Research Computing Center Wiki - Recent changes [en]

Bactopia-Sapelo2

Chelsea — Tue, 21 Apr 2026 14:36:47 GMT

Documentation

@@ Line 16: / Line 16: @@
 == Description ==
-tbd
+Assembler Parameters
-== Running Program ==
+AMRFinder+ Parameters
-tbd
+!! Hiding 110 params, use --show_hidden_params (or --help_all) to show them !!
-== Documentation ==
+* The nf-core framework
-<pre  class="gcommand">
+* Software dependencies
-tbd
+  https://bactopia.github.io/acknowledgements/
 </pre>

Bactopia-Sapelo2

Chelsea — Tue, 21 Apr 2026 14:34:52 GMT

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics == Category == Bioinformatics == Program On == Sapelo2 == Version == 3.2.0 == Author / Distributor == Please see https://bactopia.github.io/v3.1.0/ == Description == tbd == Running Program == tbd == Documentation == <pre class="gcommand"> tbd </pre> Back to Top == System == 64-bit Linux"

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
== Category ==

Bioinformatics

== Program On ==

Sapelo2

== Version ==
3.2.0

== Author / Distributor ==

Please see https://bactopia.github.io/v3.1.0/

== Description ==

tbd

== Running Program ==

tbd

== Documentation ==

<pre class="gcommand">
tbd
</pre>

[[#top|Back to Top]]

== System ==
64-bit Linux

Software

Chelsea — Tue, 21 Apr 2026 14:31:40 GMT

Partial List of Installed Software

← Older revision		Revision as of 10:31, 21 April 2026
Line 114:		Line 114:
	<!-- \| <span id ="B"></span> [[bam2fastx-Sapelo2\|bam2fastx]] \|\| 1.3.0 \|\| [[:Category:Bioinformatics\|Bioinformatics]] \|\| [[:Category:Sapelo2\|Sapelo2]] \|\| [[File:Up20.png\|20px\|link=#top]]		<!-- \| <span id ="B"></span> [[bam2fastx-Sapelo2\|bam2fastx]] \|\| 1.3.0 \|\| [[:Category:Bioinformatics\|Bioinformatics]] \|\| [[:Category:Sapelo2\|Sapelo2]] \|\| [[File:Up20.png\|20px\|link=#top]]
	\|- -->		\|- -->
			\| [[Bactopia-Sapelo2\|Bactopia]] \|\| 3.2.0 \|\| [[:Category:Bioinformatics\|Bioinformatics]] \|\| [[:Category:Sapelo2\|Sapelo2]] \|\| [[File:Up20.png\|20px\|link=#top]]
			\|- -->
	<!-- \| [[BamTools-Sapelo2\|BamTools]] \|\| 2.4.1, 2.5.1 \|\| [[:Category:Bioinformatics\|Bioinformatics]] \|\| [[:Category:Sapelo2\|Sapelo2]] \|\| [[File:Up20.png\|20px\|link=#top]]		<!-- \| [[BamTools-Sapelo2\|BamTools]] \|\| 2.4.1, 2.5.1 \|\| [[:Category:Bioinformatics\|Bioinformatics]] \|\| [[:Category:Sapelo2\|Sapelo2]] \|\| [[File:Up20.png\|20px\|link=#top]]
	\|- -->		\|- -->

Trinity-HpcGridRunner

Chelsea — Tue, 21 Apr 2026 13:47:35 GMT

Running Program

← Older revision		Revision as of 09:47, 21 April 2026
Line 42:		Line 42:

	# template for a grid submission:		# template for a grid submission:
	cmd=sbatch -p batch --mem 80gb -n 1 -t 01:00:00		cmd=sbatch -p batch --mem 80gb -n 1 --cpus-per-task 24 -t 01:00:00

	##########################################################################################		##########################################################################################

Visual Studio Code SSH

Moses — Mon, 20 Apr 2026 18:47:40 GMT

1. Prepare a batch job submission script for VSCode tunnel session

Show changes

Training

Chelsea — Fri, 17 Apr 2026 13:25:28 GMT

← Older revision		Revision as of 09:25, 17 April 2026
Line 10:		Line 10:


	In '''~~March~~ 2026''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.
			In '''April 2026''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

	We will offer:		We will offer:
Line 25:		Line 26:


	In '''~~April~~ 2026''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.		In '''May 2026''', the GACRC is hosting 9 training sessions listed below. These training workshops will be offered remotely via Zoom Meeting. Detailed instructions for joining the Zoom meeting will be sent to your UGA email account before each training session you register for.

	We will offer:		We will offer:
Line 32:		Line 33:

	2. Sapelo2 cluster new user training (3 sessions)		2. Sapelo2 cluster new user training (3 sessions)

	~~3. Sapelo2 Part II (1 session)~~

	~~4. Job Parallelization with GNU Parallel and Slurm Arrays (1 session)~~

	~~5. Installing Software Packages in Virtual Environments on Sapelo2 (1 session)~~

	==Event Schedule==		==Event Schedule==
Line 77:		Line 72:
	\|-		\|-
	\|Using Sapelo2 Cluster at the GACRC		\|Using Sapelo2 Cluster at the GACRC
	\|~~March 18th~~, Wednesday, 2:00 PM - 4:00 PM		\|April 17th, Friday, 2:00 PM - 4:00 PM
			\|-
			\|Using Sapelo2 Cluster at the GACRC
			\|April 22nd, Wednesday, 2:00 PM - 4:00 PM
	\|-		\|-
	\|Using Sapelo2 Cluster at the GACRC		\|Using Sapelo2 Cluster at the GACRC
	\|~~April 9th~~, ~~Thursday~~, 2:00 PM - 4:00 PM		\|May 8th, Friday, 2:00 PM - 4:00 PM
	\|-		\|-
	\|Using Sapelo2 Cluster at the GACRC		\|Using Sapelo2 Cluster at the GACRC
	\|~~April 17th~~, ~~Friday~~, 2:00 PM - 4:00 PM		\|May 14th, Thursday, 2:00 PM - 4:00 PM
	\|-		\|-
	\|Using Sapelo2 Cluster at the GACRC		\|Using Sapelo2 Cluster at the GACRC
	\|~~April 22nd~~, Wednesday, 2:00 PM - 4:00 PM		\|May 20th, Wednesday, 2:00 PM - 4:00 PM
	\|}		\|}

Line 119:		Line 117:
	\|-		\|-
	\|Use Linux on Cluster		\|Use Linux on Cluster
	\|~~March 16th~~, Monday, 1:00 PM - 3:00 PM		\|April 20th, Monday, 1:00 PM - 3:00 PM
	\|-		\|-
	\|Use Linux on Cluster		\|Use Linux on Cluster
	\|~~April 7th~~, ~~Tuesday~~, 1:00 PM - 3:00 PM		\|May 6th, Wednesday, 1:00 PM - 3:00 PM
	\|-		\|-
	\|Use Linux on Cluster		\|Use Linux on Cluster
	\|~~April 15th~~, ~~Wednesday~~, 1:00 PM - 3:00 PM		\|May 12th, Tuesday, 1:00 PM - 3:00 PM
	\|-		\|-
	\|Use Linux on Cluster		\|Use Linux on Cluster
	\|~~April 20th~~, Monday, 1:00 PM - 3:00 PM		\|May 18th, Monday, 1:00 PM - 3:00 PM
	\|}		\|}

Line 157:		Line 155:
	! scope="col" \|Title		! scope="col" \|Title
	! scope="col" \|Date/Time		! scope="col" \|Date/Time
	\|-
	~~\|Using Sapelo2 Cluster at the GACRC, Part II~~
	~~\|March 20th, Friday, 1:00 - 3:00 PM~~
	\|-		\|-
	\|Using Sapelo2 Cluster at the GACRC, Part II		\|Using Sapelo2 Cluster at the GACRC, Part II
Line 187:		Line 182:
	! scope="col" \|Title		! scope="col" \|Title
	! scope="col" \|Date/Time		! scope="col" \|Date/Time
	\|-
	~~\|Installing Software Packages in Virtual Environments on Sapelo2~~
	~~\|March 26th, Thursday, 2:00 - 3:00 PM~~
	\|-		\|-
	\|Installing Software Packages in Virtual Environments on Sapelo2		\|Installing Software Packages in Virtual Environments on Sapelo2
Line 217:		Line 209:
	! scope="col" \|Title		! scope="col" \|Title
	! scope="col" \|Date/Time		! scope="col" \|Date/Time
	\|-
	~~\|Job Parallelization with GNU Parallel and Slurm Arrays~~
	~~\|March 23rd, Monday, 1:00 - 2:30 PM~~
	\|-		\|-
	\|Job Parallelization with GNU Parallel and Slurm Arrays		\|Job Parallelization with GNU Parallel and Slurm Arrays

Visual Studio Code SSH

Moses — Fri, 17 Apr 2026 13:23:00 GMT

← Older revision		Revision as of 09:23, 17 April 2026
Line 292:		Line 292:

	* Always treat VSCode as a '''compute workload'''		* Always treat VSCode as a '''compute workload'''
	* Always run it inside a Slurm allocation, either via an interactive job (as shown above), a batch job, or an Open OnDemand (OOD) VSCode session		* Always run it inside a Slurm allocation, either via an interactive job (as shown above), a batch job, or an [[OnDemand\|Open OnDemand]] (OOD) VSCode session
	* Avoid launching it directly on login nodes, especially when using the SSH Remote extension.		* Avoid launching it directly on login nodes, especially when using the SSH Remote extension.

SignalIP-Sapelo2

Shtsai — Fri, 17 Apr 2026 03:04:37 GMT

Shtsai deleted page SignalIP-Sapelo2 content before blanking was: "Category:Sapelo2 Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 4.1f === Author / Distributor === [http://www.cbs.dtu.dk/services/SignalP SignalP] === Description === "SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes.". More detai..."

Univa Grid Engine

Shtsai — Fri, 17 Apr 2026 03:00:50 GMT

Shtsai deleted page Univa Grid Engine content was: "#REDIRECT KB:Univa Grid Engine", and the only contributor was "Curtis E. Combs Jr." (talk)

UGE Replacement

Shtsai — Fri, 17 Apr 2026 03:00:45 GMT

Shtsai deleted page UGE Replacement content was: "#REDIRECT KB:UGE Replacement", and the only contributor was "Jerky" (talk)

Thumper rccstor notes

Shtsai — Fri, 17 Apr 2026 03:00:40 GMT

Shtsai deleted page Thumper rccstor notes content was: "#REDIRECT KB:Thumper rccstor notes", and the only contributor was "Derda" (talk)

Scyld Evaluation

Shtsai — Fri, 17 Apr 2026 03:00:34 GMT

Shtsai deleted page Scyld Evaluation content was: "#REDIRECT KB:Scyld Evaluation", and the only contributor was "Jerky" (talk)

Resources

Shtsai — Fri, 17 Apr 2026 03:00:28 GMT

Shtsai deleted page Resources content was: "#REDIRECT KB:Resources", and the only contributor was "Curtis E. Combs Jr." (talk)

Research & Academic Community

Shtsai — Fri, 17 Apr 2026 03:00:22 GMT

Shtsai deleted page Research & Academic Community content was: "#REDIRECT KB:Research & Academic Community", and the only contributor was "Curtis E. Combs Jr." (talk)

Operations

Shtsai — Fri, 17 Apr 2026 03:00:16 GMT

Shtsai deleted page Operations content was: "#REDIRECT KB:Operations", and the only contributor was "Curtis E. Combs Jr." (talk)

Old Data Management

Shtsai — Fri, 17 Apr 2026 03:00:11 GMT

Shtsai deleted page Old Data Management content was: "#REDIRECT KB:Old Data Management", and the only contributor was "Derda" (talk)

Networking

Shtsai — Fri, 17 Apr 2026 03:00:05 GMT

Shtsai deleted page Networking content was: "#REDIRECT KB:Networking", and the only contributor was "Derda" (talk)