KAMO をテンプレートにして作成
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開始行:
&size(10){過去ページ [[KAMO20220728]]};
本家様 [[https://github.com/keitaroyam/yamtbx/blob/master...
***ccp4 [#ve78dca6]
#code(nonumber){{
[root@centos7 ~]# mkdir -p /apps
[root@centos7 ~]# cd /apps/
[root@centos7 apps]# tar xf /Public/em/ccp4-8.0.002-linux...
[root@centos7 apps]# cd ccp4-8.0/
[root@centos7 ccp4-8.0]# ./BINARY.setup
:
:
Before running CCP4 programs from command line,
source bin/ccp4.setup-sh
(or bin/ccp4.setup-csh if you use csh).
[root@centos7 ccp4-8.0]#
}}
これで完了ですが、環境変数を有効にしておきます
#code(nonumber){{
[root@centos7 ccp4-8.0]# source bin/ccp4.setup-sh
}}
***R [#x1a7f754]
#code(nonumber){{
[root@centos7 ~]# yum install epel-release
[root@centos7 ~]# yum install R-core R-core-devel
[root@centos7 ~]# R
:
:
> install.packages("rjson")
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
Warning message:
package ‘rjson’ is not available (for R version 3.6.0)
>
}}
と言われる。CRANで提供している rjsonパッケージは現在 vers...
[[https://cran.ism.ac.jp/web/packages/rjson/index.html>+h...
これは「R (≥ 4.0.0)」対応なので CentOS7のepelリポジ...
アーカイブを探してひとつ前の「rjson_0.2.20.tar.gz」なら R...
対応としてはこの「rjson_0.2.20.tar.gz」を入れるか、Rを最...
ここでは古い「rjson_0.2.20.tar.gz」を入れて回避してみる
#code(nonumber){{
[root@centos7 ~]# wget https://cran.r-project.org/src/con...
[root@centos7 ~]# R
:
> install.packages("./rjson_0.2.20.tar.gz",repos=NULL)
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘rjson’ ...
** package ‘rjson’ successfully unpacked and MD5 sums che...
** using staged installation
:
* DONE (rjson)
Making 'packages.html' ... done
>
> installed.packages() <-- 確認
:
rjson "yes" "3.6.0"
:
> q()
Save workspace image? [y/n/c]: n
[root@centos7 ~]#
}}
***xds [#bca8515e]
#code(nonumber){{
[root@centos7 ~]# mkdir -p /apps/src
[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]# cd /apps/xds
[root@centos7 xds]# ls -CF
2cbf* forkxds* mcolspot_par* mintegrate* pix...
cellparm* mcolspot* merge2cbf* mintegrate_par* 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]# python2 --version
Python 2.7.5
[root@centos7 xdsme]# ./compile.sh
:
[root@centos7 xdsme]# ls -CF bin/
Darwin_i386@ Linux_i586@ noarch/
[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]#
}}
他のアプリ
参照先 [[https://strucbio.biologie.uni-konstanz.de/xdswik...
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://wiki.uni-konstanz.de/pub...
[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]#
}}
&color(magenta){adxv};、&color(magenta){dectris-neggia.so...
追加パッケージと修正を施す
#code(nonumber){{
[root@centos7 ~]# yum install hdf5
[root@centos7 ~]# mv /apps/xtal/H5ToXds /apps/xtal/H5ToXd...
[root@centos7 ~]# vi /apps/xtal/H5ToXds
#!/bin/sh
eiger2cbf $@ 2>/dev/null
[root@centos7 ~]# chmod +x /apps/xtal/H5ToXds
}}
xdsや関連アプリ向けのEnvironmentModulesを用意する
#code(nonumber){{
[root@centos7 ~]# vi /apps/modulefiles/xtal
#%Module1.0
prepend-path PATH /apps/xds:/apps/xds/xdsme/bin/noarch:/a...
[root@centos7 ~]#
}}
***DIALSのインストール [#xf9b5321]
以前はpythonの関係でDIALS 2.2とかに制限されてましたが、現...
本家様 [[https://dials.github.io/>+https://dials.github.i...
#code(nonumber){{
[root@centos7 ~]# cd /apps/src/
[root@centos7 src]# wget https://github.com/dials/dials/r...
[root@centos7 src]# tar xf dials-v3-14-2-linux-x86_64.tar...
[root@centos7 src]# cd dials-installer/
[root@centos7 dials-installer]# ./install --prefix=/apps
}}
利用するには「/apps/dials-v3-14-2/dials_env.sh」を読み込...
ここでは EnvironmentModules でアプリ管理をするので調査し...
#code(nonumber){{
[root@centos7 ~]# vi /apps/modulefiles/DIALS
#%Module
set dials /apps/dials-v3-14-2
setenv DIALS $dials
setenv DIALS_VERSION v3-14-2
prepend-path PATH $dials/build/bin
[root@centos7 ~]#
}}
***KAMO [#e59b8350]
DIALSのEnvironmentModules を有効にして作業を進めます
#code(nonumber){{
[root@centos7 ~]# module use --append /apps/modulefiles
[root@centos7 ~]# module load DIALS
[root@centos7 ~]# cd $DIALS/build
[root@centos7 build]# pwd
/apps/dials-v3-14-2/build
[root@centos7 build]# ./bin/libtbx.python -mpip install n...
[root@centos7 build]# cd $DIALS/modules
[root@centos7 modules]# pwd
/apps/dials-v3-14-2/modules
[root@centos7 modules]# git clone https://github.com/keit...
[root@centos7 modules]# cd $DIALS/build
[root@centos7 build]# pwd
/apps/dials-v3-14-2/build
[root@centos7 build]# ./bin/libtbx.configure yamtbx
}}
っでできたかなのテスト
(別のshellを立ち上げて)
#code(nonumber){{
[root@centos7 ~]# module use --append /apps/modulefiles
[root@centos7 ~]# module load DIALS ccp4/8.0 xtal
[root@centos7 ~]# which kamo.test_installation
/apps/dials-v3-10-2/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: 3.9.13
Exec: /apps/dials-v3-10-2/build/../conda_base/bin/py...
Platform: Linux-3.10.0-1160.71.1.el7.x86_64-x86_64-with-...
Testing location..
/apps/dials-v3-10-2/modules/yamtbx/yamtbx. OK
Testing R..
OK
Testing NumPy..
1.22.4 installed. OK
Testing SciPy..
1.8.1 installed. OK
Testing networkx..
2.8.5 installed. OK
Testing Matplotlib..
3.5.2 installed. OK
Testing wxPython..
4.1.1 gtk2 (phoenix) wxWidgets 3.1.5 installed. OK
Testing XDS..
OK
Testing XDSSTAT..
OK
Testing ccp4..
OK
Testing dials (package)..
DIALS 3.10.2-g3ecfd29bc-release
Python 3.9.13
Installed in: /apps/dials-v3-14-2/modules/dials/src/dials
OK
Testing dials (module)..
DIALS 3.10.2-g3ecfd29bc-release installed. OK
Testing eiger hdf5 geometry recognition..
FormatHDFEigerNearlyNexus does not exist. This implies ...
Testing Adxv..
OK
Testing H5ToXds..
Traceback (most recent call last):
File "/apps/dials-v3-14-2/build/../modules/yamtbx/yamtb...
ret = f()
File "/apps/dials-v3-14-2/build/../modules/yamtbx/yamtb...
master_h5 = make_dummy_h5_for_test(tmpdir, data)
File "/apps/dials-v3-14-2/modules/yamtbx/yamtbx/datapro...
create_data_file(os.path.join(wdir, "test_data_000001...
File "/apps/dials-v3-14-2/modules/yamtbx/yamtbx/datapro...
dataset = compress_h5data(h5, "/entry/data/data", dat...
File "/apps/dials-v3-14-2/modules/yamtbx/yamtbx/datapro...
import bitshuffle.h5
ModuleNotFoundError: No module named 'bitshuffle'
1 Failures (tst_h5toxds)
[root@centos7 ~]#
}}
どうやら H5ToXds でエラーが発生した模様. 「ModuleNotFound...
#code(nonumber){{
[root@centos7 ~]# libtbx.python -mpip install bitshuffle
}}
っで再度テストを実行すると
#code(nonumber){{
[root@centos7 ~]# kamo.test_installation
:
Testing Adxv..
OK
Testing H5ToXds..
OK
All OK!
[root@centos7 ~]#
}}
となり完成
テスト起動
#code(nonumber){{
module load DIALS ccp4 xtal
kamo bl=32xu batch.engine=sh
}}
終了行:
&size(10){過去ページ [[KAMO20220728]]};
本家様 [[https://github.com/keitaroyam/yamtbx/blob/master...
***ccp4 [#ve78dca6]
#code(nonumber){{
[root@centos7 ~]# mkdir -p /apps
[root@centos7 ~]# cd /apps/
[root@centos7 apps]# tar xf /Public/em/ccp4-8.0.002-linux...
[root@centos7 apps]# cd ccp4-8.0/
[root@centos7 ccp4-8.0]# ./BINARY.setup
:
:
Before running CCP4 programs from command line,
source bin/ccp4.setup-sh
(or bin/ccp4.setup-csh if you use csh).
[root@centos7 ccp4-8.0]#
}}
これで完了ですが、環境変数を有効にしておきます
#code(nonumber){{
[root@centos7 ccp4-8.0]# source bin/ccp4.setup-sh
}}
***R [#x1a7f754]
#code(nonumber){{
[root@centos7 ~]# yum install epel-release
[root@centos7 ~]# yum install R-core R-core-devel
[root@centos7 ~]# R
:
:
> install.packages("rjson")
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
Warning message:
package ‘rjson’ is not available (for R version 3.6.0)
>
}}
と言われる。CRANで提供している rjsonパッケージは現在 vers...
[[https://cran.ism.ac.jp/web/packages/rjson/index.html>+h...
これは「R (≥ 4.0.0)」対応なので CentOS7のepelリポジ...
アーカイブを探してひとつ前の「rjson_0.2.20.tar.gz」なら R...
対応としてはこの「rjson_0.2.20.tar.gz」を入れるか、Rを最...
ここでは古い「rjson_0.2.20.tar.gz」を入れて回避してみる
#code(nonumber){{
[root@centos7 ~]# wget https://cran.r-project.org/src/con...
[root@centos7 ~]# R
:
> install.packages("./rjson_0.2.20.tar.gz",repos=NULL)
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘rjson’ ...
** package ‘rjson’ successfully unpacked and MD5 sums che...
** using staged installation
:
* DONE (rjson)
Making 'packages.html' ... done
>
> installed.packages() <-- 確認
:
rjson "yes" "3.6.0"
:
> q()
Save workspace image? [y/n/c]: n
[root@centos7 ~]#
}}
***xds [#bca8515e]
#code(nonumber){{
[root@centos7 ~]# mkdir -p /apps/src
[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]# cd /apps/xds
[root@centos7 xds]# ls -CF
2cbf* forkxds* mcolspot_par* mintegrate* pix...
cellparm* mcolspot* merge2cbf* mintegrate_par* 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]# python2 --version
Python 2.7.5
[root@centos7 xdsme]# ./compile.sh
:
[root@centos7 xdsme]# ls -CF bin/
Darwin_i386@ Linux_i586@ noarch/
[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]#
}}
他のアプリ
参照先 [[https://strucbio.biologie.uni-konstanz.de/xdswik...
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://wiki.uni-konstanz.de/pub...
[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]#
}}
&color(magenta){adxv};、&color(magenta){dectris-neggia.so...
追加パッケージと修正を施す
#code(nonumber){{
[root@centos7 ~]# yum install hdf5
[root@centos7 ~]# mv /apps/xtal/H5ToXds /apps/xtal/H5ToXd...
[root@centos7 ~]# vi /apps/xtal/H5ToXds
#!/bin/sh
eiger2cbf $@ 2>/dev/null
[root@centos7 ~]# chmod +x /apps/xtal/H5ToXds
}}
xdsや関連アプリ向けのEnvironmentModulesを用意する
#code(nonumber){{
[root@centos7 ~]# vi /apps/modulefiles/xtal
#%Module1.0
prepend-path PATH /apps/xds:/apps/xds/xdsme/bin/noarch:/a...
[root@centos7 ~]#
}}
***DIALSのインストール [#xf9b5321]
以前はpythonの関係でDIALS 2.2とかに制限されてましたが、現...
本家様 [[https://dials.github.io/>+https://dials.github.i...
#code(nonumber){{
[root@centos7 ~]# cd /apps/src/
[root@centos7 src]# wget https://github.com/dials/dials/r...
[root@centos7 src]# tar xf dials-v3-14-2-linux-x86_64.tar...
[root@centos7 src]# cd dials-installer/
[root@centos7 dials-installer]# ./install --prefix=/apps
}}
利用するには「/apps/dials-v3-14-2/dials_env.sh」を読み込...
ここでは EnvironmentModules でアプリ管理をするので調査し...
#code(nonumber){{
[root@centos7 ~]# vi /apps/modulefiles/DIALS
#%Module
set dials /apps/dials-v3-14-2
setenv DIALS $dials
setenv DIALS_VERSION v3-14-2
prepend-path PATH $dials/build/bin
[root@centos7 ~]#
}}
***KAMO [#e59b8350]
DIALSのEnvironmentModules を有効にして作業を進めます
#code(nonumber){{
[root@centos7 ~]# module use --append /apps/modulefiles
[root@centos7 ~]# module load DIALS
[root@centos7 ~]# cd $DIALS/build
[root@centos7 build]# pwd
/apps/dials-v3-14-2/build
[root@centos7 build]# ./bin/libtbx.python -mpip install n...
[root@centos7 build]# cd $DIALS/modules
[root@centos7 modules]# pwd
/apps/dials-v3-14-2/modules
[root@centos7 modules]# git clone https://github.com/keit...
[root@centos7 modules]# cd $DIALS/build
[root@centos7 build]# pwd
/apps/dials-v3-14-2/build
[root@centos7 build]# ./bin/libtbx.configure yamtbx
}}
っでできたかなのテスト
(別のshellを立ち上げて)
#code(nonumber){{
[root@centos7 ~]# module use --append /apps/modulefiles
[root@centos7 ~]# module load DIALS ccp4/8.0 xtal
[root@centos7 ~]# which kamo.test_installation
/apps/dials-v3-10-2/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: 3.9.13
Exec: /apps/dials-v3-10-2/build/../conda_base/bin/py...
Platform: Linux-3.10.0-1160.71.1.el7.x86_64-x86_64-with-...
Testing location..
/apps/dials-v3-10-2/modules/yamtbx/yamtbx. OK
Testing R..
OK
Testing NumPy..
1.22.4 installed. OK
Testing SciPy..
1.8.1 installed. OK
Testing networkx..
2.8.5 installed. OK
Testing Matplotlib..
3.5.2 installed. OK
Testing wxPython..
4.1.1 gtk2 (phoenix) wxWidgets 3.1.5 installed. OK
Testing XDS..
OK
Testing XDSSTAT..
OK
Testing ccp4..
OK
Testing dials (package)..
DIALS 3.10.2-g3ecfd29bc-release
Python 3.9.13
Installed in: /apps/dials-v3-14-2/modules/dials/src/dials
OK
Testing dials (module)..
DIALS 3.10.2-g3ecfd29bc-release installed. OK
Testing eiger hdf5 geometry recognition..
FormatHDFEigerNearlyNexus does not exist. This implies ...
Testing Adxv..
OK
Testing H5ToXds..
Traceback (most recent call last):
File "/apps/dials-v3-14-2/build/../modules/yamtbx/yamtb...
ret = f()
File "/apps/dials-v3-14-2/build/../modules/yamtbx/yamtb...
master_h5 = make_dummy_h5_for_test(tmpdir, data)
File "/apps/dials-v3-14-2/modules/yamtbx/yamtbx/datapro...
create_data_file(os.path.join(wdir, "test_data_000001...
File "/apps/dials-v3-14-2/modules/yamtbx/yamtbx/datapro...
dataset = compress_h5data(h5, "/entry/data/data", dat...
File "/apps/dials-v3-14-2/modules/yamtbx/yamtbx/datapro...
import bitshuffle.h5
ModuleNotFoundError: No module named 'bitshuffle'
1 Failures (tst_h5toxds)
[root@centos7 ~]#
}}
どうやら H5ToXds でエラーが発生した模様. 「ModuleNotFound...
#code(nonumber){{
[root@centos7 ~]# libtbx.python -mpip install bitshuffle
}}
っで再度テストを実行すると
#code(nonumber){{
[root@centos7 ~]# kamo.test_installation
:
Testing Adxv..
OK
Testing H5ToXds..
OK
All OK!
[root@centos7 ~]#
}}
となり完成
テスト起動
#code(nonumber){{
module load DIALS ccp4 xtal
kamo bl=32xu batch.engine=sh
}}
ページ名:
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