 135 |
fi |
| 136 |
fi |
| 137 |
|
| 138 |
-# |
| 139 |
-# Setting up library path for SGI |
| 140 |
-if [[ "${namesystem}" = 'IRIX64' || "${namesystem}" = 'IRIX' ]]; then |
| 141 |
- if test "$LD_LIBRARY_PATH"; then |
| 142 |
- export LD_LIBRARY_PATH=${warpbin}:${LD_LIBRARY_PATH} |
| 143 |
- else |
| 144 |
- export LD_LIBRARY_PATH=${warpbin} |
| 145 |
- fi |
| 146 |
-fi |
| 147 |
-# echo |
| 148 |
-# echo 'ARP/wARP Version 7.0.1 has been setup' |
| 149 |
-# |
| 150 |
- |
| 151 |
- |
| 152 |
diff -Nu -Nu -uarN arp_warp_7.0.1.orig/share/arpwarp_setup_base.csh arp_warp_7.0.1/share/arpwarp_setup_base.csh |
| 153 |
--- arp_warp_7.0.1.orig/share/arpwarp_setup_base.csh 2007-10-21 21:46:13.000000000 +0200 |
| 154 |
+++ arp_warp_7.0.1/share/arpwarp_setup_base.csh 2008-04-06 13:32:48.000000000 +0200 |
| 155 |
@@ -13,10 +13,10 @@ |
| 156 |
set identifier = ${nameprocessor}'-'${namesystem} |
| 157 |
endif |
| 158 |
# |
| 159 |
-set arpwarphome = '$1X' |
| 160 |
+set arpwarphome = '/opt/arp-warp-bin' |
| 161 |
# |
| 162 |
setenv warpbin ${arpwarphome}/bin/bin-${identifier} |
| 163 |
-setenv warpdoc ${arpwarphome}/manual |
| 164 |
+setenv warpdoc /usr/share/doc/arp-warp-bin-7.0.1/html/ |
| 165 |
set path = ( $warpbin $path ) |
| 166 |
# |
| 167 |
# Settings for python |
| 168 |
@@ -47,7 +47,7 @@ |
| 169 |
endif |
| 170 |
|
| 171 |
## 2. Complement by other potential places for python : |
| 172 |
-set search_list = "${search_list} /usr/local/bin/python /usr/bin/python" |
| 173 |
+set search_list = "${search_list} /usr/bin/python" |
| 174 |
setenv flex_wARP_python "/dev/null" |
| 175 |
|
| 176 |
## 3. Pick up the first one of the list which seems reasonable : |
| 177 |
@@ -71,30 +71,6 @@ |
| 178 |
setenv flex_wARP_bin ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2} |
| 179 |
break |
| 180 |
endif |
| 181 |
-# 3.c Otherwise, we should be able to create the byte-code using the python. |
| 182 |
- /bin/mkdir -p ${arpwarphome}/byte-code/python-${pythonvrs1}.${pythonvrs2} >& /dev/null |
| 183 |
- if ( 0 != $status ) then |
| 184 |
- /bin/mkdir -p ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2} >& /dev/null |
| 185 |
- setenv flex_wARP_bin ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2} |
| 186 |
- else |
| 187 |
- setenv flex_wARP_bin ${arpwarphome}/byte-code/python-${pythonvrs1}.${pythonvrs2} |
| 188 |
- endif |
| 189 |
- pushd ${flex_wARP_bin} >& /dev/null |
| 190 |
- if ( 0 != $status ) then |
| 191 |
- setenv flex_wARP_bin ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2} |
| 192 |
- /bin/mkdir -p ${flex_wARP_bin} >& /dev/null |
| 193 |
- pushd ${flex_wARP_bin} >& /dev/null |
| 194 |
- endif |
| 195 |
- /bin/cp -p ${arpwarphome}/flex-wARP-src/*.py . |
| 196 |
- ${python_to_test} ./compile.py |
| 197 |
- /bin/rm -f *.py |
| 198 |
- popd >& /dev/null |
| 199 |
- if ( -e ${flex_wARP_bin}/CPyWARP.pyc ) then |
| 200 |
- setenv flex_wARP_python ${python_to_test} |
| 201 |
- echo "Created a new set of flex-wARP byte code in the directory :" |
| 202 |
- echo " '${flex_wARP_bin}'" |
| 203 |
- break |
| 204 |
- endif |
| 205 |
end |
| 206 |
## 4. If nothing is available, print out a message. |
| 207 |
if ( "/dev/null" != ${flex_wARP_python} ) then |
| 208 |
@@ -105,22 +81,13 @@ |
| 209 |
echo "WARNING while setting up ARP/wARP" |
| 210 |
echo "No valid 'python' command was found" |
| 211 |
echo "flex-warp ('ARP/wARP Expert System' in the GUI) will not be available." |
| 212 |
+ echo "Did you upgrade your python? Reemerge ArpWarp!" |
| 213 |
echo |
| 214 |
setenv flex_wARP_warpbin "Unavailable" |
| 215 |
setenv flex_wARP_cbin "Unavailable" |
| 216 |
setenv flex_wARP_python "/dev/null" |
| 217 |
setenv flex_wARP_bin "Unavailable" |
| 218 |
endif |
| 219 |
- |
| 220 |
-# |
| 221 |
-# Setting up library path for SGI |
| 222 |
-if ( ${namesystem} == 'IRIX64' || ${namesystem} == 'IRIX' ) then |
| 223 |
- if ( ${?LD_LIBRARY_PATH} ) then |
| 224 |
- setenv LD_LIBRARY_PATH ${warpbin}:${LD_LIBRARY_PATH} |
| 225 |
- else |
| 226 |
- setenv LD_LIBRARY_PATH ${warpbin} |
| 227 |
- endif |
| 228 |
-endif |
| 229 |
# |
| 230 |
goto endsetup |
| 231 |
# |
| 232 |
@@ -132,7 +99,4 @@ |
| 233 |
# |
| 234 |
endsetup: |
| 235 |
# |
| 236 |
-#echo |
| 237 |
-#echo 'ARP/wARP Version 7.0.1 has been setup' |
| 238 |
-# |
Archives