CB DOCK 3.8 tutorial - Revision history

Cbedart: /* Pydock3 dockopt */

2022-12-15T18:37:40Z

Pydock3 dockopt

← Older revision		Revision as of 18:37, 15 December 2022
Line 41:		Line 41:

	3) Initialization of dockopt :		3) Initialization of dockopt :
	<nowiki>pydock3 dockopt - init ~~--job_dir_name=~~JobName</nowiki>		<nowiki>pydock3 dockopt - init JobName</nowiki>

	~~4) Run dockopt :~~

			4) Define environment variables and run dockopt :
			<nowiki>cd JobName/
			export SBATCH_EXEC=/usr/bin/sbatch
			export SQUEUE_EXEC=/usr/bin/squeue
			export TMPDIR=/scratch
			pydock3 dockopt - run slurm</nowiki>

	== DOCK 3.8 docking ==		== DOCK 3.8 docking ==

Cbedart at 16:42, 15 December 2022

2022-12-15T16:42:46Z

@@ Line 25: / Line 25: @@
 * Protein preparation
 * WIP
 ==  DOCK 3.8 docking ==

Cbedart: /* top_poses.py */

2022-12-15T16:19:15Z

top_poses.py

← Older revision		Revision as of 16:19, 15 December 2022
Line 56:		Line 56:
	1) Load a specific python environment :		1) Load a specific python environment :
	* (why is it different from the version used to run pydock3 ?)		* (why is it different from the version used to run pydock3 ?)
	<nowiki>source /nfs/soft/python/versions~~/python-3.8-install~~/python-3.8-install/bin/env.sh</nowiki>		<nowiki>source /nfs/soft/python/versions/python-3.8-install/bin/env.sh</nowiki>

	2) Main commands :		2) Main commands :
	* https://wiki.docking.org/index.php/Docking_Analysis_in_DOCK3.8#Note_on_Parallel_Processing		* https://wiki.docking.org/index.php/Docking_Analysis_in_DOCK3.8#Note_on_Parallel_Processing
	* 2022/12/13 : instructions doesn't seem to work, only the script and the main path		* 2022/12/13 : instructions doesn't seem to work, only the script and the main path
	<nowiki>python3 ~~../pydock3/DOCK/ucsfdock~~/analysis/top_poses.py output/</nowiki>		<nowiki>python3 $DOCKBASE/analysis/top_poses.py output/</nowiki>

Cbedart: /* DOCK 3.8 analysis */

2022-12-13T20:49:34Z

DOCK 3.8 analysis

← Older revision		Revision as of 20:49, 13 December 2022
Line 50:		Line 50:

	== DOCK 3.8 analysis ==		== DOCK 3.8 analysis ==
	* ~~WIP~~

			=== top_poses.py ===

			1) Load a specific python environment :
			* (why is it different from the version used to run pydock3 ?)
			<nowiki>source /nfs/soft/python/versions/python-3.8-install/python-3.8-install/bin/env.sh</nowiki>

			2) Main commands :
			* https://wiki.docking.org/index.php/Docking_Analysis_in_DOCK3.8#Note_on_Parallel_Processing
			* 2022/12/13 : instructions doesn't seem to work, only the script and the main path
			<nowiki>python3 ../pydock3/DOCK/ucsfdock/analysis/top_poses.py output/</nowiki>

Cbedart: /* DOCK 3.8 docking */

2022-12-13T20:10:07Z

DOCK 3.8 docking

← Older revision		Revision as of 20:10, 13 December 2022
Line 47:		Line 47:
	* In gimel5, --use-slurm=true is mandatory		* In gimel5, --use-slurm=true is mandatory
	<nowiki>		<nowiki>
	bash ~~/nfs/home/cbedart/exk/DOCK/ucsfdock~~/docking/submit/subdock.bash --use-db2=true --use-db2-tgz=false --use-slurm=true</nowiki>		bash $DOCKBASE/docking/submit/subdock.bash --use-db2=true --use-db2-tgz=false --use-slurm=true</nowiki>

	== DOCK 3.8 analysis ==		== DOCK 3.8 analysis ==
	* WIP		* WIP

Cbedart: Creation

2022-12-13T16:20:06Z

Creation

New page

== Things to remember ==
* Be in gimel5 : ''ssh gimel5''

== DOCK 3.8 installation ==

1) Download pydock3 :
<nowiki>
git clone https://github.com/docking-org/pydock3</nowiki>

2) Download DOCK engine :
<nowiki>
cd ./pydock3/
git clone https://github.com/docking-org/DOCK.git</nowiki>

3) Add in your ~/.profile file :
* python 3.8.5 environment (gimel5)
* DOCKEXEC & DOCKBASE environment variables
<nowiki>
source /nfs/soft/ian/python3.8.5.sh
export DOCKEXEC=''>PATH<''/pydock3/DOCK/ucsfdock/docking/DOCK/dock64
export DOCKBASE=''>PATH<''/pydock3/DOCK/ucsfdock</nowiki>
* Do not forget to source ~/.profile in case you plan to use DOCK & pydock3 immediately

== Pydock3 blastermaster ==
* Protein preparation
* WIP

== DOCK 3.8 docking ==

1) Create your run directory and copy dockfiles from blastermaster :

2) Import ligands, and create ligand index file :
* Important notice : The index file '''must''' be filled with absolute paths
<nowiki>
find $PWD -type f -name '*.db2*' > sdi.in</nowiki>

3) Create an init.sh file to initialize the main environment variables that will be used during docking :
<nowiki>export INPUT_SOURCE=$PWD/sdi.in
export EXPORT_DEST=$PWD/output
export DOCKFILES=$PWD/dockfiles</nowiki>

4) Load your init.sh file :
<nowiki>source ./init.sh</nowiki>

5) Run docking :
* In case of db2.gz files from TLDR, use --use-db2=true --use-db2-tgz=false options
* In gimel5, --use-slurm=true is mandatory
<nowiki>
bash /nfs/home/cbedart/exk/DOCK/ucsfdock/docking/submit/subdock.bash --use-db2=true --use-db2-tgz=false --use-slurm=true</nowiki>

== DOCK 3.8 analysis ==
* WIP