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Add CNS installation instructions #469
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General instructions for installing/recompiling CNS for HADDOCK added to INSTALL.md.
I would suggest to create a separate document just for CNS and refer to it in the INSTALLATION.md file |
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This is a rather simple description. We need to extend to put some compiler requirements if needed and also make a separate document just for CNS.
docs/INSTALL.md
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#### Add HADDOCK routines | ||
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HADDOCK requires some adjustments in CNS to function properly. Download the [set of routines to add](https://www.dropbox.com/s/wliubqovuusqdvr/cns.tgz?dl=0). Uncompress the archive and move all of its files into the CNS source directory (`PATH/TO/cns_solve_1.3/source/`). |
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Where is the code coming from? Is this something we are providing? If not, may-be we better create our own archive and provide it under SURF drive for example (I can handle that)
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This is a link that was provided to a user under #329 , but can of course be replaced with anything more appropriate.
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Is this the same as haddock2.4/cns1.3? Since these might be crucial for the proper work of cns and haddock3, would it not be better if we package it together with the repo?
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I would be happy to also add these to the repository and update the instructions accordingly, would just need to know where.
Added a link to the CNS instructions at the beginning of INSTALL.md, but if/when we add these files to the haddock3 repository it should probably be moved down to a step after cloning.
docs/INSTALL.md
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HADDOCK requires some adjustments in CNS to function properly. Download the [set of routines to add](https://www.dropbox.com/s/wliubqovuusqdvr/cns.tgz?dl=0). Uncompress the archive and move all of its files into the CNS source directory (`PATH/TO/cns_solve_1.3/source/`). | ||
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#### Recompile CNS |
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What about the compiler requirements? And any OS-specific instructions?
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Will add more details once I've moved the CNS instructions to a separate file!
Codecov Report
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## main #469 +/- ##
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Coverage 72.41% 72.41%
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Files 95 95
Lines 6124 6124
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Hits 4435 4435
Misses 1689 1689
Continue to review full report at Codecov.
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Should be indeed.
A good idea to package it together I would say.
… Is this the same as https://github.com/haddocking/haddock/tree/haddock2.4/cns1.3? Since these might be crucial for the proper work of cns and haddock3, would it not be better if we package it together with the repo
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Moving CNS installation instructions from INSTALL.md to its own file (CNS.md).
…nto documentation
Expanded information on the compilation of CNS. More details to be added particularly about the Makefile and different compilers/systems.
Updated to link directly to the "Installation" page of the CNS website, rather than to the main menu.
Some information on Makefile headers with specific details for gfortran.
Replacing the link path for mac to show an example of a self-compiled executable instead of the precompiled UU-specific one. For both mac and linux, specify the name of the CNS_FOLDER (cns_solve_1.3).
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Great work @cvnoort! Left some some comments on the pertinent lines 👍
docs/CNS.md
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source .cns_solve_env_sh | ||
``` | ||
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To avoid having to repeat this step each time you open a terminal window to run CNS/HADDOCK, you may want to add the relevant `source` line to your `~/.cshrc`, `~/.tcshrc`, `~/.bashrc`, or `~/.bash_profile`. When doing this, make sure to use the full path instead of only the file name. |
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I think this is not needed to run HADDOCK. At least, I don't have it in my .bashrc
. It doesn't hurt, though
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# on linux | ||
ln -s /PATH/TO/CNS_FOLDER/intel-x86_64bit-linux/source/cns_solve-2002171359.exe bin/cns | ||
ln -s /PATH/TO/cns_solve_1.3/intel-x86_64bit-linux/source/cns_solve-2002171359.exe bin/cns |
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I suggest keeping the CNS_FOLDER
instead of cns_solve_1.3
because it better explains the command, as it is more general.
docs/CNS.md
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## 3 Compile CNS | ||
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#### Start compilation |
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This head should have 3 #
instead of 4.
### Start compilation
docs/CNS.md
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If this worked, you can continue to the [next step](#4-Source-CNS). | ||
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#### Install a compiler |
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I suggest moving this section and the next one to a Troubleshooting
section at the end of the file. Like that, we can continue adding examples and solutions to possible future problems without perturbing the reading flow.
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This sounds great to me, I was thinking something similar to prevent confusing users with too much information when everything runs smoothly for them.
Moving some compilation details to a separate Troubleshooting section at the bottom of the file.
Brief statement about importance of CNS and extra link to INSTALL.md to make sure repository (eventually with the additional CNS routines) is cloned before CNS installation.
Update of the CNS instructions to point to the custom CNS routines that are now provided in the haddock3 repository, instead of a Dropbox link.
Point users to the CNS installation instructions after cloning the haddock3 repository.
General instructions for installing/recompiling CNS for HADDOCK added to INSTALL.md.
You are about to submit a new Pull Request. Before continuing make sure you read the contributing guidelines and you comply with the following criteria:
tox
tests pass. Runtox
command inside the repository folder-test.cfg
examples execute without errors. Insideexamples/
runpython run_tests.py -b
Added section to INSTALL.md that lists the basic steps for installing CNS.
For now, it links to the CNS routines to add on Dropbox. I would be happy to also add these to the repository and update the instructions accordingly, would just need to know where.