# Issue in HADDOCK2.5 local installation / config.local **URL:** \ **Category:** HADDOCK\ **Created:** [September 2, 2024, 2:37pm UTC](https://ask.bioexcel.eu/t/issue-in-haddock2-5-local-installation-config-local/5241 "2024-09-02T14:37:27Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![Sura](https://avatars.discourse-cdn.com/v4/letter/s/4da419/32.png) [@Sura](https://ask.bioexcel.eu/u/Sura)\ **Post date:** [September 2, 2024, 2:37pm UTC](https://ask.bioexcel.eu/t/issue-in-haddock2-5-local-installation-config-local/5241/1 "2024-09-02T14:37:27Z")
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 ``` CNS_EXE = ~/software/cns_solve_1.3/intel-x86_64bit- linux/source/cns_solve-2408261614.exe QUEUE_CMD = /bin/bash ``` 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 ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [September 2, 2024, 2:54pm UTC](https://ask.bioexcel.eu/t/issue-in-haddock2-5-local-installation-config-local/5241/2 "2024-09-02T14:54:28Z")
Try adding ./ before the config.local file, e.g.: python install.py ./config.local Is it in the directory where you give that command? ---
**Author:** ![Sura](https://avatars.discourse-cdn.com/v4/letter/s/4da419/32.png) [@Sura](https://ask.bioexcel.eu/u/Sura)\ **Post date:** [September 2, 2024, 9:28pm UTC](https://ask.bioexcel.eu/t/issue-in-haddock2-5-local-installation-config-local/5241/3 "2024-09-02T21:28:24Z")
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. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [September 3, 2024, 6:51am UTC](https://ask.bioexcel.eu/t/issue-in-haddock2-5-local-installation-config-local/5241/4 "2024-09-03T06:51:19Z")
Then you need to specify the subdirectory! ---
**Author:** ![Sura](https://avatars.discourse-cdn.com/v4/letter/s/4da419/32.png) [@Sura](https://ask.bioexcel.eu/u/Sura)\ **Post date:** [September 3, 2024, 3:23pm UTC](https://ask.bioexcel.eu/t/issue-in-haddock2-5-local-installation-config-local/5241/5 "2024-09-03T15:23:42Z")
Dear Prof. Alexandre Bonvin 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 [2024/09/03 18:06:06] Reading configuration file [2024/09/03 18:06:06] success! [2024/09/03 18:06:06] Editing run.cns [2024/09/03 18:06:06] success! [2024/09/03 18:06:06] Configuring queue submission scripts [2024/09/03 18:06:06] success! [2024/09/03 18:06:06] Compiling C/C++ tools [2024/09/03 18:06:06] error compiling source files: make[2]: g++: No such file or directory make[2]: *** [Makefile:16: cluster_struc] Error 127 make[1]: *** [Makefile:13: all] Error 2 make: *** [Makefile:8: all] Error 2 Traceback (most recent call last): File "/home/sura/software/haddock2.5-2023-01/install.py", line 513, in setup(settings) File "/home/sura/software/haddock2.5-2023-01/install.py", line 482, in setup compile_tools() File "/home/sura/software/haddock2.5-2023-01/install.py", line 367, in compile_tools raise Exception Exception ``` Best regards ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [September 3, 2024, 5:45pm UTC](https://ask.bioexcel.eu/t/issue-in-haddock2-5-local-installation-config-local/5241/6 "2024-09-03T17:45:58Z")
Your need the g++ compiler installed on your system. ---
**Author:** ![Sura](https://avatars.discourse-cdn.com/v4/letter/s/4da419/32.png) [@Sura](https://ask.bioexcel.eu/u/Sura)\ **Post date:** [September 4, 2024, 3:44pm UTC](https://ask.bioexcel.eu/t/issue-in-haddock2-5-local-installation-config-local/5241/7 "2024-09-04T15:44:50Z")
Dear prof. Alexandre Bonvin Thanks a lot, after I install g++ I got ``` (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. Thank you very much for your help and time ? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [September 5, 2024, 7:04am UTC](https://ask.bioexcel.eu/t/issue-in-haddock2-5-local-installation-config-local/5241/8 "2024-09-05T07:04:53Z")
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: ```auto ~> 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 > ``` ---
**Author:** ![Sura](https://avatars.discourse-cdn.com/v4/letter/s/4da419/32.png) [@Sura](https://ask.bioexcel.eu/u/Sura)\ **Post date:** [September 5, 2024, 1:17pm UTC](https://ask.bioexcel.eu/t/issue-in-haddock2-5-local-installation-config-local/5241/9 "2024-09-05T13:17:02Z")
Dear prof. Alexandre Bonvin 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](http://www.bioinf.org.uk/software/profit/) but not the ProFit V3.3 protein least squares fitting. Thank you