Applications/BayesTraits - Revision history

Pysdlb at 09:49, 23 March 2023

2023-03-23T09:49:07Z

Pysdlb at 15:10, 16 November 2022

2022-11-16T15:10:28Z

Pysdlb: /* Further Information */

2022-11-16T15:09:07Z

‎Further Information

Pysdlb at 15:07, 16 November 2022

2022-11-16T15:07:52Z

Pysdlb: /* Navigation */

2022-11-16T10:37:17Z

‎Navigation

Pysdlb at 08:58, 24 May 2021

2021-05-24T08:58:26Z

Pysdlb at 11:11, 24 May 2019

2019-05-24T11:11:34Z

Pysdlb at 11:10, 24 May 2019

2019-05-24T11:10:38Z

Chris.collins: /* Usage Examples */

2019-05-10T12:00:53Z

‎Usage Examples

Pysdlb at 14:19, 7 June 2018

2018-06-07T14:19:33Z

@@ Line 6: / Line 6: @@
 * Version: 3.0.0 (supplied compiled binaries)
 * Modules: bayes/3.0.0 (apps)
-* Licence: Free (http://www.evolution.rdg.ac.uk/index.html)
+* Licence: Free
 ==Introduction==
@@ Line 14: / Line 14: @@
 This new package incorporates our earlier and separate programs Multistate, Discrete and Continuous.
-BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, ancestral states and about correlations among pairs of traits.
+BayesTraits can be applied to analysing traits that adopt a finite number of discrete states, or to analysing continuously varying traits. Hypotheses can be tested about models of evolution, ancestral states and correlations among pairs of traits.
 ==Usage Examples==

@@ Line 100: / Line 100: @@
 </pre>
-The job is submitted in the same way as a standard batch job.
+<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 ==Next Steps==

@@ Line 102: / Line 102: @@
 The job is submitted in the same way as a standard batch job.
-==Further Information==
+==Next Steps==
 * [http://http://www.evolution.rdg.ac.uk/index.html http://www.evolution.rdg.ac.uk/index.html]
 {{Modulepagenav}}

@@ Line 7: / Line 7: @@
 * Modules: bayes/3.0.0 (apps)
 * Licence: Free (http://www.evolution.rdg.ac.uk/index.html)
 ==Usage Examples==
@@ Line 52: / Line 60: @@
 ===Multi-Batch Jobs===
 The following job script will automatically run 3 identical BayesTrait jobs in an array so that three outputs can be compared. It takes care of separating the jobs, running them, and then bringing the outputs together.
@@ Line 86: / Line 95: @@
 cd $RUNDIR
-# Copy the output files from each of the 3 run directories into a files called run_1_<data_file>.log.txt
+# Copy the output files from each of the 3 run directories into a file called run_1_<data_file>.log.txt
 cp $SLURM_ARRAY_TASK_ID/${DATA_FILE}.Log.txt run_${SLURM_ARRAY_TASK_ID}_${DATA_FILE}.Log.txt
 cp $SLURM_ARRAY_TASK_ID/${DATA_FILE}.Schedule.txt run_${SLURM_ARRAY_TASK_ID}_${DATA_FILE}.Schedule.txt

← Older revision		Revision as of 10:37, 16 November 2022
Line 97:		Line 97:
	* [http://http://www.evolution.rdg.ac.uk/index.html http://www.evolution.rdg.ac.uk/index.html]		* [http://http://www.evolution.rdg.ac.uk/index.html http://www.evolution.rdg.ac.uk/index.html]

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

@@ Line 37: / Line 37: @@
 #SBATCH -p compute       # Partition to run on
 #SBATCH --exclusive       # Instructs SLURM to not run any other job in the node(s) selected
 module add bayesTraits/3.0.0
@@ Line 51: / Line 52: @@
 ===Multi-Batch Jobs===
-The following job script will automatically run 3 identical BayesTrait jobs in an array, so that three outputs can be compared. It takes care of separating the jobs, running them and then bringing the outputs together.
+The following job script will automatically run 3 identical BayesTrait jobs in an array so that three outputs can be compared. It takes care of separating the jobs, running them, and then bringing the outputs together.
 <pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
@@ Line 71: / Line 72: @@
 cd $SLURM_ARRAY_TASK_ID
-# Update here to set command, tree and data files
+# Update here to set command, tree, and data files
 COMMAND_FILE=MCcSM_RJHPexp05_WCLCBNoZero_command.txt
 TREE_FILE=FritzHARD_WCLCBNoZero.trees

← Older revision		Revision as of 11:11, 24 May 2019
Line 95:		Line 95:

	* [http://http://www.evolution.rdg.ac.uk/index.html http://www.evolution.rdg.ac.uk/index.html]		* [http://http://www.evolution.rdg.ac.uk/index.html http://www.evolution.rdg.ac.uk/index.html]
		+
		+	==Navigation==
		+
		+	* [[Main_Page\|Home]]
		+	* [[Applications\|Application support]] *
		+	* [[General\|General]]
		+	* [[Programming\|Programming support]]

← Older revision		Revision as of 11:10, 24 May 2019
Line 95:		Line 95:

	* [http://http://www.evolution.rdg.ac.uk/index.html http://www.evolution.rdg.ac.uk/index.html]		* [http://http://www.evolution.rdg.ac.uk/index.html http://www.evolution.rdg.ac.uk/index.html]
−
−
−
−	{\|
−	~~\|style="width:5%; border-width: 0" \| [[File:icon_home.png]]~~
−	~~\|style="width:95%; border-width: 0" \|~~
−	* [[Main_Page\|Home]]
−	* [[Applications\|Application support]]
−	* [[General\|General]]
−	* [[Training\|Training]]
−	* [[Programming\|Programming support]]
−	\|-
−	\|}

← Older revision		Revision as of 12:00, 10 May 2019
Line 49:		Line 49:

	</pre>		</pre>
		+
		+	===Multi-Batch Jobs===
		+	The following job script will automatically run 3 identical BayesTrait jobs in an array, so that three outputs can be compared. It takes care of separating the jobs, running them and then bringing the outputs together.
		+
		+	<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
		+	#!/bin/bash
		+	#SBATCH -J BayesTrait_array
		+	#SBATCH -N 1
		+	#SBATCH -n 28
		+	#SBATCH -o %N.%j.%a.out
		+	#SBATCH -e %N.%j.%a.err
		+	#SBATCH -pcompute
		+	#SBATCH --exclusive
		+	#SBATCH --array 1-3
		+
		+	module add bayesTraits/3.0/intel-2017
		+
		+	# Create 3 sub-directories inside which each job will run
		+	RUNDIR=`pwd`
		+	mkdir $SLURM_ARRAY_TASK_ID
		+	cd $SLURM_ARRAY_TASK_ID
		+
		+	# Update here to set command, tree and data files
		+	COMMAND_FILE=MCcSM_RJHPexp05_WCLCBNoZero_command.txt
		+	TREE_FILE=FritzHARD_WCLCBNoZero.trees
		+	DATA_FILE=MCcSM_RJHPexp05_WCLCBNoZero.txt
		+
		+	# Make a 'copy' of the command, tree and data files in the job sub-directories
		+	ln -s ../$COMMAND_FILE .
		+	ln -s ../$TREE_FILE .
		+	ln -s ../$DATA_FILE .
		+
		+	BayesTraitsV3 $TREE_FILE $DATA_FILE < $COMMAND_FILE
		+
		+	cd $RUNDIR
		+
		+	# Copy the output files from each of the 3 run directories into a files called run_1_<data_file>.log.txt
		+	cp $SLURM_ARRAY_TASK_ID/${DATA_FILE}.Log.txt run_${SLURM_ARRAY_TASK_ID}_${DATA_FILE}.Log.txt
		+	cp $SLURM_ARRAY_TASK_ID/${DATA_FILE}.Schedule.txt run_${SLURM_ARRAY_TASK_ID}_${DATA_FILE}.Schedule.txt
		+	</pre>
		+
		+	The job is submitted in the same way as a standard batch job.

	==Further Information==		==Further Information==

@@ Line 17: / Line 17: @@
 salloc: Granted job allocation 409670
 Job ID 409670 connecting to c128, please wait...
-[username@c128 ~]$ module load bayesTrait/3.0.0
+[username@c128 ~]$ module add bayesTrait/3.0.0
 [username@c128 ~]$ BayesTraitsV3 /trinity/clustervision/CentOS/7/apps/bayesTraits/3.0.0/Mammal.trees bob.tress
 BayesTraits V3.0 (Mar  2 2017)