KAMO20220728 の変更点

• 追加された行はこの色です。
• 削除された行はこの色です。
• KAMO20220728 へ行く。
• KAMO20220728 の差分を削除

#author("2022-01-23T14:10:37+00:00","default:sysosa","sysosa")
#author("2022-01-23T15:37:14+00:00","default:sysosa","sysosa")
本家様
[[https://github.com/keitaroyam/yamtbx/blob/master/doc/kamo-ja.md>+https://github.com/keitaroyam/yamtbx/blob/master/doc/kamo-ja.md]]

ドキュメントを拝読するとCCP4, R, xds, Xdxv の実行環境があって、DIALS2.2のCCTBXに組み込む感じかな.

***ccp4 [#h375ed2b]
ccp4本家様 [[https://www.ccp4.ac.uk/>+https://www.ccp4.ac.uk/]] から入手します
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.tar.gz
[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向けの追加パッケージを入れます
#code(nonumber){{
[root@centos7 ~]# R
 :
>
> install.packages("rjson")
 :
>  quit()
[root@centos7 ~]#
}}
途中、「--- Please select a CRAN mirror for use in this session ---」と言われミラーサイトの選択が要求されるが、適当に。
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、インストールされる.

インストール済みのパッケージは「library()」で確認可能. パッケージの削除は「remove.packages('rjson')」


***xds [#k9963967]
[[xray/XDS#a2d21caa]]参照


#code(nonumber){{
[root@centos7 ~]# cd /apps/src/
[root@centos7 src]# wget https://xds.mr.mpg.de/XDS-INTEL64_Linux_x86_64.tar.gz
[root@centos7 src]# tar xf XDS-INTEL64_Linux_x86_64.tar.gz -C /apps
[root@centos7 src]# mv /apps/XDS-INTEL64_Linux_x86_64 /apps/xds

[root@centos7 src]# ls -CF /apps/xds/
2cbf*      forkxds*   mcolspot_par*  mintegrate*      pix2lab*  xdsconv*  xscale*
cellparm*  mcolspot*  merge2cbf*     mintegrate_par*  xds*      xds_par*  xscale_par*
[root@centos7 src]#

[root@centos7 src]# cd /apps/xds

[root@centos7 xds]# git clone https://github.com/legrandp/xdsme
[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@       xdsHKLinfos.pyc          xio_info@
2pck.pyc        mos2dnz.py@            runxds.pyc       xdslog.py@               XIO_info.py@
check_bgk.py@   mos2dnz.pyc            xds2dnz.py@      xdslog.pyc               XIO_info.pyc
check_bgk.pyc   mos2xds.py@            xds2dnz.pyc      xdsme@                   XOalign.py@
daccor.py@      mos2xds.pyc            xds2mos.py@      xds_phiRotationAxis.py@  XOalign.pyc
daccor.pyc      oxford2adsc.py@        xds2mos.pyc      xds_phiRotationAxis.pyc  XOcompare.py@
diffxdsinp.py@  oxford2adsc.pyc        xdsauto.py@      XDS.py@                  XOcompare.pyc
diffxdsinp.pyc  resumxds.py@           xdsauto.pyc      XDS.pyc                  xscale2.py@
dnz2mos.py@     resumxds.pyc           xdsconv.py@      xdsreport@               xscale2.pyc
dnz2mos.pyc     run_xds2aimless.sh*    xdsconv.pyc      XIO_collect_info.py@     xscale.py@
dnz2xds.py@     run_xds2staraniso.sh*  xdsHKLinfos.py@  XIO_collect_info.pyc     xscale.pyc
[root@centos7 xdsme]# pwd
/apps/xds/xdsme
[root@centos7 xdsme]#
}}





他のアプリ
参照 [[https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Installation>+https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Installation]]
参照先の「get_folder.sh」の内容から xds_extra_linux.tar (42MB) を取得します

#code(nonumber){{
[root@centos7 ~]# cd /apps/src/
[root@centos7 src]# wget https://strucbio.biologie.uni-konstanz.de/pub/linux_bin/xds_extra_linux.tar

[root@centos7 src]# mkdir /apps/xtal
[root@centos7 src]# tar xf xds_extra_linux.tar -C /apps/xtal/

[root@centos7 src]# ls -CF /apps/xtal/
adxv*               get_folder.sh*         README.durin     xds_nonisomorphism*  xscale_maxcc12*
checkcentering*     h5dump*                README.xds-zcbf  xdsstat*             xxdiff.centos7*
dectris-neggia.so*  H5ToXds*               spot2pdb*        XDS-viewer*
durin-plugin.so*    hdf2mini-cbf*          xdscc12*         XDS-viewer.qt4*
eiger2cbf*          nxds_getcc*            xdsgui*          xds-zcbf.so*
generate_XDS.INP*   README.dectris-neggia  xdsgui.qt4*      xscale_isocluster*

[root@centos7 src]# yum install hdf5
}}

&color(magenta){dectris-neggia.so}; とか &color(magenta){H5ToXds}; が入っていることに驚く
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:/apps/xtal
}}

***DIALS 2.2 [#l004162b]
[[https://github.com/dials/dials/releases/tag/v2.2.0>+https://github.com/dials/dials/releases/tag/v2.2.0]]にて
「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/releases/download/v2.2.0/dials-v2-2-10-linux-x86_64.tar.xz

[root@centos7 src]# tar xf dials-v2-2-10-linux-x86_64.tar.xz
[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 decorator==4.3.0
 :
Successfully installed decorator-4.3.0
 :
[root@centos7 build]# ./bin/libtbx.python -mpip install networkx==2.2
 :
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/keitaroyam/yamtbx.git

[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 all outputs:
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-centos-7.9.2009-Core

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 h5-recorded geometry can be no longer extracted using dxtbx. I hope it works. OK
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