KAMO

[root@centos7 ~]# mkdir -p /apps
[root@centos7 ~]# cd /apps/
[root@centos7 apps]# tar xf /Public/em/ccp4-8.0.002-linux64.tar.gz 
[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]#

[root@centos7 ccp4-8.0]# source bin/ccp4.setup-sh

[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)
>

[root@centos7 ~]# wget https://cran.r-project.org/src/contrib/Archive/rjson/rjson_0.2.20.tar.gz
 
[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 checked
** 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 ~]#

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

[root@centos7 ~]# cd /apps/src/
[root@centos7 src]# wget https://wiki.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.qt4*
dectris-neggia.so*  H5ToXds*               spot2pdb*        XDS-viewer*          xxdiff.qt5*
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]#

[root@centos7 ~]# yum install hdf5
[root@centos7 ~]# mv /apps/xtal/H5ToXds /apps/xtal/H5ToXds.orig
[root@centos7 ~]# vi /apps/xtal/H5ToXds
#!/bin/sh
eiger2cbf $@ 2>/dev/null
 
[root@centos7 ~]# chmod +x /apps/xtal/H5ToXds

[root@centos7 ~]# vi /apps/modulefiles/xtal
#%Module1.0
 
prepend-path PATH /apps/xds:/apps/xds/xdsme/bin/noarch:/apps/xtal
 
[root@centos7 ~]#

[root@centos7 ~]# cd /apps/src/
[root@centos7 src]# wget https://github.com/dials/dials/releases/download/v3.14.2/dials-v3-14-2-linux-x86_64.tar.xz
[root@centos7 src]# tar xf dials-v3-14-2-linux-x86_64.tar.xz
[root@centos7 src]# cd dials-installer/
 
[root@centos7 dials-installer]# ./install --prefix=/apps

[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 ~]#

[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 networkx
 
 
[root@centos7 build]# cd $DIALS/modules
[root@centos7 modules]# pwd
/apps/dials-v3-14-2/modules
 
[root@centos7 modules]# git clone https://github.com/keitaroyam/yamtbx.git
[root@centos7 modules]# cd $DIALS/build
[root@centos7 build]# pwd
/apps/dials-v3-14-2/build
 
[root@centos7 build]# ./bin/libtbx.configure yamtbx

[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 all outputs:
Info:
   Python: 3.9.13
     Exec: /apps/dials-v3-10-2/build/../conda_base/bin/python
 Platform: Linux-3.10.0-1160.71.1.el7.x86_64-x86_64-with-glibc2.17
 
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 h5-recorded geometry can be no longer extracted using dxtbx. I hope it works. OK
Testing Adxv..
  OK
Testing H5ToXds..
Traceback (most recent call last):
  File "/apps/dials-v3-14-2/build/../modules/yamtbx/yamtbx/command_line/kamo_test_installation.py", line 367, in run
    ret = f()
  File "/apps/dials-v3-14-2/build/../modules/yamtbx/yamtbx/command_line/kamo_test_installation.py", line 84, in tst_h5toxds
    master_h5 = make_dummy_h5_for_test(tmpdir, data)
  File "/apps/dials-v3-14-2/modules/yamtbx/yamtbx/dataproc/eiger.py", line 293, in make_dummy_h5_for_test
    create_data_file(os.path.join(wdir, "test_data_000001.h5"), data, None, 1, 1, compression="bslz4")
  File "/apps/dials-v3-14-2/modules/yamtbx/yamtbx/dataproc/eiger.py", line 270, in create_data_file
    dataset = compress_h5data(h5, "/entry/data/data", data, chunks, compression)
  File "/apps/dials-v3-14-2/modules/yamtbx/yamtbx/dataproc/eiger.py", line 237, in compress_h5data
    import bitshuffle.h5
ModuleNotFoundError: No module named 'bitshuffle'
 
 
1 Failures (tst_h5toxds)
[root@centos7 ~]#

[root@centos7 ~]# libtbx.python -mpip install bitshuffle

[root@centos7 ~]# kamo.test_installation
 :
Testing Adxv..
  OK
Testing H5ToXds..
  OK
 
All OK!
[root@centos7 ~]#

module load DIALS ccp4 xtal
kamo bl=32xu batch.engine=sh