Dear haddock assistance team
I am trying to install haddock 2.5 following INSTALLATION.md. I start with install conda environment named haddock_env by command below
conda env create --file requirements.yml
Haddock2.5 environment is installed and activated then I edited a config. local file to define the location of CNS executable
After that I run the command below as mention in INSTALLATION.md file
~/software/haddock2.5-2023-01$ python install.py config.local
I got the following
[2024/09/02 11:57:33] Reading configuration file
[2024/09/02 11:57:33] file not found: config.local
Traceback (most recent call last):
File “/home/sura/software/haddock2.5-2023-01/install.py”, line 510, in
settings = read_config(args.config_file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/sura/software/haddock2.5-2023-01/install.py”, line 238, in read_config
fpath = fpath.resolve(strict=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/sura/miniconda3/envs/haddock2.5/lib/python3.12/pathlib.py”, line 1240, in resolve
s = self._flavour.realpath(self, strict=strict)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “”, line 427, in realpath
File “”, line 462, in _joinrealpath
FileNotFoundError: [Errno 2] No such file or directory: ‘config.local’
I am using
Ubuntu 22.04.3 LTS,
bash shell, Python 3.12.1
My operating system is: intel-x86_64bit-linux
Please can you help me to understand and fix this issue?
Thank you very much for your reply. I run the command
python install.py ./config.local
But I got the same error
(haddock2.5) sura@DESKTOP-AUQVN3U: ~/software/haddock2.5-2023-01$ python install.py ./config.local
[2024/09/02 23:35:41] Reading configuration file
[2024/09/02 23:35:41] file not found: config.local
Traceback (most recent call last):
File “/home/sura/software/haddock2.5-2023-01/install.py”, line 510, in
settings = read_config(args.config_file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/sura/software/haddock2.5-2023-01/install.py”, line 238, in read_config
fpath = fpath.resolve(strict=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/sura/miniconda3/envs/haddock2.5/lib/python3.12/pathlib.py”, line 1240, in resolve
s = self._flavour.realpath(self, strict=strict)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “”, line 427, in realpath
File “”, line 462, in _joinrealpath
FileNotFoundError: [Errno 2] No such file or directory: ‘config.local’
The config.local file is found in the subdirectory (configs) of the haddock2.5-2023-01 directory where I run the command.
Thank you for your prompt response. I specify where is the config.local script found and I run the script via command below
python install.py ./configs/config.local
I got the following error
(haddock2.5) sura@DESKTOP-
AUQVN3U:~/software/haddock2.5-2023-01$ python install.py
./configs/config.local
[2024/09/04 16:50:53] Reading configuration file
[2024/09/04 16:50:53] success!
[2024/09/04 16:50:53] Editing run.cns
[2024/09/04 16:50:53] success!
[2024/09/04 16:50:53] Configuring queue submission scripts
[2024/09/04 16:50:53] success!
[2024/09/04 16:50:53] Compiling C/C++ tools
[2024/09/04 16:50:57] success!
[2024/09/04 16:50:57] Writing source files
[2024/09/04 16:50:57] third-party executable not found in
PATH: NACCESS
[2024/09/04 16:50:58] third-party executable not found in
PATH: PALES
[2024/09/04 16:50:58] third-party executable not found in
PATH: PROFIT
[2024/09/04 16:50:58] third-party executable not found in
PATH: TENSOR2
[2024/09/04 16:50:58] success!
In terms of config.local script, I edited the config.local to define the location of CNS executable as below
[HADDOCK]
CNS_EXE = ~/software/cns_solve_1.3/intel-x86_64bit-linux/source/cns_solve-2408261614.exe
QUEUE_CMD = /bin/bash
NUM_JOBS = 5
[THIRD_PARTY]
NACCESS = auto
PALES = auto
PROFIT = auto
TENSOR2 = auto
However, in the [THIRD_PARTY] part, I did not change “auto” into to
NACCESS = which NACCESS
PALES = which PALES
PROFIT = which PROFIT
TENSOR2 = which TENSOR2
As from my understanding and navigating through bioexcel that this changing will perform when I want to run example or task not before that. It is right ?
In terms of path of NACCESS, PALES, PROFIT, TENSOR2
I installed freesasa, ProFit using conda in miniconda3 directory which is not in the software directory where is the haddock2.5 installed.
freesasa is not really needed - only for some tutorials.
ProFit (for RMSD calculations) is required if you want to do some analysis.
And it should be accessible in the path of your HADDOCK installation. You can also specify the full path to the executable.
There is another profit software that does something completely different. Make sure you install the correct one.
When calling at at the command line level you should see something like:
~> profit
PPPPP FFFFFF ii tt
PP PP FF tt
PP PP rrrrr oooo FF ii ttttt
PPPPP rr rr oo oo FFFF ii tt
PP rr oo oo FF ii tt
PP rr oo oo FF ii tt
PP rr oooo FF ii ttt
Protein Least Squares Fitting
Version 3.1
Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2009
Copyright (c) Dr. Craig T. Porter, UCL 2008-2009
>
I tried to install most of auxiliary software as my plan is going through several haddock tutorials to learn and gain more knowledge. For profit software, I install the ProFit V3.3 linux binary distribution using bioinf.org.uk - Prof. Andrew C.R. Martin's group at UCL but not the ProFit V3.3 protein least squares fitting.