How to install the phenix suite in archlinux?

murpholinox · 2017-02-13 18:34:16

Dear all...
Phenix (http://www.phenix-online.org/) is a suite of programs to do x-ray crystallography stuff (https://en.wikipedia.org/wiki/X-ray_crystallography).
Normally (ubuntu, fedora) ..One would have to download the tar.gz (registration required, password required), untar the thing, cd into the new dir, become root and do `./install` which looks like a little script that looks for a python version (between 2-2.7) and then executes the installation script located in a subdirectory.
Here is the little script (http://pastebin.com/fVvhdkcD) and here is the installation script (http://pastebin.com/s24D2MHT). Maybe it would be better if you download the whole thing (unfortunately it takes a while because it weighs about ~ 1000Mb...this plus the registration process...is too much to ask and I am sorry for that). I am asking because is the only thing I need to make my thesis (plus maybe coot, pymol and latex)..and because I am lost. I read about the ABS in the wiki but I think this package autobuilds itself (so it won't help here, please correct me if I am wrong).
The error produced by the `./install` in archlinux is here (http://pastebin.com/mmmMiBrT).

I have contacted the developers and one told me to download the source (~780M) and install the development packages for zlib, openSSL, freeglut, mesa (maybe), X11 and Xft (I think I have all the libraries installed http://pastebin.com/ZqKCXnK9). The error produced is here (http://pastebin.com/W1KiFQik).

So...How to install the phenix suite in archlinux?
Any help is appreciated.

PS Although I know linux since 2009 (first ubuntu...then fedora..just recently arch (actually this is my second attempt at arch)) I do not consider myself an expert in linux (it took me a night to install arch and about 2 hours to get my usb printer ready )

jasonwryan · 2017-02-13 18:43:57

Moving to AUR Issues...

Laurenz · 2017-04-01 09:53:15

Hey murpholinox,

did you manage to install phenix yet? I'm having the exact same problem that you seem to have. Are you sure you installed devel versions of the libraries? May I ask how you did this? I tried but couldn't figure out how to install devel version from the source.

Trilby · 2017-04-01 10:50:41

Arch linux does not split packages: there are no "-devel" versions and you don't need to install them from source. Install the dependencies with pacman. But, frankly, it sounds like upstream is full of crap - that error is next to meaningless, but it certainly doesn't suggest that there is a missing depenency. It looks like there is an unspecified problem in their installer class. But as their code is all hush-hush we can't really help debug it.

Laurenz · 2017-04-01 12:49:56

Okay thanks anyways. Maybe I will also contact the developers. Murpholinox, I installed ccp4 now which seems to work. It has a lot of the programs integraded that would come with phenix..

Lone_Wolf · 2017-04-03 14:02:00

Laurenz,

those errors look very much like the ones you get when a python2 file is ran with python3 .
Ask the devs if they tested install on systems where /usr/bin/python is a symlink to python3 and pythonn2 is also installed.
If they don't understand, show them, show them ls -l /usr/bin/python* output.

Another potential problem cause is they seem to target kernel 2.6 , can their installer handle 3.x and 4.x kernel versions ?

murpholinox · 2017-04-08 01:58:40

Dear Lone_Wolf:
The python version problem is solved by the "little script".
The kernel version problem....I think it is not a problem because I can install phenix on fedora 25 (kernel 4.9.x)
Dear Laurenz:
So you are a crystallographer?
I know that ccp4 works, Thing is that I can work better with phenix (I do have a few bash scripts with phenix commands wich make my work easier...I tried the same with ccp4 but it was too cumbersome for me).
Dear Trilby:
Thanks for the info.
The exact words from the developer were:
"you will need the development files for,

zlib
openSSL
freeglut
mesa (maybe)
X11
Xft

Phenix builds its own versions of Python and some other dependencies, but the above are needed."

PS. I guess that I can upload the source to dropbox and make a link if someone wants to help. Just say the word.

Dear all: Thanks for reading.

Lone_Wolf · 2017-04-08 14:40:01

I checked the license[1] and non-commercial users do have some freedoms, but redistribution is not among them.

section 1 (i) wrote:

you may not distribute, rent,
lease, loan, or sublicense the Software to any third party

IANAL, but making the source you downloaded available for others in any way seems a violation of the license.

The "little script" appears to be meant to make sure the installer is run with python2 .
(why didn't i realise that before ? )

Try running the install like this :

/usr/bin/python2 ./bin/install.py

[1] http://www.phenix-online.org/license/LICENSE

murpholinox · 2017-04-08 17:51:36

@Lone_Wolf:
You are right. Sorry. A guess this is the end
Ps I try running `sudo /usr/bin/python2 ./bin/install.py`
The error is the same

Arch Linux

#1 2017-02-13 18:34:16

How to install the phenix suite in archlinux?

#2 2017-02-13 18:43:57

Re: How to install the phenix suite in archlinux?

#3 2017-04-01 09:53:15

Re: How to install the phenix suite in archlinux?

#4 2017-04-01 10:50:41

Re: How to install the phenix suite in archlinux?

#5 2017-04-01 12:49:56

Re: How to install the phenix suite in archlinux?

#6 2017-04-03 14:02:00

Re: How to install the phenix suite in archlinux?

#7 2017-04-08 01:58:40

Re: How to install the phenix suite in archlinux?

#8 2017-04-08 14:40:01

Re: How to install the phenix suite in archlinux?

#9 2017-04-08 17:51:36

Re: How to install the phenix suite in archlinux?

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