Updated PIrANHA versioning in function scripts

Update in prep for v0.2-alpha.2 release
justincbagley · Apr 9, 2019 · 6ae7614 · 6ae7614
1 parent 520a5af
commit 6ae7614
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diff --git a/bin/2logeB10.r b/bin/2logeB10.r
@@ -20,7 +20,7 @@
 ######################################## START ###########################################
 
 cat('INFO      | $(date) |----------------------------------------------------------------\n')
-cat('INFO      | $(date) | 2logeB10.r, v1.2 March 2019  (part of PIrANHA v0.2-alpha.1c)   \n')
+cat('INFO      | $(date) | 2logeB10.r, v1.2 March 2019  (part of PIrANHA v0.2-alpha.2)   \n')
 cat('INFO      | $(date) | Copyright (c) 2016-2019 Justin C. Bagley. All rights reserved. \n')
 cat('INFO      | $(date) |----------------------------------------------------------------\n')
 

diff --git a/bin/AnouraNEXUSPrepper b/bin/AnouraNEXUSPrepper
@@ -138,7 +138,7 @@ AnouraNEXUSPrepper () {
 ##########################################################################################
 
 echo "INFO      | $(date) |----------------------------------------------------------------"
-echo "INFO      | $(date) | AnouraNEXUSPrepper, v1.3.1 March 2019  (in PIrANHA v0.2-alpha.1c)"
+echo "INFO      | $(date) | AnouraNEXUSPrepper, v1.3.1 March 2019  (in PIrANHA v0.2-alpha.2)"
 echo "INFO      | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved.      "
 echo "INFO      | $(date) |----------------------------------------------------------------"
 
@@ -277,7 +277,7 @@ USAGE="Usage: $(basename $0) [OPTION]...
  Sierra (10.13+) and many earlier macOS or OSX versions.
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/BEASTPostProc b/bin/BEASTPostProc
@@ -136,7 +136,7 @@ BEASTPostProc () {
 ##########################################################################################
 
 echo "INFO      | $(date) |----------------------------------------------------------------"
-echo "INFO      | $(date) | BEASTPostProc, v1.6.3 March 2019  (in PIrANHA v0.2-alpha.1c)   "
+echo "INFO      | $(date) | BEASTPostProc, v1.6.3 March 2019  (in PIrANHA v0.2-alpha.2)   "
 echo "INFO      | $(date) | Copyright (c) 2016-2019 Justin C. Bagley. All rights reserved. "
 echo "INFO      | $(date) |----------------------------------------------------------------"
 
@@ -459,7 +459,7 @@ USAGE="Usage: $(basename $0) [OPTION]...
     piranha -f BEASTPostProc --args='-h'
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/BEASTReset b/bin/BEASTReset
@@ -137,7 +137,7 @@ BEASTReset () {
 ##########################################################################################
 
 echo "INFO      | $(date) |----------------------------------------------------------------"
-echo "INFO      | $(date) | BEASTReset, v1.0.0 March 2019  (in PIrANHA v0.2-alpha.1c)      "
+echo "INFO      | $(date) | BEASTReset, v1.0.0 March 2019  (in PIrANHA v0.2-alpha.2)      "
 echo "INFO      | $(date) | Copyright (c) 2017-2019 Justin C. Bagley. All rights reserved. "
 echo "INFO      | $(date) |----------------------------------------------------------------"
 
@@ -292,11 +292,11 @@ USAGE="Usage: $(basename $0) [OPTION]...
     piranha -f BEASTReset --args='-h'	  Print help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  Created by Justin Bagley on Thu, 24 Aug 2017 11:30:42 -0400.

diff --git a/bin/BEASTRunner b/bin/BEASTRunner
@@ -136,7 +136,7 @@ BEASTRunner () {
 ##########################################################################################
 
 echo "INFO      | $(date) |----------------------------------------------------------------"
-echo "INFO      | $(date) | BEASTRunner, v1.4.1 March 2019  (in PIrANHA v0.2-alpha.1c)     "
+echo "INFO      | $(date) | BEASTRunner, v1.4.1 March 2019  (in PIrANHA v0.2-alpha.2)     "
 echo "INFO      | $(date) | Copyright (c) 2016-2019 Justin C. Bagley. All rights reserved. "
 echo "INFO      | $(date) |----------------------------------------------------------------"
 
@@ -419,7 +419,7 @@ USAGE="Usage: $(basename $0) [OPTION]...
     piranha -f BEASTRunner --args='-n 10 -w 24:00:00 -m 2048M'        Change memory (RAM) allocation to 2GB
 	
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}
@@ -497,7 +497,7 @@ VERBOSE_USAGE="Usage: $(basename $0) [OPTION]...
     piranha -f BEASTRunner --args='-n 10 -w 24:00:00 -m 2048M'        Change memory (RAM) allocation to 2GB
 	
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/BEAST_PSPrepper b/bin/BEAST_PSPrepper
@@ -136,7 +136,7 @@ BEAST_PSPrepper () {
 ##########################################################################################
 
 echo "INFO      | $(date) |----------------------------------------------------------------"
-echo "INFO      | $(date) | BEAST_PSPrepper, v1.0.0 March 2019  (in PIrANHA v0.2-alpha.1c)   "
+echo "INFO      | $(date) | BEAST_PSPrepper, v1.0.0 March 2019  (in PIrANHA v0.2-alpha.2)   "
 echo "INFO      | $(date) | Copyright (c) 2017-2019 Justin C. Bagley. All rights reserved. "
 echo "INFO      | $(date) |----------------------------------------------------------------"
 
@@ -358,7 +358,7 @@ USAGE="Usage: $(basename $0) [OPTION]...
     piranha -f BEAST_PSPrepper --args='-h'
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/ExaBayesPostProc b/bin/ExaBayesPostProc
@@ -136,7 +136,7 @@ ExaBayesPostProc () {
 ##########################################################################################
 
 echo "INFO      | $(date) |----------------------------------------------------------------"
-echo "INFO      | $(date) | ExaBayesPostProc, v1.3.2 March 2019  (in PIrANHA v0.2-alpha.1c)"
+echo "INFO      | $(date) | ExaBayesPostProc, v1.3.2 March 2019  (in PIrANHA v0.2-alpha.2)"
 echo "INFO      | $(date) | Copyright (c) 2016-2019 Justin C. Bagley. All rights reserved. "
 echo "INFO      | $(date) |----------------------------------------------------------------"
 
@@ -436,7 +436,7 @@ USAGE="Usage: $(basename $0) [OPTION]...
     piranha -f ExaBayesPostProc --args='-h'       Print this help text
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/FASTA2PHYLIP b/bin/FASTA2PHYLIP
@@ -139,7 +139,7 @@ FASTA2PHYLIP () {
 ##########################################################################################
 
 echo "INFO      | $(date) |----------------------------------------------------------------"
-echo "INFO      | $(date) | FASTA2PHYLIP, v1.0.0 March 2019  (in PIrANHA v0.2-alpha.1c)    "
+echo "INFO      | $(date) | FASTA2PHYLIP, v1.0.0 March 2019  (in PIrANHA v0.2-alpha.2)    "
 echo "INFO      | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved.      "
 echo "INFO      | $(date) |----------------------------------------------------------------"
 
@@ -619,7 +619,7 @@ USAGE="Usage: $(basename $0) [OPTION]...
     piranha -f FASTA2PHYLIP -a '-k 1 -v 1'     Same as above, but passing arguments with -a flag
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}
@@ -684,7 +684,7 @@ VERBOSE_USAGE="Usage: $(basename $0) [OPTION]...
     piranha -f FASTA2PHYLIP -a '-k 1 -v 1'     Same as above, but passing arguments with -a flag
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/FASTA2VCF b/bin/FASTA2VCF
@@ -141,7 +141,7 @@ FASTA2VCF () {
 ##########################################################################################
 
 echo "INFO      | $(date) |----------------------------------------------------------------"
-echo "INFO      | $(date) | FASTA2VCF, v1.0.0 March 2019  (in PIrANHA v0.2-alpha.1c)    "
+echo "INFO      | $(date) | FASTA2VCF, v1.0.0 March 2019  (in PIrANHA v0.2-alpha.2)    "
 echo "INFO      | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved.      "
 echo "INFO      | $(date) |----------------------------------------------------------------"
 
@@ -388,7 +388,7 @@ USAGE="Usage: $(basename $0) [OPTION]...
     piranha -f FASTA2VCF --args='-h'
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/MAGNET-1.0.0/MAGNET b/bin/MAGNET-1.0.0/MAGNET
@@ -136,7 +136,7 @@ MAGNET () {
 ##########################################################################################
 
 echo "INFO      | $(date) |----------------------------------------------------------------"
-echo "INFO      | $(date) | MAGNET, v1.0.0 March 2019  (part of PIrANHA v0.2-alpha.1c)     "
+echo "INFO      | $(date) | MAGNET, v1.0.0 March 2019  (part of PIrANHA v0.2-alpha.2)     "
 echo "INFO      | $(date) | Copyright (c) 2016-2019 Justin C. Bagley. All rights reserved. "
 echo "INFO      | $(date) |----------------------------------------------------------------"
 
@@ -985,7 +985,7 @@ USAGE="Usage: $(basename $0) [OPTION]...
      											    	  HKY85 substitution model for all loci    
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}
@@ -1101,7 +1101,7 @@ VERBOSE_USAGE="Usage: $(basename $0) [OPTION]...
      											    	  HKY85 substitution model for all loci    
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/MAGNET-1.0.0/README.md b/bin/MAGNET-1.0.0/README.md
@@ -12,7 +12,7 @@ All code within the PIrANHA repository, including MAGNET v1.0.0 pipeline code, i
 
 If you use scripts from this repository as part of your published research, then I require you to cite the PIrANHA repository and/or MAGNET package as follows (also see DOI information below):
 
-  Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at: http://github.com/justincbagley/piranha/.
+  Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at: http://github.com/justincbagley/piranha/.
 
   Bagley, J.C. 2019. MAGNET v1.0.0. GitHub package, Available at: http://github.com/justincbagley/MAGNET. 
 
@@ -186,7 +186,7 @@ Usage: MAGNET [OPTION]...
      											    	  HKY85 substitution model for all loci    
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/PIrANHA>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/MAGNET-1.0.0/shell/NEXUS2gphocs b/bin/MAGNET-1.0.0/shell/NEXUS2gphocs
@@ -136,7 +136,7 @@ function NEXUS2gphocs () {
 ##########################################################################################
 
 echo "INFO      | $(date) |----------------------------------------------------------------"
-echo "INFO      | $(date) | NEXUS2gphocs, v1.5.0 March 2019  (part of PIrANHA v1.0.0)      "
+echo "INFO      | $(date) | NEXUS2gphocs, v1.5.0 March 2019  (part of PIrANHA v0.2-alpha.2)      "
 echo "INFO      | $(date) | Copyright (c) 2016-2019 Justin C. Bagley. All rights reserved. "
 echo "INFO      | $(date) |----------------------------------------------------------------"
 
@@ -329,7 +329,7 @@ USAGE="Usage: $(basename $0) [OPTION]...
     piranha -f MAGNET-1.0.0/NEXUS2gphocs --args='-h'
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v1.0.0. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/PIrANHA>.
 
  ${bold}REFERENCES${reset}
@@ -402,4 +402,4 @@ set -o pipefail
 NEXUS2gphocs
 
 # Exit cleanly
-safeExit
+safeExit
diff --git a/bin/MAGNET-1.0.0/shell/NEXUS2gphocs.sh b/bin/MAGNET-1.0.0/shell/NEXUS2gphocs.sh
@@ -136,7 +136,7 @@ function NEXUS2gphocs () {
 ##########################################################################################
 
 echo "INFO      | $(date) |----------------------------------------------------------------"
-echo "INFO      | $(date) | NEXUS2gphocs, v1.5.0 March 2019  (part of PIrANHA v1.0.0)      "
+echo "INFO      | $(date) | NEXUS2gphocs, v1.5.0 March 2019  (part of PIrANHA v0.2-alpha.2)      "
 echo "INFO      | $(date) | Copyright (c) 2016-2019 Justin C. Bagley. All rights reserved. "
 echo "INFO      | $(date) |----------------------------------------------------------------"
 
@@ -329,7 +329,7 @@ USAGE="Usage: $(basename $0) [OPTION]...
     piranha -f MAGNET-1.0.0/NEXUS2gphocs --args='-h'
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v1.0.0. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/PIrANHA>.
 
  ${bold}REFERENCES${reset}
@@ -402,4 +402,4 @@ set -o pipefail
 NEXUS2gphocs
 
 # Exit cleanly
-safeExit
+safeExit
diff --git a/bin/MAGNET-1.0.0/shell/RAxMLRunChecker b/bin/MAGNET-1.0.0/shell/RAxMLRunChecker
@@ -136,7 +136,7 @@ function RAxMLRunChecker () {
 ##########################################################################################
 
 echo "INFO      | $(date) |----------------------------------------------------------------"
-echo "INFO      | $(date) | RAxMLRunChecker, v1.3.0 March 2019  (part of PIrANHA v1.0.0)   "
+echo "INFO      | $(date) | RAxMLRunChecker, v1.3.0 March 2019  (part of PIrANHA v0.2-alpha.2)   "
 echo "INFO      | $(date) | Copyright (c) 2018-2019 Justin C. Bagley. All rights reserved. "
 echo "INFO      | $(date) |----------------------------------------------------------------"
 
@@ -260,7 +260,7 @@ USAGE="Usage: $(basename $0) [OPTION]...
 
  ${bold}OVERVIEW${reset}
  THIS SCRIPT was designed to run in a current working directory where the MAGNET pipeline
- in PIrANHA v1.0.0 (Bagley 2019) is being run, or has completed a run, to estimate maximum-
+ in PIrANHA v0.2-alpha.2 (Bagley 2019) is being run, or has completed a run, to estimate maximum-
  likelihood (ML) gene trees in RAxML v8+ (Stamatakis 2014) for a set of loci from DNA 
  sequence data. Given such a workspace, this script counts the number of loci or data 
  partitions (each assigned a separate RAxML run in MAGNET) with completed RAxML runs and 
@@ -278,11 +278,11 @@ USAGE="Usage: $(basename $0) [OPTION]...
     piranha -f RAxMLRunChecker --args='-h'      Print this help text
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v1.0.0. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/PIrANHA>.
 
  ${bold}REFERENCES${reset}
- Bagley, J.C. 2019. PIrANHA v1.0.0. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/PIrANHA>.
  Stamatakis, A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of 
 	large phylogenies. Bioinformatics, 30, 1312-1313.
@@ -336,4 +336,4 @@ set -o pipefail
 RAxMLRunChecker
 
 # Exit cleanly
-safeExit
+safeExit
diff --git a/bin/MAGNET-1.0.0/shell/RAxMLRunChecker.sh b/bin/MAGNET-1.0.0/shell/RAxMLRunChecker.sh
@@ -136,7 +136,7 @@ function RAxMLRunChecker () {
 ##########################################################################################
 
 echo "INFO      | $(date) |----------------------------------------------------------------"
-echo "INFO      | $(date) | RAxMLRunChecker, v1.3.0 March 2019  (part of PIrANHA v1.0.0)   "
+echo "INFO      | $(date) | RAxMLRunChecker, v1.3.0 March 2019  (part of PIrANHA v0.2-alpha.2)   "
 echo "INFO      | $(date) | Copyright (c) 2018-2019 Justin C. Bagley. All rights reserved. "
 echo "INFO      | $(date) |----------------------------------------------------------------"
 
@@ -260,7 +260,7 @@ USAGE="Usage: $(basename $0) [OPTION]...
 
  ${bold}OVERVIEW${reset}
  THIS SCRIPT was designed to run in a current working directory where the MAGNET pipeline
- in PIrANHA v1.0.0 (Bagley 2019) is being run, or has completed a run, to estimate maximum-
+ in PIrANHA v0.2-alpha.2 (Bagley 2019) is being run, or has completed a run, to estimate maximum-
  likelihood (ML) gene trees in RAxML v8+ (Stamatakis 2014) for a set of loci from DNA 
  sequence data. Given such a workspace, this script counts the number of loci or data 
  partitions (each assigned a separate RAxML run in MAGNET) with completed RAxML runs and 
@@ -278,11 +278,11 @@ USAGE="Usage: $(basename $0) [OPTION]...
     piranha -f RAxMLRunChecker --args='-h'      Print this help text
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2019. PIrANHA v1.0.0. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/PIrANHA>.
 
  ${bold}REFERENCES${reset}
- Bagley, J.C. 2019. PIrANHA v1.0.0. GitHub repository, Available at:
+ Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at:
 	<https://github.com/justincbagley/PIrANHA>.
  Stamatakis, A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of 
 	large phylogenies. Bioinformatics, 30, 1312-1313.
@@ -336,4 +336,4 @@ set -o pipefail
 RAxMLRunChecker
 
 # Exit cleanly
-safeExit
+safeExit