Applications/Cufflinks - Revision history

Pysdlb: /* Batch Job */

2022-11-16T16:55:35Z

‎Batch Job

2022-11-16T16:54:51Z

‎Batch Job

2022-11-16T16:54:35Z

‎Usage Examples

2022-11-16T16:53:28Z

‎Usage Examples

2022-11-16T10:41:19Z

‎Further Information

2022-11-16T10:41:11Z

‎Navigation

2019-05-24T11:20:53Z

2018-06-07T13:26:12Z

2017-04-06T08:31:44Z

2017-04-06T07:57:19Z

@@ Line 41: / Line 41: @@
 <pre>
 #!/bin/bash
 #SBATCH -J cufflinks-test
 #SBATCH -n 1

@@ Line 51: / Line 51: @@
 module purge
-module load apps/cufflinks/2.2.1
+module load cufflinks/2.2.1
 CUFFLINKS_OUTPUT="${PWD}"

@@ Line 37: / Line 37: @@
 </pre>
+===Batch Job===
 <pre>
 #!/bin/bash
@@ Line 44: / Line 45: @@
 #SBATCH -n 1
 #SBATCH --ntasks-per-node=2
-#SBATCH --output=output.%j.cufflinks-test
+#SBATCH --output=output.%j.out
 #SBATCH --time=00:10:00

← Older revision		Revision as of 16:53, 16 November 2022
Line 35:		Line 35:
	[username@login01 ~]$ module add cufflinks/2.2.1		[username@login01 ~]$ module add cufflinks/2.2.1

		+	</pre>
		+
		+
		+	<pre>
		+	#!/bin/bash
		+	#
		+	#SBATCH -J cufflinks-test
		+	#SBATCH -n 1
		+	#SBATCH --ntasks-per-node=2
		+	#SBATCH --output=output.%j.cufflinks-test
		+	#SBATCH --time=00:10:00
		+
		+	#### SLURM task using 1 Node with 2 Processors per Node cufflinks test to run for 10 minutes.
		+
		+	module purge
		+	module load apps/cufflinks/2.2.1
		+
		+	CUFFLINKS_OUTPUT="${PWD}"
		+
		+	cufflinks --quiet --num-threads $SLURM_NTASKS --output-dir $CUFFLINKS_OUTPUT input.bam
	</pre>		</pre>

← Older revision		Revision as of 10:41, 16 November 2022
Line 40:		Line 40:

	* [http://cole-trapnell-lab.github.io/cufflinks/ http://cole-trapnell-lab.github.io/cufflinks/]		* [http://cole-trapnell-lab.github.io/cufflinks/ http://cole-trapnell-lab.github.io/cufflinks/]
−

	{{Modulepagenav}}		{{Modulepagenav}}

← Older revision		Revision as of 10:41, 16 November 2022
Line 42:		Line 42:


−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

@@ Line 42: / Line 42: @@
-{|
+==Navigation==
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

@@ Line 33: / Line 33: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-[username@login01 ~]$ module load cufflinks/2.2.1
+[username@login01 ~]$ module add cufflinks/2.2.1
 </pre>

@@ Line 24: / Line 24: @@
 With linkages to the following modules too:
 * [[applications/Samtools|Samtools]]
 * [[applications/Tophat|Tophat]]