KAMO20220728 をテンプレートにして作成
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開始行:
本家様
[[https://github.com/keitaroyam/yamtbx/blob/master/doc/ka...
ドキュメントを拝読するとCCP4, R, xds, Xdxv の実行環境があ...
***ccp4 [#h375ed2b]
ccp4本家様 [[https://www.ccp4.ac.uk/>+https://www.ccp4.ac...
ここでは「ccp4-7.1.015-linux64.tar.gz」を取得しました
これを展開します
#code(nonumber){{
[root@centos7 ~]# cd /apps/
[root@centos7 apps]# tar xf ../src/ccp4-7.1.015-linux64.t...
[root@centos7 apps]# ./ccp4-7.1/BINARY.setup
}}
EnvironmentModulesは[[EnvironmentModules/sample]]参照
***R [#e43e854f]
epelリポジトリにあるR-3.6.0を使います
#code(nonumber){{
[root@centos7 ~]# yum install R-core R-core-devel
RHEL8系なら
dnf install --enablerepo=powertools R-core R-core-devel
}}
その後に「rjson packageも含め」ってあるのでRにR向けの追加...
#code(nonumber){{
[root@centos7 ~]# R
:
>
> install.packages("rjson")
:
> quit()
[root@centos7 ~]#
}}
途中、「--- Please select a CRAN mirror for use in this s...
パッケージがダウンロードされ、展開され、コンパイルされ、...
インストール済みのパッケージは「library()」で確認可能. パ...
***xds [#k9963967]
[[xray/XDS#a2d21caa]]参照
#code(nonumber){{
[root@centos7 ~]# cd /apps/src/
[root@centos7 src]# wget https://xds.mr.mpg.de/XDS-INTEL6...
[root@centos7 src]# tar xf XDS-INTEL64_Linux_x86_64.tar.g...
[root@centos7 src]# mv /apps/XDS-INTEL64_Linux_x86_64 /ap...
[root@centos7 src]# ls -CF /apps/xds/
2cbf* forkxds* mcolspot_par* mintegrate* pix...
cellparm* mcolspot* merge2cbf* mintegrate_par* xds...
[root@centos7 src]#
[root@centos7 src]# cd /apps/xds
[root@centos7 xds]# git clone https://github.com/legrandp...
[root@centos7 xds]# cd xdsme/
[root@centos7 xdsme]# which python2
/usr/bin/python2
[root@centos7 xdsme]# ./compile.sh
[root@centos7 xdsme]# ls -CF bin/noarch/
2pck.py@ dnz2xds.pyc runxds.py@ x...
2pck.pyc mos2dnz.py@ runxds.pyc x...
check_bgk.py@ mos2dnz.pyc xds2dnz.py@ x...
check_bgk.pyc mos2xds.py@ xds2dnz.pyc x...
daccor.py@ mos2xds.pyc xds2mos.py@ x...
daccor.pyc oxford2adsc.py@ xds2mos.pyc x...
diffxdsinp.py@ oxford2adsc.pyc xdsauto.py@ X...
diffxdsinp.pyc resumxds.py@ xdsauto.pyc X...
dnz2mos.py@ resumxds.pyc xdsconv.py@ x...
dnz2mos.pyc run_xds2aimless.sh* xdsconv.pyc X...
dnz2xds.py@ run_xds2staraniso.sh* xdsHKLinfos.py@ X...
[root@centos7 xdsme]# pwd
/apps/xds/xdsme
[root@centos7 xdsme]#
}}
他のアプリ
参照 [[https://strucbio.biologie.uni-konstanz.de/xdswiki/...
参照先の「get_folder.sh」の内容から xds_extra_linux.tar (...
#code(nonumber){{
[root@centos7 ~]# cd /apps/src/
[root@centos7 src]# wget https://strucbio.biologie.uni-ko...
[root@centos7 src]# mkdir /apps/xtal
[root@centos7 src]# tar xf xds_extra_linux.tar -C /apps/x...
[root@centos7 src]# ls -CF /apps/xtal/
adxv* get_folder.sh* README.durin ...
checkcentering* h5dump* README.xds-zcb...
dectris-neggia.so* H5ToXds* spot2pdb* ...
durin-plugin.so* hdf2mini-cbf* xdscc12* ...
eiger2cbf* nxds_getcc* xdsgui* ...
generate_XDS.INP* README.dectris-neggia xdsgui.qt4* ...
[root@centos7 src]# yum install hdf5
}}
&color(magenta){dectris-neggia.so}; とか &color(magenta){...
っが、KAMOのkamo.test_installationを通らないので修正
#code(nonumber){{
[root@centos7 ~]# cd /apps/xtal
[root@centos7 xtal]# mv H5ToXds H5ToXds.orig
[root@centos7 xtal]# vi H5ToXds
#!/bin/sh
eiger2cbf $@ 2>/dev/null
[root@centos7 xtal]# chmod +x H5ToXds
}}
EnvironmentModules
「/etc/modulefiles/xtal」
#code(nonumber){{
#%Module1.0
prepend-path PATH /apps/xds:/apps/xds/xdsme/bin/noarch:/a...
}}
***DIALS 2.2 [#l004162b]
[[https://github.com/dials/dials/releases/tag/v2.2.0>+htt...
「dials-v2-2-10-linux-x86_64.tar.xz」を取得します
#code(nonumber){{
[root@centos7 ~]# cd /apps/src/
[root@centos7 src]# wget https://github.com/dials/dials/r...
[root@centos7 src]# tar xf dials-v2-2-10-linux-x86_64.tar...
[root@centos7 src]# cd dials-installer/
[root@centos7 dials-installer]# ./install --help
:
:
[root@centos7 dials-installer]# ./install --prefix=/apps
}}
これでDIALSのインストールは完了
その後で調整を加える
#code(nonumber){{
[root@centos7 ~]# source /apps/dials-v2-2-10/dials_env.sh
[root@centos7 ~]# echo $DIALS
/apps/dials-v2-2-10
[root@centos7 ~]# cd $DIALS/build
[root@centos7 build]# ./bin/libtbx.python -mpip install d...
:
Successfully installed decorator-4.3.0
:
[root@centos7 build]# ./bin/libtbx.python -mpip install n...
:
Successfully installed networkx-2.2
:
[root@centos7 build]#
}}
EnvironmentModules
「/etc/modulefiles/DIALS/v2-2-10」
#code(nonumber){{
#%Module1.0
set dials /apps/dials-v2-2-10
setenv DIALS $dials
setenv DIALS_VERSION v2-2-10
prepend-path PATH $dials/build/bin
}}
「/etc/modulefiles/DIALS/.version」
#code(nonumber){{
#%Module1.0
set ModulesVersion v2-2-10
}}
***kamo [#a6606b5f]
っで最後にkamoをインストール
#code(nonumber){{
[root@centos7 ~]# module load DIALS
[root@centos7 ~]# cd $DIALS/modules
[root@centos7 modules]# git clone https://github.com/keit...
[root@centos7 modules]# cd $DIALS/build
[root@centos7 build]# ./bin/libtbx.configure yamtbx
(確認)
[root@centos7 ~]# module load DIALS ccp4 xtal
[root@centos7 ~]# which kamo.test_installation
/apps/dials-v2-2-10/build/bin/kamo.test_installation
[root@centos7 ~]# kamo.test_installation
Testing installation of KAMO.
If you have trouble, please report the issue including al...
Info:
Python: 2.7.18
Exec: /apps/dials-v2-2-10/build/../base/bin/python2.7
Platform: Linux-3.10.0-1160.36.2.el7.x86_64-x86_64-with-...
Testing location..
/apps/dials-v2-2-10/modules/yamtbx/yamtbx. OK
Testing R..
OK
Testing NumPy..
1.15.4 installed. OK
Testing SciPy..
1.2.1 installed. OK
Testing networkx..
2.2 installed. OK
Testing Matplotlib..
2.2.3 installed. OK
Testing wxPython..
3.0.2.0 gtk2 (classic) installed. OK
Testing XDS..
OK
Testing XDSSTAT..
OK
Testing ccp4..
OK
Testing dials (package)..
DIALS 2.2.10-g6dafd9427-release
Python 2.7.18
Installed in: /apps/dials-v2-2-10/modules/dials
OK
Testing dials (module)..
DIALS 2.2.10-g6dafd9427-release installed. OK
Testing eiger hdf5 geometry recognition..
FormatHDFEigerNearlyNexus does not exist. This implies ...
Testing Adxv..
OK
Testing H5ToXds..
OK
All OK!
[root@centos7 ~]#
}}
起動は
#code(nonumber){{
module load DIALS ccp4 xtal
kamo bl=32xu batch.engine=sh
}}
とかで
終了行:
本家様
[[https://github.com/keitaroyam/yamtbx/blob/master/doc/ka...
ドキュメントを拝読するとCCP4, R, xds, Xdxv の実行環境があ...
***ccp4 [#h375ed2b]
ccp4本家様 [[https://www.ccp4.ac.uk/>+https://www.ccp4.ac...
ここでは「ccp4-7.1.015-linux64.tar.gz」を取得しました
これを展開します
#code(nonumber){{
[root@centos7 ~]# cd /apps/
[root@centos7 apps]# tar xf ../src/ccp4-7.1.015-linux64.t...
[root@centos7 apps]# ./ccp4-7.1/BINARY.setup
}}
EnvironmentModulesは[[EnvironmentModules/sample]]参照
***R [#e43e854f]
epelリポジトリにあるR-3.6.0を使います
#code(nonumber){{
[root@centos7 ~]# yum install R-core R-core-devel
RHEL8系なら
dnf install --enablerepo=powertools R-core R-core-devel
}}
その後に「rjson packageも含め」ってあるのでRにR向けの追加...
#code(nonumber){{
[root@centos7 ~]# R
:
>
> install.packages("rjson")
:
> quit()
[root@centos7 ~]#
}}
途中、「--- Please select a CRAN mirror for use in this s...
パッケージがダウンロードされ、展開され、コンパイルされ、...
インストール済みのパッケージは「library()」で確認可能. パ...
***xds [#k9963967]
[[xray/XDS#a2d21caa]]参照
#code(nonumber){{
[root@centos7 ~]# cd /apps/src/
[root@centos7 src]# wget https://xds.mr.mpg.de/XDS-INTEL6...
[root@centos7 src]# tar xf XDS-INTEL64_Linux_x86_64.tar.g...
[root@centos7 src]# mv /apps/XDS-INTEL64_Linux_x86_64 /ap...
[root@centos7 src]# ls -CF /apps/xds/
2cbf* forkxds* mcolspot_par* mintegrate* pix...
cellparm* mcolspot* merge2cbf* mintegrate_par* xds...
[root@centos7 src]#
[root@centos7 src]# cd /apps/xds
[root@centos7 xds]# git clone https://github.com/legrandp...
[root@centos7 xds]# cd xdsme/
[root@centos7 xdsme]# which python2
/usr/bin/python2
[root@centos7 xdsme]# ./compile.sh
[root@centos7 xdsme]# ls -CF bin/noarch/
2pck.py@ dnz2xds.pyc runxds.py@ x...
2pck.pyc mos2dnz.py@ runxds.pyc x...
check_bgk.py@ mos2dnz.pyc xds2dnz.py@ x...
check_bgk.pyc mos2xds.py@ xds2dnz.pyc x...
daccor.py@ mos2xds.pyc xds2mos.py@ x...
daccor.pyc oxford2adsc.py@ xds2mos.pyc x...
diffxdsinp.py@ oxford2adsc.pyc xdsauto.py@ X...
diffxdsinp.pyc resumxds.py@ xdsauto.pyc X...
dnz2mos.py@ resumxds.pyc xdsconv.py@ x...
dnz2mos.pyc run_xds2aimless.sh* xdsconv.pyc X...
dnz2xds.py@ run_xds2staraniso.sh* xdsHKLinfos.py@ X...
[root@centos7 xdsme]# pwd
/apps/xds/xdsme
[root@centos7 xdsme]#
}}
他のアプリ
参照 [[https://strucbio.biologie.uni-konstanz.de/xdswiki/...
参照先の「get_folder.sh」の内容から xds_extra_linux.tar (...
#code(nonumber){{
[root@centos7 ~]# cd /apps/src/
[root@centos7 src]# wget https://strucbio.biologie.uni-ko...
[root@centos7 src]# mkdir /apps/xtal
[root@centos7 src]# tar xf xds_extra_linux.tar -C /apps/x...
[root@centos7 src]# ls -CF /apps/xtal/
adxv* get_folder.sh* README.durin ...
checkcentering* h5dump* README.xds-zcb...
dectris-neggia.so* H5ToXds* spot2pdb* ...
durin-plugin.so* hdf2mini-cbf* xdscc12* ...
eiger2cbf* nxds_getcc* xdsgui* ...
generate_XDS.INP* README.dectris-neggia xdsgui.qt4* ...
[root@centos7 src]# yum install hdf5
}}
&color(magenta){dectris-neggia.so}; とか &color(magenta){...
っが、KAMOのkamo.test_installationを通らないので修正
#code(nonumber){{
[root@centos7 ~]# cd /apps/xtal
[root@centos7 xtal]# mv H5ToXds H5ToXds.orig
[root@centos7 xtal]# vi H5ToXds
#!/bin/sh
eiger2cbf $@ 2>/dev/null
[root@centos7 xtal]# chmod +x H5ToXds
}}
EnvironmentModules
「/etc/modulefiles/xtal」
#code(nonumber){{
#%Module1.0
prepend-path PATH /apps/xds:/apps/xds/xdsme/bin/noarch:/a...
}}
***DIALS 2.2 [#l004162b]
[[https://github.com/dials/dials/releases/tag/v2.2.0>+htt...
「dials-v2-2-10-linux-x86_64.tar.xz」を取得します
#code(nonumber){{
[root@centos7 ~]# cd /apps/src/
[root@centos7 src]# wget https://github.com/dials/dials/r...
[root@centos7 src]# tar xf dials-v2-2-10-linux-x86_64.tar...
[root@centos7 src]# cd dials-installer/
[root@centos7 dials-installer]# ./install --help
:
:
[root@centos7 dials-installer]# ./install --prefix=/apps
}}
これでDIALSのインストールは完了
その後で調整を加える
#code(nonumber){{
[root@centos7 ~]# source /apps/dials-v2-2-10/dials_env.sh
[root@centos7 ~]# echo $DIALS
/apps/dials-v2-2-10
[root@centos7 ~]# cd $DIALS/build
[root@centos7 build]# ./bin/libtbx.python -mpip install d...
:
Successfully installed decorator-4.3.0
:
[root@centos7 build]# ./bin/libtbx.python -mpip install n...
:
Successfully installed networkx-2.2
:
[root@centos7 build]#
}}
EnvironmentModules
「/etc/modulefiles/DIALS/v2-2-10」
#code(nonumber){{
#%Module1.0
set dials /apps/dials-v2-2-10
setenv DIALS $dials
setenv DIALS_VERSION v2-2-10
prepend-path PATH $dials/build/bin
}}
「/etc/modulefiles/DIALS/.version」
#code(nonumber){{
#%Module1.0
set ModulesVersion v2-2-10
}}
***kamo [#a6606b5f]
っで最後にkamoをインストール
#code(nonumber){{
[root@centos7 ~]# module load DIALS
[root@centos7 ~]# cd $DIALS/modules
[root@centos7 modules]# git clone https://github.com/keit...
[root@centos7 modules]# cd $DIALS/build
[root@centos7 build]# ./bin/libtbx.configure yamtbx
(確認)
[root@centos7 ~]# module load DIALS ccp4 xtal
[root@centos7 ~]# which kamo.test_installation
/apps/dials-v2-2-10/build/bin/kamo.test_installation
[root@centos7 ~]# kamo.test_installation
Testing installation of KAMO.
If you have trouble, please report the issue including al...
Info:
Python: 2.7.18
Exec: /apps/dials-v2-2-10/build/../base/bin/python2.7
Platform: Linux-3.10.0-1160.36.2.el7.x86_64-x86_64-with-...
Testing location..
/apps/dials-v2-2-10/modules/yamtbx/yamtbx. OK
Testing R..
OK
Testing NumPy..
1.15.4 installed. OK
Testing SciPy..
1.2.1 installed. OK
Testing networkx..
2.2 installed. OK
Testing Matplotlib..
2.2.3 installed. OK
Testing wxPython..
3.0.2.0 gtk2 (classic) installed. OK
Testing XDS..
OK
Testing XDSSTAT..
OK
Testing ccp4..
OK
Testing dials (package)..
DIALS 2.2.10-g6dafd9427-release
Python 2.7.18
Installed in: /apps/dials-v2-2-10/modules/dials
OK
Testing dials (module)..
DIALS 2.2.10-g6dafd9427-release installed. OK
Testing eiger hdf5 geometry recognition..
FormatHDFEigerNearlyNexus does not exist. This implies ...
Testing Adxv..
OK
Testing H5ToXds..
OK
All OK!
[root@centos7 ~]#
}}
起動は
#code(nonumber){{
module load DIALS ccp4 xtal
kamo bl=32xu batch.engine=sh
}}
とかで
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