From 6ae7614eeef9660f11ec01b11ffb23c4d1817a9c Mon Sep 17 00:00:00 2001 From: "Justin C. Bagley" Date: Tue, 9 Apr 2019 07:50:01 -0500 Subject: [PATCH] Updated PIrANHA versioning in function scripts Update in prep for v0.2-alpha.2 release --- bin/2logeB10.r | 2 +- bin/AnouraNEXUSPrepper | 4 ++-- bin/BEASTPostProc | 4 ++-- bin/BEASTReset | 6 +++--- bin/BEASTRunner | 6 +++--- bin/BEAST_PSPrepper | 4 ++-- bin/ExaBayesPostProc | 4 ++-- bin/FASTA2PHYLIP | 6 +++--- bin/FASTA2VCF | 4 ++-- bin/MAGNET-1.0.0/MAGNET | 6 +++--- bin/MAGNET-1.0.0/README.md | 4 ++-- bin/MAGNET-1.0.0/shell/NEXUS2gphocs | 6 +++--- bin/MAGNET-1.0.0/shell/NEXUS2gphocs.sh | 6 +++--- bin/MAGNET-1.0.0/shell/RAxMLRunChecker | 10 +++++----- bin/MAGNET-1.0.0/shell/RAxMLRunChecker.sh | 10 +++++----- bin/MAGNET-1.0.0/shell/getBootTrees | 10 +++++----- bin/MAGNET-1.0.0/shell/getBootTrees.sh | 10 +++++----- bin/MAGNET-1.0.0/shell/phyNcharSumm | 4 ++-- bin/MAGNET-1.0.0/shell/phyNcharSumm.sh | 4 ++-- bin/MLEResultsProc | 4 ++-- bin/Mega2PHYLIP | 4 ++-- bin/MrBayesPostProc | 4 ++-- bin/NEXUS2MultiPHYLIP | 4 ++-- bin/NEXUS2PHYLIP | 4 ++-- bin/PFSubsetSum | 4 ++-- bin/PHYLIP2FASTA | 4 ++-- bin/PHYLIP2Mega | 4 ++-- bin/PHYLIP2NEXUS | 4 ++-- bin/PHYLIP2PFSubsets | 4 ++-- bin/PHYLIPsubsampler | 4 ++-- bin/PhyloMapperNullProc | 2 +- bin/RAxMLRunChecker | 2 +- bin/RAxMLRunner | 4 ++-- bin/SNAPPRunner | 2 +- bin/SpeciesIdentifier | 4 ++-- bin/calcAlignmentPIS | 4 ++-- bin/completeConcatSeqs | 4 ++-- bin/completeSeqs | 4 ++-- bin/concatenateSeqs | 4 ++-- bin/dadiPostProc | 6 +++--- bin/dadiRunner | 6 +++--- bin/dadiUncertainty | 4 ++-- bin/dropRandomHap | 4 ++-- bin/fastSTRUCTURE | 4 ++-- bin/getBootTrees | 4 ++-- bin/getTaxonNames | 4 ++-- bin/makePartitions | 4 ++-- bin/phyNcharSumm | 4 ++-- bin/pyRAD2PartitionFinder | 4 ++-- bin/pyRADLocusVarSites | 4 ++-- bin/renameForStarBeast2 | 4 ++-- bin/taxonCompFilter | 4 ++-- bin/treeThinner | 4 ++-- bin/vcfSubsampler | 4 ++-- 54 files changed, 124 insertions(+), 124 deletions(-) diff --git a/bin/2logeB10.r b/bin/2logeB10.r index c48be624..17bf05fc 100644 --- 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 index 0df386d8..3b0f4bcd 100644 --- 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: . ${bold}REFERENCES${reset} diff --git a/bin/BEASTPostProc b/bin/BEASTPostProc index e3b1c7ff..91dafd99 100644 --- 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: . ${bold}REFERENCES${reset} diff --git a/bin/BEASTReset b/bin/BEASTReset index 7421fdc2..6f008894 100644 --- 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: . ${bold}REFERENCES${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: . Created by Justin Bagley on Thu, 24 Aug 2017 11:30:42 -0400. diff --git a/bin/BEASTRunner b/bin/BEASTRunner index 87432df4..2349d0b3 100644 --- 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: . ${bold}REFERENCES${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: . ${bold}REFERENCES${reset} diff --git a/bin/BEAST_PSPrepper b/bin/BEAST_PSPrepper index 1c3b3582..fb9174cf 100644 --- 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: . ${bold}REFERENCES${reset} diff --git a/bin/ExaBayesPostProc b/bin/ExaBayesPostProc index 9f7788b8..f81461b3 100644 --- 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: . ${bold}REFERENCES${reset} diff --git a/bin/FASTA2PHYLIP b/bin/FASTA2PHYLIP index 5f0b1a6b..2a0e851f 100644 --- 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: . ${bold}REFERENCES${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: . ${bold}REFERENCES${reset} diff --git a/bin/FASTA2VCF b/bin/FASTA2VCF index d23942f6..fceef3e4 100644 --- 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: . ${bold}REFERENCES${reset} diff --git a/bin/MAGNET-1.0.0/MAGNET b/bin/MAGNET-1.0.0/MAGNET index 9b4262d8..d681da73 100644 --- 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: . ${bold}REFERENCES${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: . ${bold}REFERENCES${reset} diff --git a/bin/MAGNET-1.0.0/README.md b/bin/MAGNET-1.0.0/README.md index 0e0cb2a2..07f14ecd 100644 --- 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: . ${bold}REFERENCES${reset} diff --git a/bin/MAGNET-1.0.0/shell/NEXUS2gphocs b/bin/MAGNET-1.0.0/shell/NEXUS2gphocs index 920e2c67..ff6e2650 100644 --- 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: . ${bold}REFERENCES${reset} @@ -402,4 +402,4 @@ set -o pipefail NEXUS2gphocs # Exit cleanly -safeExit \ No newline at end of file +safeExit diff --git a/bin/MAGNET-1.0.0/shell/NEXUS2gphocs.sh b/bin/MAGNET-1.0.0/shell/NEXUS2gphocs.sh index 920e2c67..ff6e2650 100644 --- 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: . ${bold}REFERENCES${reset} @@ -402,4 +402,4 @@ set -o pipefail NEXUS2gphocs # Exit cleanly -safeExit \ No newline at end of file +safeExit diff --git a/bin/MAGNET-1.0.0/shell/RAxMLRunChecker b/bin/MAGNET-1.0.0/shell/RAxMLRunChecker index cfdeb074..b14e2005 100644 --- 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: . ${bold}REFERENCES${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: . 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 \ No newline at end of file +safeExit diff --git a/bin/MAGNET-1.0.0/shell/RAxMLRunChecker.sh b/bin/MAGNET-1.0.0/shell/RAxMLRunChecker.sh index cfdeb074..b14e2005 100644 --- 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: . ${bold}REFERENCES${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: . 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 \ No newline at end of file +safeExit diff --git a/bin/MAGNET-1.0.0/shell/getBootTrees b/bin/MAGNET-1.0.0/shell/getBootTrees index 5731f76d..9999661f 100644 --- a/bin/MAGNET-1.0.0/shell/getBootTrees +++ b/bin/MAGNET-1.0.0/shell/getBootTrees @@ -136,7 +136,7 @@ function getBootTrees () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | getBootTrees, v1.0.0 March 2019 (part of PIrANHA v1.0.0) " +echo "INFO | $(date) | getBootTrees, v1.0.0 March 2019 (part of PIrANHA v0.2-alpha.2) " echo "INFO | $(date) | Copyright (c) 2017-2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -220,7 +220,7 @@ 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) has been run to estimate maximum-likelihood (ML) gene trees + in PIrANHA v0.2-alpha.2 (Bagley 2019) has been 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 organizes the bootstrap trees resulting from all RAxML runs, in subfolders of the current directory. The getBootTrees function is already run during the @@ -241,11 +241,11 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f getBootTrees --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: . ${bold}REFERENCES${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: . Stamatakis, A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312-1313. @@ -299,4 +299,4 @@ set -o pipefail getBootTrees # Exit cleanly -safeExit \ No newline at end of file +safeExit diff --git a/bin/MAGNET-1.0.0/shell/getBootTrees.sh b/bin/MAGNET-1.0.0/shell/getBootTrees.sh index 5731f76d..9999661f 100644 --- a/bin/MAGNET-1.0.0/shell/getBootTrees.sh +++ b/bin/MAGNET-1.0.0/shell/getBootTrees.sh @@ -136,7 +136,7 @@ function getBootTrees () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | getBootTrees, v1.0.0 March 2019 (part of PIrANHA v1.0.0) " +echo "INFO | $(date) | getBootTrees, v1.0.0 March 2019 (part of PIrANHA v0.2-alpha.2) " echo "INFO | $(date) | Copyright (c) 2017-2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -220,7 +220,7 @@ 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) has been run to estimate maximum-likelihood (ML) gene trees + in PIrANHA v0.2-alpha.2 (Bagley 2019) has been 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 organizes the bootstrap trees resulting from all RAxML runs, in subfolders of the current directory. The getBootTrees function is already run during the @@ -241,11 +241,11 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f getBootTrees --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: . ${bold}REFERENCES${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: . Stamatakis, A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312-1313. @@ -299,4 +299,4 @@ set -o pipefail getBootTrees # Exit cleanly -safeExit \ No newline at end of file +safeExit diff --git a/bin/MAGNET-1.0.0/shell/phyNcharSumm b/bin/MAGNET-1.0.0/shell/phyNcharSumm index dff5dbff..2a836b22 100644 --- a/bin/MAGNET-1.0.0/shell/phyNcharSumm +++ b/bin/MAGNET-1.0.0/shell/phyNcharSumm @@ -136,7 +136,7 @@ function phyNcharSumm () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | phyNcharSumm, v1.0.0 March 2019 (part of PIrANHA v1.0.0) " +echo "INFO | $(date) | phyNcharSumm, 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) |----------------------------------------------------------------" @@ -223,4 +223,4 @@ set -o pipefail phyNcharSumm # Exit cleanly -safeExit \ No newline at end of file +safeExit diff --git a/bin/MAGNET-1.0.0/shell/phyNcharSumm.sh b/bin/MAGNET-1.0.0/shell/phyNcharSumm.sh index dff5dbff..2a836b22 100644 --- a/bin/MAGNET-1.0.0/shell/phyNcharSumm.sh +++ b/bin/MAGNET-1.0.0/shell/phyNcharSumm.sh @@ -136,7 +136,7 @@ function phyNcharSumm () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | phyNcharSumm, v1.0.0 March 2019 (part of PIrANHA v1.0.0) " +echo "INFO | $(date) | phyNcharSumm, 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) |----------------------------------------------------------------" @@ -223,4 +223,4 @@ set -o pipefail phyNcharSumm # Exit cleanly -safeExit \ No newline at end of file +safeExit diff --git a/bin/MLEResultsProc b/bin/MLEResultsProc index 3185b2de..c5f5511a 100644 --- a/bin/MLEResultsProc +++ b/bin/MLEResultsProc @@ -137,7 +137,7 @@ MLEResultsProc () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | MLEResultsProc, v1.4.0 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | MLEResultsProc, v1.4.0 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) |----------------------------------------------------------------" @@ -337,7 +337,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f MLEResultsProc --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: . Created by Justin Bagley on Fri, 29 Jul 2016 11:21:37 -0300. diff --git a/bin/Mega2PHYLIP b/bin/Mega2PHYLIP index 67698923..45ea3671 100644 --- a/bin/Mega2PHYLIP +++ b/bin/Mega2PHYLIP @@ -136,7 +136,7 @@ Mega2PHYLIP () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | Mega2PHYLIP, v1.0.2 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | Mega2PHYLIP, v1.0.2 March 2019 (part of PIrANHA v0.2-alpha.2)" echo "INFO | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -377,7 +377,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f Mega2PHYLIP --args='-m1 -k 1' Convert multiple Mega files to PHYLIP, keeping original files ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/MrBayesPostProc b/bin/MrBayesPostProc index b36c2027..4930ec11 100644 --- a/bin/MrBayesPostProc +++ b/bin/MrBayesPostProc @@ -137,7 +137,7 @@ MrBayesPostProc () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | MrBayesPostProc, v1.6.0 March 2019 (in PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | MrBayesPostProc, v1.6.0 March 2019 (in PIrANHA v0.2-alpha.2)" echo "INFO | $(date) | Copyright (c) 2017–2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -384,7 +384,7 @@ USAGE="Usage: $(basename $0) [OPTION]... to MrBayesPostProc). ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/NEXUS2MultiPHYLIP b/bin/NEXUS2MultiPHYLIP index 1b176c33..9d05b287 100644 --- a/bin/NEXUS2MultiPHYLIP +++ b/bin/NEXUS2MultiPHYLIP @@ -138,7 +138,7 @@ NEXUS2MultiPHYLIP () { if [[ "$MY_VERBOSE_OUT_SWITCH" != "0" ]]; then echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | NEXUS2MultiPHYLIP, v1.5.3 March 2019 (in PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | NEXUS2MultiPHYLIP, v1.5.3 March 2019 (in PIrANHA v0.2-alpha.2)" echo "INFO | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" fi @@ -560,7 +560,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f NEXUS2MultiPHYLIP -a '-i -v 1' Same as above, but 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: . ${bold}REFERENCES${reset} diff --git a/bin/NEXUS2PHYLIP b/bin/NEXUS2PHYLIP index a380d013..bde110c7 100644 --- a/bin/NEXUS2PHYLIP +++ b/bin/NEXUS2PHYLIP @@ -136,7 +136,7 @@ NEXUS2PHYLIP () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | NEXUS2PHYLIP, v1.4.2 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | NEXUS2PHYLIP, v1.4.2 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) |----------------------------------------------------------------" @@ -419,7 +419,7 @@ VERBOSE_USAGE="Usage: $(basename $0) [OPTION]... piranha -f NEXUS2PHYLIP -a '-i -v 1 -k 1' Same as above, but 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: . ${bold}REFERENCES${reset} diff --git a/bin/PFSubsetSum b/bin/PFSubsetSum index 4b3f2d60..d4df2414 100644 --- a/bin/PFSubsetSum +++ b/bin/PFSubsetSum @@ -136,7 +136,7 @@ PFSubsetSum () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | PFSubsetSum, v1.3.3 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | PFSubsetSum, v1.3.3 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) |----------------------------------------------------------------" @@ -291,7 +291,7 @@ if [[ "$1" == "-V" ]] || [[ "$1" == "--version" ]]; then fi if [[ "$1" == "-citation" ]] || [[ "$1" == "--citation" ]]; then - echo " Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at: + echo " Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at: . " exit diff --git a/bin/PHYLIP2FASTA b/bin/PHYLIP2FASTA index d6462257..3ee43fb1 100644 --- a/bin/PHYLIP2FASTA +++ b/bin/PHYLIP2FASTA @@ -136,7 +136,7 @@ PHYLIP2FASTA () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | PHYLIP2FASTA, v1.1.2 March 2019 (in PIrANHA v0.2-alpha.1c) " +echo "INFO | $(date) | PHYLIP2FASTA, v1.1.2 March 2019 (in PIrANHA v0.2-alpha.2) " echo "INFO | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -260,7 +260,7 @@ USAGE="Usage: $(basename $0) [OPTION]... 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: . ${bold}REFERENCES${reset} diff --git a/bin/PHYLIP2Mega b/bin/PHYLIP2Mega index a2d06b0a..3fca2f62 100644 --- a/bin/PHYLIP2Mega +++ b/bin/PHYLIP2Mega @@ -135,7 +135,7 @@ PHYLIP2Mega () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | PHYLIP2Mega, v1.1.2 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | PHYLIP2Mega, v1.1.2 March 2019 (part of PIrANHA v0.2-alpha.2)" echo "INFO | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -355,7 +355,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f PHYLIP2Mega --args='-m1 -k 1' Convert multiple PHYLIP files to Mega, keeping original files ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/PHYLIP2NEXUS b/bin/PHYLIP2NEXUS index 7b4efc53..0b2f846d 100644 --- a/bin/PHYLIP2NEXUS +++ b/bin/PHYLIP2NEXUS @@ -136,7 +136,7 @@ PHYLIP2NEXUS () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | PHYLIP2NEXUS, v1.1.5 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | PHYLIP2NEXUS, v1.1.5 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) |----------------------------------------------------------------" @@ -298,7 +298,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f PHYLIP2NEXUS --args='-i -p -f SVDquartets' ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/PHYLIP2PFSubsets b/bin/PHYLIP2PFSubsets index bdd16237..9cb4c766 100644 --- a/bin/PHYLIP2PFSubsets +++ b/bin/PHYLIP2PFSubsets @@ -137,7 +137,7 @@ PHYLIP2PFSubsets () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | PHYLIP2PFSubsets, v1.0.1 March 2019 (in PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | PHYLIP2PFSubsets, v1.0.1 March 2019 (in PIrANHA v0.2-alpha.2)" echo "INFO | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -450,7 +450,7 @@ USAGE="Usage: $(basename $0) [OPTION]... files must have the extension '.phy'. ${bold}CITATION${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: . Created by Justin Bagley on Tue, Mar 5 09:53:04 CST 2019. diff --git a/bin/PHYLIPsubsampler b/bin/PHYLIPsubsampler index dd6e0f8f..08c66aeb 100644 --- a/bin/PHYLIPsubsampler +++ b/bin/PHYLIPsubsampler @@ -139,7 +139,7 @@ PHYLIPsubsampler () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | PHYLIPsubsampler, v1.1.4 March 2019 (in PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | PHYLIPsubsampler, v1.1.4 March 2019 (in PIrANHA v0.2-alpha.2)" echo "INFO | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -342,7 +342,7 @@ USAGE="Usage: $(basename $0) [OPTION]... specified assignment file 'species.txt' ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/PhyloMapperNullProc b/bin/PhyloMapperNullProc index 2b2e3901..bdf4bbc7 100644 --- a/bin/PhyloMapperNullProc +++ b/bin/PhyloMapperNullProc @@ -220,7 +220,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f PhyloMapperNullProc --args='-h' Print the 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: . ${bold}REFERENCES${reset} diff --git a/bin/RAxMLRunChecker b/bin/RAxMLRunChecker index 2f482ae5..4c17c495 100644 --- a/bin/RAxMLRunChecker +++ b/bin/RAxMLRunChecker @@ -278,7 +278,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f RAxMLRunChecker --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: . ${bold}REFERENCES${reset} diff --git a/bin/RAxMLRunner b/bin/RAxMLRunner index dbb7ab5e..c532046e 100644 --- a/bin/RAxMLRunner +++ b/bin/RAxMLRunner @@ -137,7 +137,7 @@ RAxMLRunner () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | RAxMLRunner, v1.4.1 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | RAxMLRunner, v1.4.1 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) |----------------------------------------------------------------" @@ -316,7 +316,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f RAxMLRunner --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: . ${bold}REFERENCES${reset} diff --git a/bin/SNAPPRunner b/bin/SNAPPRunner index 6bf43571..6cc4c2b2 100644 --- a/bin/SNAPPRunner +++ b/bin/SNAPPRunner @@ -640,7 +640,7 @@ VERBOSE_USAGE="Usage: $(basename $0) [OPTION]... piranha -f SNAPPRunner --args='-n 10 -w 24:00:00 -m 2048M' Also increase the default walltime and memory (RAM) settings ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/SpeciesIdentifier b/bin/SpeciesIdentifier index 91d59fbf..136e3760 100644 --- a/bin/SpeciesIdentifier +++ b/bin/SpeciesIdentifier @@ -136,7 +136,7 @@ SpeciesIdentifier () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | SpeciesIdentifier, v1.0.0 March 2019 (in PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | SpeciesIdentifier, 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) |----------------------------------------------------------------" @@ -306,7 +306,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f SpeciesIdentifier -a '-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: . ${bold}REFERENCES${reset} diff --git a/bin/calcAlignmentPIS b/bin/calcAlignmentPIS index 50a40f8d..37a09e15 100644 --- a/bin/calcAlignmentPIS +++ b/bin/calcAlignmentPIS @@ -136,7 +136,7 @@ calcAlignmentPIS () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | calcAlignmentPIS, v1.4.0 March 2019 (in PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | calcAlignmentPIS, v1.4.0 March 2019 (in PIrANHA v0.2-alpha.2)" echo "INFO | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -331,7 +331,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f calcAlignmentPIS -a '-t 150' 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: . ${bold}REFERENCES${reset} diff --git a/bin/completeConcatSeqs b/bin/completeConcatSeqs index 020f75e1..6af6d405 100644 --- a/bin/completeConcatSeqs +++ b/bin/completeConcatSeqs @@ -137,7 +137,7 @@ completeConcatSeqs () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | completeConcatSeqs, v1.0.0 March 2019 (in PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | completeConcatSeqs, 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) |----------------------------------------------------------------" @@ -383,7 +383,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f completeConcatSeqs --args='-t taxon_name_spaces12.txt -v 1' ${bold}CITATION${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: . Created by Justin Bagley on Tue, Mar 12 19:11:08 CDT 2019. diff --git a/bin/completeSeqs b/bin/completeSeqs index 3eef77d5..dec8ba6a 100644 --- a/bin/completeSeqs +++ b/bin/completeSeqs @@ -141,7 +141,7 @@ completeSeqs () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | completeSeqs, v1.0.0 March 2019 (in PIrANHA v0.2-alpha.1c) " +echo "INFO | $(date) | completeSeqs, 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) |----------------------------------------------------------------" @@ -326,7 +326,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f completeSeqs --args='-t taxon_name_spaces12.txt' ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/concatenateSeqs b/bin/concatenateSeqs index ca2a9fe6..715f3d81 100644 --- a/bin/concatenateSeqs +++ b/bin/concatenateSeqs @@ -136,7 +136,7 @@ concatenateSeqs () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | concatenateSeqs, v1.0.0 March 2019 (in PIrANHA v0.2-alpha.1c) " +echo "INFO | $(date) | concatenateSeqs, 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) |----------------------------------------------------------------" @@ -318,7 +318,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f concatenateSeqs --args='-t taxon_name_spaces12.txt' ${bold}CITATION${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: . Created by Justin Bagley on Tue, Mar 12 21:23:30 CDT 2019. diff --git a/bin/dadiPostProc b/bin/dadiPostProc index 742389f0..aa1d8a78 100644 --- a/bin/dadiPostProc +++ b/bin/dadiPostProc @@ -137,7 +137,7 @@ dadiPostProc () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | dadiPostProc, v1.0.0 March 2019 (in PIrANHA v0.2-alpha.1c) " +echo "INFO | $(date) | dadiPostProc, 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) |----------------------------------------------------------------" @@ -413,7 +413,7 @@ USAGE="Usage: $(basename $0) [OPTION]... ranges starting from values other than 1 ${bold}CITATION${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: . ${bold}REFERENCES${reset} @@ -465,7 +465,7 @@ VERBOSE_USAGE="Usage: $(basename $0) [OPTION]... ranges starting from values other than 1 ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/dadiRunner b/bin/dadiRunner index a6166fa1..3c947a06 100644 --- a/bin/dadiRunner +++ b/bin/dadiRunner @@ -135,7 +135,7 @@ dadiRunner () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | dadiRunner, v1.0.0 March 2019 (in PIrANHA v0.2-alpha.1c) " +echo "INFO | $(date) | dadiRunner, 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) |----------------------------------------------------------------" @@ -421,7 +421,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f dadiRunner --args='-i -n 20 -w 24:00:00' Changing run walltime. ${bold}CITATION${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: . ${bold}REFERENCES${reset} @@ -497,7 +497,7 @@ VERBOSE_USAGE="Usage: $(basename $0) [OPTION]... piranha -f dadiRunner --args='-i -n 20 -w 24:00:00' Changing run walltime. ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/dadiUncertainty b/bin/dadiUncertainty index 072641e4..f2c5ada0 100644 --- a/bin/dadiUncertainty +++ b/bin/dadiUncertainty @@ -137,7 +137,7 @@ dadiUncertainty () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | dadiUncertainty, v1.0.0 March 2019 (in PIrANHA v0.2-alpha.1c) " +echo "INFO | $(date) | dadiUncertainty, 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) |----------------------------------------------------------------" @@ -969,7 +969,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f dadiUncertainty --args='-a assignments.txt -i \'LP\',\'core\',\'periphery\' -p 98,46,156 -n 250 -m 2 -s M4.py -e 0.72828532,0.29458734,0.96806661,5.30191219,6.90827885,4.35076242,8.80921022,0.0349316,0.00881585 55Pops.recode.6330IDs.vcf' ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/dropRandomHap b/bin/dropRandomHap index 00da6c10..e5b006b5 100644 --- a/bin/dropRandomHap +++ b/bin/dropRandomHap @@ -142,7 +142,7 @@ dropRandomHap () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | dropRandomHap, v1.4.0 March 2019 (in PIrANHA v0.2-alpha.1c) " +echo "INFO | $(date) | dropRandomHap, v1.4.0 March 2019 (in PIrANHA v0.2-alpha.2) " echo "INFO | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -367,7 +367,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f dropRandomHap --args='-t ' ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/fastSTRUCTURE b/bin/fastSTRUCTURE index 03e1c33f..db47ab44 100644 --- a/bin/fastSTRUCTURE +++ b/bin/fastSTRUCTURE @@ -136,7 +136,7 @@ fastSTRUCTURE () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | fastSTRUCTURE, v1.1.2 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | fastSTRUCTURE, v1.1.2 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) |----------------------------------------------------------------" @@ -222,7 +222,7 @@ USAGE="Usage: $(basename $0) [OPTION]... including Python, and automatically generates random number seeds. ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/getBootTrees b/bin/getBootTrees index 9922cedd..74168adc 100644 --- a/bin/getBootTrees +++ b/bin/getBootTrees @@ -136,7 +136,7 @@ getBootTrees () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | getBootTrees, v1.0.0 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | getBootTrees, v1.0.0 March 2019 (part of PIrANHA v0.2-alpha.2)" echo "INFO | $(date) | Copyright (c) 2017-2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -241,7 +241,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f getBootTrees --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: . ${bold}REFERENCES${reset} diff --git a/bin/getTaxonNames b/bin/getTaxonNames index d8e402e0..86eee67c 100644 --- a/bin/getTaxonNames +++ b/bin/getTaxonNames @@ -136,7 +136,7 @@ getTaxonNames () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | getTaxonNames, v1.0.0 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | getTaxonNames, v1.0.0 March 2019 (part of PIrANHA v0.2-alpha.2)" echo "INFO | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -246,7 +246,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f getTaxonNames --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: . Created by Justin Bagley on Wed, Mar 13 17:17:41 CDT 2019. diff --git a/bin/makePartitions b/bin/makePartitions index 0b865347..de8716a1 100644 --- a/bin/makePartitions +++ b/bin/makePartitions @@ -145,7 +145,7 @@ makePartitions () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | makePartitions, v1.2.1 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | makePartitions, v1.2.1 March 2019 (part of PIrANHA v0.2-alpha.2)" echo "INFO | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -303,7 +303,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f makePartitions --args='-h' Get this makePartitions-specific 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: . ${bold}REFERENCES${reset} diff --git a/bin/phyNcharSumm b/bin/phyNcharSumm index 80c87ebe..01e4aef4 100644 --- a/bin/phyNcharSumm +++ b/bin/phyNcharSumm @@ -136,7 +136,7 @@ phyNcharSumm () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | phyNcharSumm, v1.0.0 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | phyNcharSumm, 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) |----------------------------------------------------------------" @@ -189,7 +189,7 @@ if [[ "$1" == "-V" ]] || [[ "$1" == "--version" ]]; then fi if [[ "$1" == "-citation" ]] || [[ "$1" == "--citation" ]]; then - echo " Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at: + echo " Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at: . " exit diff --git a/bin/pyRAD2PartitionFinder b/bin/pyRAD2PartitionFinder index 3f051a41..73b3833f 100644 --- a/bin/pyRAD2PartitionFinder +++ b/bin/pyRAD2PartitionFinder @@ -136,7 +136,7 @@ pyRAD2PartitionFinder () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | pyRAD2PartitionFinder, v1.2.3 March 2019 (in PIrANHA v0.2-alpha.1c) " +echo "INFO | $(date) | pyRAD2PartitionFinder, v1.2.3 March 2019 (in PIrANHA v0.2-alpha.2) " echo "INFO | $(date) | Copyright (c) 2016-2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -389,7 +389,7 @@ USAGE="Usage: $(basename $0) [OPTION]... by pyRAD, the -s setting is set to rcluster by default. ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/pyRADLocusVarSites b/bin/pyRADLocusVarSites index 759445f1..3f37a568 100644 --- a/bin/pyRADLocusVarSites +++ b/bin/pyRADLocusVarSites @@ -140,7 +140,7 @@ pyRADLocusVarSites () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | pyRADLocusVarSites, v1.0.0 March 2019 (in PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | pyRADLocusVarSites, 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) |----------------------------------------------------------------" @@ -258,7 +258,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f pyRADLocusVarSites ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/renameForStarBeast2 b/bin/renameForStarBeast2 index 52cbac70..9dbed8e7 100644 --- a/bin/renameForStarBeast2 +++ b/bin/renameForStarBeast2 @@ -146,7 +146,7 @@ renameForStarBEAST2 () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | renameForStarBEAST2, v1.2.2 March 2019 (in PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | renameForStarBEAST2, v1.2.2 March 2019 (in PIrANHA v0.2-alpha.2)" echo "INFO | $(date) | Copyright (c) 2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -272,7 +272,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f renameForStarBEAST2 --args='-f phylip -a assignment.txt' ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/taxonCompFilter b/bin/taxonCompFilter index 72eff529..6e5954e3 100644 --- a/bin/taxonCompFilter +++ b/bin/taxonCompFilter @@ -136,7 +136,7 @@ taxonCompFilter () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | taxonCompFilter, v1.0.0 March 2019 (in PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | taxonCompFilter, 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) |----------------------------------------------------------------" @@ -319,7 +319,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f taxonCompFilter --args='-p 1 -n 43 -t 0.75' Empirical 75% taxon sampling example ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/treeThinner b/bin/treeThinner index c1fbea3d..7b9e1d3c 100644 --- a/bin/treeThinner +++ b/bin/treeThinner @@ -148,7 +148,7 @@ treeThinner () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | treeThinner, v1.2.1 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | treeThinner, v1.2.1 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) |----------------------------------------------------------------" @@ -206,7 +206,7 @@ USAGE="Usage: $(basename $0) [OPTION]... b) detect tree file type, and c) conduct thinning. ${bold}CITATION${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: . ${bold}REFERENCES${reset} diff --git a/bin/vcfSubsampler b/bin/vcfSubsampler index c1860f36..21c60fda 100644 --- a/bin/vcfSubsampler +++ b/bin/vcfSubsampler @@ -136,7 +136,7 @@ vcfSubsampler () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | vcfSubsampler, v0.2.1 March 2019 (part of PIrANHA v0.2-alpha.1c)" +echo "INFO | $(date) | vcfSubsampler, v0.2.1 March 2019 (part of PIrANHA v0.2-alpha.2)" echo "INFO | $(date) | Copyright (c) 2017-2019 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -202,7 +202,7 @@ USAGE="Usage: $(basename $0) [OPTION]... piranha -f vcfSubsampler --args='-i -s ' ${bold}CITATION${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: . Created by Justin Bagley on Thu, Sep 28 09:31:25 2017 -0400.