CTF Tools - Revision history

Tomh at 19:54, 15 September 2023

2023-09-15T19:54:38Z

← Older revision		Revision as of 15:54, 15 September 2023
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	; Singularity container running CentOS 6.9 with the CTF tools		; Singularity container running CentOS 6.9 with the CTF tools
	: [https://megcore.nih.gov/MEG/ctf-6.2-sing.tar Singularity container ctf-6.2-sing.tar download]		: [https://megcore.nih.gov/MEG/ctf-6.1-sing.tar Singularity container ctf-6.1-sing.tar download]
	: {\| width=70% style="border: 1px solid black;"		: {\| width=70% style="border: 1px solid black;"
	\|<u>Example usage</u>: singularity shell --bind /data:/mnt/data ctf6.2.sif		\|<u>Example usage</u>: singularity shell --bind /data:/mnt/data ctf6.1.sif
	\|-		\|-
	\| where the ''/data'' file system holds your CTF data set and mounts under /mnt/data inside the container		\| where the ''/data'' file system holds your CTF data set and mounts under /mnt/data inside the container
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	\|}		\|}

	Note that the ctf6.2.sif file is inside the .tar file.		Note that the ctf6.1.sif file is inside the .tar file.

	Another way to use the Singularity container is to use a wrapper script. This allows you to run CTF commands from outside the Singularity environment.		Another way to use the Singularity container is to use a wrapper script. This allows you to run CTF commands from outside the Singularity environment.
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	mkdir tmp		mkdir tmp
	cd tmp		cd tmp
	tar -xf /path/to/ctf-6.2-sing.tar		tar -xf /path/to/ctf-6.1-sing.tar
	./mkwrappers		./mkwrappers

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	# goctf.sh		# goctf.sh

	singularity shell --bind /data/username:/mnt/data ctf6.2.sif		singularity shell --bind /data/username:/mnt/data ctf6.1.sif
	killall -s msgd 2>/dev/null		killall -s msgd 2>/dev/null
	</syntaxhighlight>		</syntaxhighlight>
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	----		----

	; CTF tools native download
	Instead of installing the Singularity container, you can also install the tools natively; you will need to install the necessary 32-bit libraries by hand.

	: [https://megcore.nih.gov/MEG/ctf-6.2.tar ctf-6.2.tar download]

Tomh at 16:44, 2 March 2022

2022-03-02T16:44:08Z

← Older revision		Revision as of 12:44, 2 March 2022
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	; biowulf.nih.gov users		; biowulf.nih.gov users
	: module load ctf~~/6.1.14-beta~~		: module load ctf

	The ctf container is already installed on biowulf.		The ctf container is already installed on biowulf.
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	# goctf.sh		# goctf.sh

	singularity shell --bind /data/username:/mnt/data ~~ctf-6~~.1.~~14-beta.img~~		singularity shell --bind /data/username:/mnt/data ctf6.2.sif
	killall -s msgd 2>/dev/null		killall -s msgd 2>/dev/null
	</syntaxhighlight>		</syntaxhighlight>

Tomh: added 6.2 native download

2022-03-02T16:16:57Z

added 6.2 native download

← Older revision		Revision as of 12:16, 2 March 2022
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	Instead of installing the Singularity container, you can also install the tools natively; you will need to install the necessary 32-bit libraries by hand.		Instead of installing the Singularity container, you can also install the tools natively; you will need to install the necessary 32-bit libraries by hand.

	: [https://megcore.nih.gov/MEG/ctf-6.1.~~14.tgz~~ ctf-6.~~1.14~~.~~tgz~~ download]		: [https://megcore.nih.gov/MEG/ctf-6.2.tar ctf-6.2.tar download]

Tomh at 15:50, 7 September 2021

2021-09-07T15:50:17Z

← Older revision		Revision as of 11:50, 7 September 2021
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	\| (your /home directory and the /tmp file systems are automatically visible inside the container)		\| (your /home directory and the /tmp file systems are automatically visible inside the container)
	\|}		\|}

			Note that the ctf6.2.sif file is inside the .tar file.

	Another way to use the Singularity container is to use a wrapper script. This allows you to run CTF commands from outside the Singularity environment.		Another way to use the Singularity container is to use a wrapper script. This allows you to run CTF commands from outside the Singularity environment.

	To do this, unpack the .tar file above, and run the ~~mkwrapper~~ script.		To do this, unpack the .tar file above, and run the mkwrappers script.

	mkdir tmp		mkdir tmp

Tomh at 15:47, 7 September 2021

2021-09-07T15:47:38Z

← Older revision		Revision as of 11:47, 7 September 2021
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	To do this, unpack the .tar file above, and run the mkwrapper script.		To do this, unpack the .tar file above, and run the mkwrapper script.

			mkdir tmp
	<syntaxhighlight lang="bash">
	~~mkdir~~ tmp		cd tmp
		⚫	tar -xf /path/to/ctf-6.2-sing.tar
	cd tmp
		⚫	./mkwrappers
⚫	tar -x /path/to/ctf-6.2-sing.tar
⚫	./mkwrappers
	</syntaxhighlight>

	You don't need the tmp directory after that. The wrappers are installed in /usr/local/ctf/bin, so put that in your path.		You don't need the tmp directory after that. The wrappers are installed in /usr/local/ctf/bin, so put that in your path.

Tomh at 15:40, 7 September 2021

2021-09-07T15:40:55Z

@@ Line 23: / Line 23: @@
 To do this, unpack the .tar file above, and run the mkwrapper script.
-| mkdir tmp
+mkdir tmp
 You don't need the tmp directory after that. The wrappers are installed in /usr/local/ctf/bin, so put that in your path.

Tomh at 15:39, 7 September 2021

2021-09-07T15:39:31Z

← Older revision		Revision as of 11:39, 7 September 2021
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	: {\| width=70% style="border: 1px solid black;"		: {\| width=70% style="border: 1px solid black;"
	\| mkdir tmp		\| mkdir tmp
			\|-
	\| cd tmp		\| cd tmp
			\|-
	\| tar -x /path/to/ctf-6.2-sing.tar		\| tar -x /path/to/ctf-6.2-sing.tar
			\|-
	\| ./mkwrappers		\| ./mkwrappers
	\|}		\|}

Tomh at 15:38, 7 September 2021

2021-09-07T15:38:58Z

← Older revision		Revision as of 11:38, 7 September 2021
Line 23:		Line 23:
	To do this, unpack the .tar file above, and run the mkwrapper script.		To do this, unpack the .tar file above, and run the mkwrapper script.

			: {\| width=70% style="border: 1px solid black;"
	\| mkdir tmp		\| mkdir tmp
	\| cd tmp		\| cd tmp
	\| tar -x /path/to/ctf-6.2-sing.tar		\| tar -x /path/to/ctf-6.2-sing.tar
	\| ./mkwrappers		\| ./mkwrappers
			\|}

	You don't need the tmp directory after that. The wrappers are installed in /usr/local/ctf/bin, so put that in your path.		You don't need the tmp directory after that. The wrappers are installed in /usr/local/ctf/bin, so put that in your path.

Tomh at 15:37, 7 September 2021

2021-09-07T15:37:14Z

← Older revision		Revision as of 11:37, 7 September 2021
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	; Singularity container running CentOS 6.9 with the CTF tools		; Singularity container running CentOS 6.9 with the CTF tools
	: [https://megcore.nih.gov/MEG/ctf-6.~~1.14~~-~~beta~~.~~img~~ Singularity container ctf-6.~~1.14~~-~~beta~~.~~img~~ download]		: [https://megcore.nih.gov/MEG/ctf-6.2-sing.tar Singularity container ctf-6.2-sing.tar download]
	: {\| width=70% style="border: 1px solid black;"		: {\| width=70% style="border: 1px solid black;"
	\|<u>Example usage</u>: singularity shell --bind /data:/mnt/data ~~ctf-6~~.1.~~14-beta.img~~		\|<u>Example usage</u>: singularity shell --bind /data:/mnt/data ctf6.2.sif
	\|-		\|-
	\| where the ''/data'' file system holds your CTF data set and mounts under /mnt/data inside the container		\| where the ''/data'' file system holds your CTF data set and mounts under /mnt/data inside the container
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	\| (your /home directory and the /tmp file systems are automatically visible inside the container)		\| (your /home directory and the /tmp file systems are automatically visible inside the container)
	\|}		\|}

			Another way to use the Singularity container is to use a wrapper script. This allows you to run CTF commands from outside the Singularity environment.

			To do this, unpack the .tar file above, and run the mkwrapper script.

			\| mkdir tmp
			\| cd tmp
			\| tar -x /path/to/ctf-6.2-sing.tar
			\| ./mkwrappers

			You don't need the tmp directory after that. The wrappers are installed in /usr/local/ctf/bin, so put that in your path.

	----		----

Tomh: reorganizing page names and other updates

2020-09-23T19:55:23Z

reorganizing page names and other updates

← Older revision		Revision as of 15:55, 23 September 2020
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	==== Using the CTF ~~DataEditor~~ with a Singularity Container ====		==== Using the CTF tools with a Singularity Container ====

	The current version of the ~~'''~~CTF ~~DataEditor~~ ~~tool''' runs~~ under CentOS (Linux) version 6.9. To support the MEG user community, we have a [https://singularity.lbl.gov/index.html Singularity] container for CentOS 6.9 containing the necessary libraries to run ~~the DataEditor tool~~. This allows MEG users to run the ~~DataEditor~~ under the operating system (Windows, Mac OSX, Linux) of their choice.		The current version of the CTF tools run under CentOS (Linux) version 6.9. To support the MEG user community, we have a [https://singularity.lbl.gov/index.html Singularity] container for CentOS 6.9 containing the necessary libraries to run them. This allows MEG users to run the tools under the operating system (Windows, Mac OSX, Linux) of their choice.

	Singularity is a		Singularity is a
	[https://en.wikipedia.org/wiki/Operating-system-level_virtualization Operating-system-level virtualization] solution where an operating system		[https://en.wikipedia.org/wiki/Operating-system-level_virtualization Operating-system-level virtualization] solution where an operating system
	can host another operating system in an isolated container. To run a Singularity container on your operating system, you need to install the Singularity software for your operating system. There are install packages for the major operating systems from the [https://www.sylabs.io/ Singularity website.]		can host another operating system in an isolated container. To run a Singularity container on your operating system, you need to install the Singularity software for your operating system. There are install packages for the major operating systems from the [https://www.sylabs.io/ Singularity website.]

	----		----

	; Singularity container running CentOS 6.9 with the CTF ~~DataEditor tool~~		; Singularity container running CentOS 6.9 with the CTF tools
	: [https://megcore.nih.gov/MEG/ctf-6.1.14-beta.img Singularity container ctf-6.1.14-beta.img download]		: [https://megcore.nih.gov/MEG/ctf-6.1.14-beta.img Singularity container ctf-6.1.14-beta.img download]
	: {\| width=70% style="border: 1px solid black;"		: {\| width=70% style="border: 1px solid black;"
	\|<u>~~Usage~~</u>: singularity shell --bind /data:/mnt/data ctf-6.1.14-beta.img		\|<u>Example usage</u>: singularity shell --bind /data:/mnt/data ctf-6.1.14-beta.img
	\|-		\|-
	\| where the ''/data'' file system holds your CTF data set and mounts under /mnt/data inside the container		\| where the ''/data'' file system holds your CTF data set and mounts under /mnt/data inside the container
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	\| (your /home directory and the /tmp file systems are automatically visible inside the container)		\| (your /home directory and the /tmp file systems are automatically visible inside the container)
	\|}		\|}

	----		----

	; biowulf.nih.gov users		; biowulf.nih.gov users
	: module load ctf/6.1.14-beta		: module load ctf/6.1.14-beta

	The ctf container is already installed on biowulf.		The ctf container is already installed on biowulf.

			----

			; General use
	For other machines, use the following bash script to shell into the singularity container.		For other machines, use the following bash script to shell into the singularity container.

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	</syntaxhighlight>		</syntaxhighlight>

	DataEditor ~~communicates~~ ~~with~~ other CTF tools using the '''msgd''' service, ~~and DataEditor~~ will automatically ~~launch~~ ~~this service~~ if it isn't running. This service is not killed when you exit from the singularity container, so you will end up with a persistent process. To prevent this from occurring, just kill it, as above.		'''DataEditor''' and the other CTF tools communicate with each other using the '''msgd''' service, which will automatically be launched if it isn't already running. This service is not killed when you exit from the singularity container, so you will end up with a persistent process. To prevent this from occurring, just kill it, as above.

	You may want to add this stanza to your ~/.bashrc file.		You may want to add this stanza to your ~/.bashrc file.
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	----		----

	; CTF tools native download		; CTF tools native download
	Instead of installing the Singularity container, you can also install the tools natively; you will need to install the necessary 32-bit libraries by hand.		Instead of installing the Singularity container, you can also install the tools natively; you will need to install the necessary 32-bit libraries by hand.