How to use Blastermaster 2.0 on UCSF computers - Revision history

Ianscottknight: /* 1. Source the relevant pre-configured environment */

2022-06-07T19:31:22Z

1. Source the relevant pre-configured environment

← Older revision		Revision as of 19:31, 7 June 2022
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	Be aware that you will need to ssh to a node that supports Python >=3.8.5 (e.g. gimel5, n-9-38). Otherwise you will run into an error like:		Be aware that you will need to ssh to a node that supports Python >=3.8.5 (e.g. gimel5, n-9-38). Otherwise you will run into an error like:

	/lib64/libc.so.6: version `GLIBC_2.15' not found ~~(required by /nfs/soft2/ian/.pyenv/versions/3.8.5/bin/python3.8)~~		/lib64/libc.so.6: version `GLIBC_2.15' not found

	Source a Python environment		Source a Python environment

Ianscottknight: /* 1. Source the relevant pre-configured environment */

2022-06-07T19:30:52Z

1. Source the relevant pre-configured environment

← Older revision		Revision as of 19:30, 7 June 2022
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	Source a Python environment		Source a Python environment

	source /nfs/~~soft2~~/ian/python<PYTHON_VERSION>.sh		source /nfs/soft/ian/python<PYTHON_VERSION>.sh

	where <PYTHON_VERSION> is replaced with one of the available python versions. E.g. python3.8.5.sh		where <PYTHON_VERSION> is replaced with one of the available python versions. E.g.:
			source /nfs/soft/ian/python3.8.5.sh

	To check which python versions are available, run		To check which python versions are available, run

Ianscottknight at 20:57, 28 April 2022

2022-04-28T20:57:27Z

← Older revision		Revision as of 20:57, 28 April 2022
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	To check which python versions are available, run		To check which python versions are available, run
	ls /nfs/~~soft2~~/ian/python*.sh		ls /nfs/soft/ian/python*.sh

	== 2. Generate a blaster config file to your directory ==		== 2. Generate a blaster config file to your directory ==
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	The parameters in the config file govern the behavior of blastermaster.		The parameters in the config file govern the behavior of blastermaster.

	Note: if you are using your own files other than rec.pdb and xtal-lig.pdb (e.g., rec.crg.pdb), you need to point to them in the "existing_files_to_use_section". E.g., receptor_charged_file should be set to "rec.crg.pdb" if you have copied it into the directory you are working in.

	To enter the vi text editor:		To enter the vi text editor:
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	blastermaster		blastermaster
	Otherwise:		Otherwise:
	blastermaster <~~BLASTER_CONFIG_FILE_NAME~~>		blastermaster --blaster_config_file_path=<BLASTER_CONFIG_FILE_PATH>

			If you want to supply your own charged receptor file (usually called rec.crg.pdb), you can do so as follows:
			blastermaster --charged_receptor_file_path=<PATH_TO_FILE>

	= Tips for users =		= Tips for users =

	You can create and save multiple blaster config files with different settings so long as they have different names (e.g. blasterconfig_default.yaml, ~~blasterconfig_use_existing_charged_receptor~~.yaml). Then it is easy to reuse the same configuration settings at a later time.		You can create and save multiple blaster config files with different settings so long as they have different names (e.g. blasterconfig_default.yaml, blasterconfig_elec_only_thinspheres.yaml). Then it is easy to reuse the same configuration settings at a later time.

Ianscottknight: /* 1. Source the relevant pre-configured environment */

2022-04-19T20:00:01Z

1. Source the relevant pre-configured environment

← Older revision		Revision as of 20:00, 19 April 2022
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	where <PYTHON_VERSION> is replaced with one of the available python versions. E.g. python3.8.5.sh		where <PYTHON_VERSION> is replaced with one of the available python versions. E.g. python3.8.5.sh

	To check which python versions are available, run		To check which python versions are available, run
	ls /nfs/soft2/ian/python*.sh		ls /nfs/soft2/ian/python*.sh

Ianscottknight: /* 1. Source the relevant pre-configured environment */

2022-04-19T19:59:46Z

1. Source the relevant pre-configured environment

← Older revision		Revision as of 19:59, 19 April 2022
Line 12:		Line 12:
	/lib64/libc.so.6: version `GLIBC_2.15' not found (required by /nfs/soft2/ian/.pyenv/versions/3.8.5/bin/python3.8)		/lib64/libc.so.6: version `GLIBC_2.15' not found (required by /nfs/soft2/ian/.pyenv/versions/3.8.5/bin/python3.8)

	Source ~~the pre-configured~~ environment		Source a Python environment

	source /nfs/soft2/ian/python<PYTHON_VERSION>.sh		source /nfs/soft2/ian/python<PYTHON_VERSION>.sh
Line 19:		Line 19:
	To check which python versions are available, run		To check which python versions are available, run
	ls /nfs/soft2/ian/python*.sh		ls /nfs/soft2/ian/python*.sh

	~~All pre-configured environments currently use DOCK 3.8.~~

	== 2. Generate a blaster config file to your directory ==		== 2. Generate a blaster config file to your directory ==

Ianscottknight: /* 1. Source the relevant pre-configured environment */

2022-04-19T19:58:13Z

1. Source the relevant pre-configured environment

← Older revision		Revision as of 19:58, 19 April 2022
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	Source the pre-configured environment		Source the pre-configured environment

	source /nfs/soft2/ian/~~env~~.sh		source /nfs/soft2/ian/python<PYTHON_VERSION>.sh

	~~By default,~~ the ~~pre-configured environment uses DOCK-3~~.8.0. ~~If you want to use a different version of DOCK~~, ~~set the DOCKBASE parameter to the path of the desired DOCK repository:~~		where <PYTHON_VERSION> is replaced with one of the available python versions. E.g. python3.8.5.sh
			To check which python versions are available, run
			ls /nfs/soft2/ian/python*.sh

	~~export DOCKBASE=<ABSOLUTE_PATH_TO_DOCK_REPOSITORY>~~		All pre-configured environments currently use DOCK 3.8.

	== 2. Generate a blaster config file to your directory ==		== 2. Generate a blaster config file to your directory ==

Ianscottknight at 19:52, 19 April 2022

2022-04-19T19:52:52Z

← Older revision		Revision as of 19:52, 19 April 2022
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	== 4. Run ==		== 4. Run ==
			If you used the default blaster config file name, then you can simply run:
			blastermaster
			Otherwise:
	blastermaster <BLASTER_CONFIG_FILE_NAME>		blastermaster <BLASTER_CONFIG_FILE_NAME>

Ianscottknight: /* 1. Source the relevant pre-configured environment */

2022-04-08T18:58:06Z

1. Source the relevant pre-configured environment

← Older revision		Revision as of 18:58, 8 April 2022
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	=== Gimel ===		=== Gimel ===

	~~source~~ /nfs/soft2/ian/~~env~~.sh		Be aware that you will need to ssh to a node that supports Python >=3.8.5 (e.g. gimel5, n-9-38). Otherwise you will run into an error like:

			/lib64/libc.so.6: version `GLIBC_2.15' not found (required by /nfs/soft2/ian/.pyenv/versions/3.8.5/bin/python3.8)

	~~If you are using Gimel, be aware that you will need to ssh to a node that supports Python >=3.8.5 (e.g. n~~-~~9-38). Otherwise you will run into an error like:~~		Source the pre-configured environment

	~~/lib64/libc.so.6: version `GLIBC_2.15' not found (required by~~ /nfs/soft2/ian/.~~pyenv/versions/3.8.5/bin/python3.8)~~		source /nfs/soft2/ian/env.sh

	By default, the pre-configured environment uses DOCK-3.8.0. If you want to use a different version of DOCK, set the DOCKBASE parameter to the path of the desired DOCK repository:		By default, the pre-configured environment uses DOCK-3.8.0. If you want to use a different version of DOCK, set the DOCKBASE parameter to the path of the desired DOCK repository:

Ianscottknight: /* 1. Source the relevant pre-configured environment */

2022-04-08T18:51:05Z

1. Source the relevant pre-configured environment

← Older revision		Revision as of 18:51, 8 April 2022
Line 10:		Line 10:
	source /nfs/soft2/ian/env.sh		source /nfs/soft2/ian/env.sh

	If you are using Gimel, be aware that you will need to ssh to a node that supports Python >=3.8.5~~. E~~.g.:		If you are using Gimel, be aware that you will need to ssh to a node that supports Python >=3.8.5 (e.g. n-9-38). Otherwise you will run into an error like:
	~~ssh~~ n-9-38
			/lib64/libc.so.6: version `GLIBC_2.15' not found (required by /nfs/soft2/ian/.pyenv/versions/3.8.5/bin/python3.8)

	By default, the pre-configured environment uses DOCK-3.8.0. If you want to use a different version of DOCK, set the DOCKBASE parameter to the path of the desired DOCK repository:		By default, the pre-configured environment uses DOCK-3.8.0. If you want to use a different version of DOCK, set the DOCKBASE parameter to the path of the desired DOCK repository:

Ianscottknight: /* 1. Source the relevant pre-configured environment */

2022-04-08T18:49:39Z

1. Source the relevant pre-configured environment

← Older revision		Revision as of 18:49, 8 April 2022
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	== 1. Source the relevant pre-configured environment ==		== 1. Source the relevant pre-configured environment ==
	Gimel:
			=== Gimel ===

	source /nfs/soft2/ian/env.sh		source /nfs/soft2/ian/env.sh
	~~Wynton~~:
	~~N/A~~		If you are using Gimel, be aware that you will need to ssh to a node that supports Python >=3.8.5. E.g.:
			ssh n-9-38

	By default, the pre-configured environment uses DOCK-3.8.0. If you want to use a different version of DOCK, set the DOCKBASE parameter to the path of the desired DOCK repository:		By default, the pre-configured environment uses DOCK-3.8.0. If you want to use a different version of DOCK, set the DOCKBASE parameter to the path of the desired DOCK repository: