coot/source/v1 をテンプレートにして作成
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開始行:
v0.9.xと同様に 本家様で構築用のスクリプトが用意されています
そのスクリプトを実行すると [[https://github.com/pemsley/c...
でもスクリプトは rockylinux 向けではなくちょっとした修正...
***rockylinux9で coot-1.x をソースから作成してみる [#ja83...
っで実際に作ってみる
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.8 (Blue Onyx)
[root@rockylinux9 ~]# dnf groupinstall "Development Tools"
[root@rockylinux9 ~]# dnf install epel-release
[root@rockylinux9 ~]# dnf config-manager --enable crb
[root@rockylinux9 ~]# dnf install cmake texinfo gtk4-deve...
openssl-devel sqlite-devel gdbm-devel lib...
[root@rockylinux9 ~]# mkdir script ; cd script
[root@rockylinux9 script]#
[root@rockylinux9 script]# wget https://raw.githubusercon...
[root@rockylinux9 script]# grep ^script_version build-it-...
script_version=6.26
[root@rockylinux9 script]#
[root@rockylinux9 script]# vi ./build-it-3-3
}}
「build-it-3-3」の中で修正を行います.
変更項目
pygobjectが3.52.3ではgirepository-2.0を要求するがrockyl...
pygobjectを3.46.0にしたので対応するpythonは3.14ではだめ...
greg-testsを有効へ
COOT_BUILD_INFO_STRINGは文言にスペースが入って上手く処...
post_install_slimは十分に機能しないので削除
#code(diff,nonumber){{
--- build-it-3-3.orig 2026-06-24 06:08:18.706906055 +0900
+++ build-it-3-3 2026-06-24 18:50:28.650552404 +0900
@@ -1053,7 +1053,7 @@
if test -e /etc/os-release ; then
# 20240914 strip quote marks also now
dist_name=$(grep ^ID= /etc/os-release | sed...
- dist_ver=$(grep ^VERSION_ID /etc/os-release...
+ dist_ver=$(grep ^VERSION_ID /etc/os-release...
else
for i in fedora-release redhat-release redh...
rpm -q --qf '%{name}' ${i}
@@ -2141,12 +2141,12 @@
#
# python_version is the filename of the python executable.
#
-python_version=python3.14
-pver=3.14.2
-python_version_extension=3.14 # extract this
+python_version=python3.11
+pver=3.11.11
+python_version_extension=3.11 # extract this
# I think that for python to be compatible with Blender,...
# python_abiflags=d # because we use --with-pydebug on t...
-python_version_squish=314
+python_version_squish=311
# for Blender 4 in 2024, we want Python 3.10.13, so unco...
# for Blender 4.1 in June 2025, we want Python 3.11.x
@@ -2737,6 +2737,7 @@
patch -p0 < ${AUTOBUILD_SOURCES}/readline-5.1.patch
fi
do_the_sed=no
+ if [ "$dist_name" = rocky ] ; then do_the_sed=ye...
if [ "$dist_name" = arch ] ; then do_the_sed=ye...
if [ "$dist_name" = almalinux ] ; then do_the_sed=ye...
if [ "$dist_name" = ubuntu ] ; then do_the_sed=ye...
@@ -2873,7 +2874,7 @@
fi
else
# what about rocky here also?
- if test "$dist_name" = fedora ; then
+ if [ "$dist_name" = fedora ] || [ "$dist_name" = rock...
if [ -e $install_top_dir/include/openssl ] ; then
build_openssl=false
else
@@ -2977,7 +2978,7 @@
# remove --with-pydebug for now because __PyNegativeR...
#
# do we also need to use --with-threads=dir?
- if test "$dist_name" = fedora ; then
+ if [ "$dist_name" = fedora ] || [ "$dist_name" = rock...
python_install_top_dir=$HOME/building-python
python_install_top_dir=$HOME/building-python-tt
python_install_top_dir=$install_top_dir
@@ -4184,7 +4185,7 @@
if test "$dist_name" = almalinux ; then
echo don.t mess with LDFLAGS on almali...
else
- if test "$dist_name" = arch ; then
+ if [ "$dist_name" = arch ] || [ "$dist_...
echo don.t mess with LDFLAGS here o...
else
export LDFLAGS="-L$install_top_dir...
@@ -4504,10 +4505,12 @@
pygobject_major_minor_version=3.36
pygobject_major_minor_version=3.42
pygobject_major_minor_version=3.52 # 20250621-PE
+pygobject_major_minor_version=3.46
pygobject_version=3.29.1
pygobject_version=3.30.5
pygobject_version=3.42.1
pygobject_version=3.52.3
+pygobject_version=3.46.0
# pygobject_version=3.42.2 add me to the extras place!
# https://download.gnome.org/sources/pygobject/3.42/pygo...
# https://download.gnome.org/sources/pygobject/3.52/pygo...
@@ -4596,7 +4599,7 @@
echo PKG_CONFIG_PATH $PKG_CONFIG_PATH
which pip3
pip3 install wheel
- pip3 install pygobject
+ pip3 install pygobject==3.46.0
) > $HOSTLOGDIR/34-pip-wheel-pygobject.txt 2>&1
echo BUILDING: "done" install pygobject with pip3 >&2
fi
@@ -5163,7 +5166,7 @@
# 20220707-PE does this improve thie linking (get pass t...
# We get checking dynamic linker characteristics... awk:...
# on fedora if LD_LIBRARY_PATH is set
-if [ "$dist_name" = fedora ] ; then
+if [ "$dist_name" = fedora ] || [ "$dist_name" = rocky ]...
:
else
if [ "$dist_name" = arch ] ; then
@@ -5184,8 +5187,9 @@
echo bash ../coot/configure $coot_prefix \
--with-fftw-prefix=$install_top_dir \
- COOT_BUILD_INFO_STRING="$coot_build_info_string" \
SHELL=/bin/bash \
+ GEMMI_CXXFLAGS="-I/apps/coot/include" \
+ GEMMI_LIBS="-L/apps/coot/lib64 -lgemmi_cpp" \
PYTHON=python3 \
--with-boost=$install_top_dir \
--with-boost-libdir=$install_top_dir/lib \
@@ -5200,8 +5204,9 @@
bash ../coot/configure $coot_prefix \
--with-fftw-prefix=$install_top_dir \
SHELL=/bin/bash \
+ GEMMI_CXXFLAGS="-I/apps/coot/include" \
+ GEMMI_LIBS="-L/apps/coot/lib64 -lgemmi_cpp" \
PYTHON=python3 \
- COOT_BUILD_INFO_STRING="$coot_build_info_string" \
--with-boost=$install_top_dir \
--with-boost-libdir=$install_top_dir/lib \
--with-rdkit-prefix=$install_top_dir \
@@ -5391,8 +5396,8 @@
tar xzf $holding_tar_file
echo cding into `basename $slim_dir` f...
cd `basename $slim_dir`
- echo ln -s ../../$coot_dir_name/greg-te...
- ln -s ../../$coot_dir_name/greg-tests .
+ echo mkdir greg-tests
+ mkdir greg-tests
echo second coot test...
echo running second test... >&2
test_coot bin/coot > $LOGS/test-2.log 2...
}}
これでコンパイルします.
#code(nonumber){{
[root@rockylinux9 script]# AUTOBUILD_INSTALLED=/apps/coot...
:
(ケーキと紅茶)
:
[root@rockylinux9 script]#
}}
コンパイルが完了すると/appsに「coot」と「coot-Linux-x86_6...
#code(nonumber){{
[root@rockylinux9 ~]# ls -l /apps/
:
drwxr-xr-x 12 root root 4096 Jun 25 00:02 coot
drwxr-xr-x 7 root root 68 Jun 25 00:03 coot-Linux-x86_...
:
[root@rockylinux9 ~]#
}}
「/apps/coot」はbuild時に用意されてモノで、必要なファイル...
必要なファイルが適切に移っていない模様. あと移動させたと...
取り敢えずは「/apps/cooot」を使ってみる
っでEnvironment-modulesは「/apps/modulefiles/coot」を下記...
#code(nonumber){{
#%Module1.0
set root /apps/coot
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib:$root/lib64
}}
これをloadして「coot」と実行すると
&ref(2026y06m24d_231825570.png,nolink,70%);
そして本体の画面が表示され、そのヘルプは下記になります
cootのソースコードをgitで取ってきて最新版なので「1.1.x-pr...
&ref(2026y06m24d_231906890.png,nolink,80%);
リモートでX11越しに使うのは微妙でしょうか。コンソールで使...
***ubuntu24.04で [#qd9e6318]
#code(nonumber){{
root@ubuntu24:~# apt install build-essential git cmake m4...
liblapack-dev libncurses5-dev libjpeg-dev libgtk-4-dev...
root@ubuntu24:~#
root@ubuntu24:~# mkdir script
root@ubuntu24:~# cd script/
root@ubuntu24:~/script#
root@ubuntu24:~/script# wget https://raw.githubuserconten...
root@ubuntu24:~/script# grep ^script_version build-it-3-3
script_version=6.25
root@ubuntu24:~/script#
}}
ubuntu側はスクリプトの修正なしで大丈夫のようです
っで構築
#code(nonumber){{
root@ubuntu24:~/script# AUTOBUILD_INSTALLED=/apps/coot ba...
root@ubuntu24:~/script# cd /apps/
root@ubuntu24:/apps# ls -l
drwxr-xr-x 8 root root 4096 Feb 16 18:54 coot
drwxr-xr-x 7 root root 4096 Feb 16 18:55 coot-Linux-x86_6...
root@ubuntu24:/apps#
}}
インストール先を「/apps/coot」として作成しますが、その後...
なので「/apps/coot」を削除してもいいかなと思うのだが、ど...
いずれ修正されるかもしれないけどね。
なのでenvironment-modulesは、
「/apps/modulefiles/coot」
#code(nonumber){{
#%Module1.0
#set root /apps/coot-Linux-x86_64-ubuntu-24.04.4...
set root /apps/coot
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
}}
とします。
終了行:
v0.9.xと同様に 本家様で構築用のスクリプトが用意されています
そのスクリプトを実行すると [[https://github.com/pemsley/c...
でもスクリプトは rockylinux 向けではなくちょっとした修正...
***rockylinux9で coot-1.x をソースから作成してみる [#ja83...
っで実際に作ってみる
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.8 (Blue Onyx)
[root@rockylinux9 ~]# dnf groupinstall "Development Tools"
[root@rockylinux9 ~]# dnf install epel-release
[root@rockylinux9 ~]# dnf config-manager --enable crb
[root@rockylinux9 ~]# dnf install cmake texinfo gtk4-deve...
openssl-devel sqlite-devel gdbm-devel lib...
[root@rockylinux9 ~]# mkdir script ; cd script
[root@rockylinux9 script]#
[root@rockylinux9 script]# wget https://raw.githubusercon...
[root@rockylinux9 script]# grep ^script_version build-it-...
script_version=6.26
[root@rockylinux9 script]#
[root@rockylinux9 script]# vi ./build-it-3-3
}}
「build-it-3-3」の中で修正を行います.
変更項目
pygobjectが3.52.3ではgirepository-2.0を要求するがrockyl...
pygobjectを3.46.0にしたので対応するpythonは3.14ではだめ...
greg-testsを有効へ
COOT_BUILD_INFO_STRINGは文言にスペースが入って上手く処...
post_install_slimは十分に機能しないので削除
#code(diff,nonumber){{
--- build-it-3-3.orig 2026-06-24 06:08:18.706906055 +0900
+++ build-it-3-3 2026-06-24 18:50:28.650552404 +0900
@@ -1053,7 +1053,7 @@
if test -e /etc/os-release ; then
# 20240914 strip quote marks also now
dist_name=$(grep ^ID= /etc/os-release | sed...
- dist_ver=$(grep ^VERSION_ID /etc/os-release...
+ dist_ver=$(grep ^VERSION_ID /etc/os-release...
else
for i in fedora-release redhat-release redh...
rpm -q --qf '%{name}' ${i}
@@ -2141,12 +2141,12 @@
#
# python_version is the filename of the python executable.
#
-python_version=python3.14
-pver=3.14.2
-python_version_extension=3.14 # extract this
+python_version=python3.11
+pver=3.11.11
+python_version_extension=3.11 # extract this
# I think that for python to be compatible with Blender,...
# python_abiflags=d # because we use --with-pydebug on t...
-python_version_squish=314
+python_version_squish=311
# for Blender 4 in 2024, we want Python 3.10.13, so unco...
# for Blender 4.1 in June 2025, we want Python 3.11.x
@@ -2737,6 +2737,7 @@
patch -p0 < ${AUTOBUILD_SOURCES}/readline-5.1.patch
fi
do_the_sed=no
+ if [ "$dist_name" = rocky ] ; then do_the_sed=ye...
if [ "$dist_name" = arch ] ; then do_the_sed=ye...
if [ "$dist_name" = almalinux ] ; then do_the_sed=ye...
if [ "$dist_name" = ubuntu ] ; then do_the_sed=ye...
@@ -2873,7 +2874,7 @@
fi
else
# what about rocky here also?
- if test "$dist_name" = fedora ; then
+ if [ "$dist_name" = fedora ] || [ "$dist_name" = rock...
if [ -e $install_top_dir/include/openssl ] ; then
build_openssl=false
else
@@ -2977,7 +2978,7 @@
# remove --with-pydebug for now because __PyNegativeR...
#
# do we also need to use --with-threads=dir?
- if test "$dist_name" = fedora ; then
+ if [ "$dist_name" = fedora ] || [ "$dist_name" = rock...
python_install_top_dir=$HOME/building-python
python_install_top_dir=$HOME/building-python-tt
python_install_top_dir=$install_top_dir
@@ -4184,7 +4185,7 @@
if test "$dist_name" = almalinux ; then
echo don.t mess with LDFLAGS on almali...
else
- if test "$dist_name" = arch ; then
+ if [ "$dist_name" = arch ] || [ "$dist_...
echo don.t mess with LDFLAGS here o...
else
export LDFLAGS="-L$install_top_dir...
@@ -4504,10 +4505,12 @@
pygobject_major_minor_version=3.36
pygobject_major_minor_version=3.42
pygobject_major_minor_version=3.52 # 20250621-PE
+pygobject_major_minor_version=3.46
pygobject_version=3.29.1
pygobject_version=3.30.5
pygobject_version=3.42.1
pygobject_version=3.52.3
+pygobject_version=3.46.0
# pygobject_version=3.42.2 add me to the extras place!
# https://download.gnome.org/sources/pygobject/3.42/pygo...
# https://download.gnome.org/sources/pygobject/3.52/pygo...
@@ -4596,7 +4599,7 @@
echo PKG_CONFIG_PATH $PKG_CONFIG_PATH
which pip3
pip3 install wheel
- pip3 install pygobject
+ pip3 install pygobject==3.46.0
) > $HOSTLOGDIR/34-pip-wheel-pygobject.txt 2>&1
echo BUILDING: "done" install pygobject with pip3 >&2
fi
@@ -5163,7 +5166,7 @@
# 20220707-PE does this improve thie linking (get pass t...
# We get checking dynamic linker characteristics... awk:...
# on fedora if LD_LIBRARY_PATH is set
-if [ "$dist_name" = fedora ] ; then
+if [ "$dist_name" = fedora ] || [ "$dist_name" = rocky ]...
:
else
if [ "$dist_name" = arch ] ; then
@@ -5184,8 +5187,9 @@
echo bash ../coot/configure $coot_prefix \
--with-fftw-prefix=$install_top_dir \
- COOT_BUILD_INFO_STRING="$coot_build_info_string" \
SHELL=/bin/bash \
+ GEMMI_CXXFLAGS="-I/apps/coot/include" \
+ GEMMI_LIBS="-L/apps/coot/lib64 -lgemmi_cpp" \
PYTHON=python3 \
--with-boost=$install_top_dir \
--with-boost-libdir=$install_top_dir/lib \
@@ -5200,8 +5204,9 @@
bash ../coot/configure $coot_prefix \
--with-fftw-prefix=$install_top_dir \
SHELL=/bin/bash \
+ GEMMI_CXXFLAGS="-I/apps/coot/include" \
+ GEMMI_LIBS="-L/apps/coot/lib64 -lgemmi_cpp" \
PYTHON=python3 \
- COOT_BUILD_INFO_STRING="$coot_build_info_string" \
--with-boost=$install_top_dir \
--with-boost-libdir=$install_top_dir/lib \
--with-rdkit-prefix=$install_top_dir \
@@ -5391,8 +5396,8 @@
tar xzf $holding_tar_file
echo cding into `basename $slim_dir` f...
cd `basename $slim_dir`
- echo ln -s ../../$coot_dir_name/greg-te...
- ln -s ../../$coot_dir_name/greg-tests .
+ echo mkdir greg-tests
+ mkdir greg-tests
echo second coot test...
echo running second test... >&2
test_coot bin/coot > $LOGS/test-2.log 2...
}}
これでコンパイルします.
#code(nonumber){{
[root@rockylinux9 script]# AUTOBUILD_INSTALLED=/apps/coot...
:
(ケーキと紅茶)
:
[root@rockylinux9 script]#
}}
コンパイルが完了すると/appsに「coot」と「coot-Linux-x86_6...
#code(nonumber){{
[root@rockylinux9 ~]# ls -l /apps/
:
drwxr-xr-x 12 root root 4096 Jun 25 00:02 coot
drwxr-xr-x 7 root root 68 Jun 25 00:03 coot-Linux-x86_...
:
[root@rockylinux9 ~]#
}}
「/apps/coot」はbuild時に用意されてモノで、必要なファイル...
必要なファイルが適切に移っていない模様. あと移動させたと...
取り敢えずは「/apps/cooot」を使ってみる
っでEnvironment-modulesは「/apps/modulefiles/coot」を下記...
#code(nonumber){{
#%Module1.0
set root /apps/coot
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib:$root/lib64
}}
これをloadして「coot」と実行すると
&ref(2026y06m24d_231825570.png,nolink,70%);
そして本体の画面が表示され、そのヘルプは下記になります
cootのソースコードをgitで取ってきて最新版なので「1.1.x-pr...
&ref(2026y06m24d_231906890.png,nolink,80%);
リモートでX11越しに使うのは微妙でしょうか。コンソールで使...
***ubuntu24.04で [#qd9e6318]
#code(nonumber){{
root@ubuntu24:~# apt install build-essential git cmake m4...
liblapack-dev libncurses5-dev libjpeg-dev libgtk-4-dev...
root@ubuntu24:~#
root@ubuntu24:~# mkdir script
root@ubuntu24:~# cd script/
root@ubuntu24:~/script#
root@ubuntu24:~/script# wget https://raw.githubuserconten...
root@ubuntu24:~/script# grep ^script_version build-it-3-3
script_version=6.25
root@ubuntu24:~/script#
}}
ubuntu側はスクリプトの修正なしで大丈夫のようです
っで構築
#code(nonumber){{
root@ubuntu24:~/script# AUTOBUILD_INSTALLED=/apps/coot ba...
root@ubuntu24:~/script# cd /apps/
root@ubuntu24:/apps# ls -l
drwxr-xr-x 8 root root 4096 Feb 16 18:54 coot
drwxr-xr-x 7 root root 4096 Feb 16 18:55 coot-Linux-x86_6...
root@ubuntu24:/apps#
}}
インストール先を「/apps/coot」として作成しますが、その後...
なので「/apps/coot」を削除してもいいかなと思うのだが、ど...
いずれ修正されるかもしれないけどね。
なのでenvironment-modulesは、
「/apps/modulefiles/coot」
#code(nonumber){{
#%Module1.0
#set root /apps/coot-Linux-x86_64-ubuntu-24.04.4...
set root /apps/coot
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
}}
とします。
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