varioustoxins / nmrpack

A set of spack tools for installing NMR Software

nmrpack

nmrpack is a set of packages, libraries and helper programs that allow you to install nmr software.

see the website https://varioustoxins.github.io/nmrpack for details...

nmrpack's Issues

nmrpipe: talos and smile give bad checksums

talos and smile give bad checksums when installed with the nmrpipe/package.py

nmrpack needs an installation script

centos install nmrpipe identifies install.com as html

this appears to be a spack bug

spack install nmrpipe requires csh

under centos 8 csh is not installed

the user needs to sudo yum install tcsh

this needs to be added to documentation

modulecmd gives ERROR: Unknown shell type '()' on centos

nmrpack install fails with unknown variable capture_output

this is a bug in environment.py  get_environment_change which uses sub_process_run capture_output which isn't available in python3.6 which is the install python3 on centos8

required change is below

#pre = subprocess.run(['/usr/bin/env', '-i', '/bin/csh', '-c', f"{pre_command}"], capture_output=True)
#post = subprocess.run(['/usr/bin/env', '-i', '/bin/csh','-c', f"{post_command}"], capture_output=True)

# required for python 3.6 
pre = subprocess.run(['/usr/bin/env', '-i', '/bin/csh', '-c', f"{pre_command}"], stdout=PIPE, stderr=PIPE)
post = subprocess.run(['/usr/bin/env', '-i', '/bin/csh','-c', f"{post_command}"], stdout=PIPE, stderr=PIPE)

the nmrpack installation script needs to modify the users .bashrc

nmrpack needs to initialise functions when it starts up to allow easy access of paths and commands

spack load environment-modules fails

this fails to add module to the shell environment

this is a spack bug add has been added to the spack issue tracker

nmrpipe needs extra libraries on centos 8 for i686

centos 8 doesn't come with the correct libraries installed for Nmr pipe

sudo yum install xorg-x11-fonts-100dpi xorg-x11-fonts-ISO8859-1-100dpi
sudo yum install xorg-x11-fonts-misc
sudo yum install xorg-x11-fonts-75dpi xorg-x11-fonts-ISO8859-1-75dpi
sudo yum install -y libgcc.i686
sudo yum install -y glibc.i686
sudo yum install -y libX11.so.i6866
sudo yum install -y libXext.i686
sudo yum install -y libstdc++.i686
sudo yum install -y xorg-x11-fonts-75dpi
sudo yum install -y xorg-x11-fonts-ISO8859-1-75dpi

maybe these should all be run from one script under sudo

initial todo list

initial target list

program	state	ease	priority	notes
aria	partial	8	3	requires patches and python packages
xplor	partial	3	1	demonstrator of e-mail technology
cns	partial	3	2
nmrpipe	done macOS	3	0	would also like linux needs additional installs as does osx
ccpn2	none	3	4
ccpn3	none	5	5

os

only Mac OS

required technologies

1. email monitor system
2. python packaging and dependencies
3. method for providing data to Spack packages
4. web page templating
5. driver program