From 01af1534661cdffd8919e8f2420bb488b097e52a Mon Sep 17 00:00:00 2001 From: "Justin C. Bagley" Date: Wed, 16 Dec 2020 23:48:24 -0600 Subject: [PATCH] Updating piranha path in scripts Updating piranha path in scripts --- bin/FASTAsummary | 11 ++++++----- bin/alignAlleles | 8 ++++---- 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/bin/FASTAsummary b/bin/FASTAsummary index f851045a..07ead7a4 100755 --- a/bin/FASTAsummary +++ b/bin/FASTAsummary @@ -6,10 +6,10 @@ # | # # # # File: FASTAsummary.sh # - VERSION="v1.1.3" # + VERSION="v1.1.4" # # Author: Justin C. Bagley # # Date: Created by Justin Bagley on Fri, Apr 3 00:03:39 EDT 2020. # -# Last update: December 15, 2020 # +# Last update: December 16, 2020 # # Copyright (c) 2020 Justin C. Bagley. All rights reserved. # # Please report bugs to . # # # @@ -136,7 +136,7 @@ FASTAsummary () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" -echo "INFO | $(date) | FASTAsummary, v1.1.3 December 2020 " +echo "INFO | $(date) | FASTAsummary, v1.1.4 December 2020 " echo "INFO | $(date) | Copyright (c) 2020 Justin C. Bagley. All rights reserved. " echo "INFO | $(date) |----------------------------------------------------------------" @@ -227,7 +227,8 @@ if [[ "$INPUT_FASTA_FILE" != "NULL" ]] && [[ -s "$INPUT_FASTA_FILE" ]]; then ### RUN calcAlignmentPIS PIrANHA FUNCTION TO GET PARSIMONY-INFORMATIVE SITES FOR THE ### INPUT FASTA (TESTING WITH SINGLE INPUT FASTA) - MY_PIRANHA_PATH="$(echo ${SCRIPT_PATH}/../piranha | sed 's/bin\/\.\.\///g')"; + MY_PIRANHA_PATH="$(echo ${SCRIPT_PATH}/../piranha.sh | sed 's/bin\/\.\.\///g')"; + echo "INFO | $(date) | piranha path: $MY_PIRANHA_PATH" echo "#!/bin/sh @@ -318,7 +319,7 @@ count=1 ### RUN calcAlignmentPIS PIrANHA FUNCTION TO GET PARSIMONY-INFORMATIVE SITES FOR ### MULTIPLE FASTA FILES IN CURRENT WORKING DIRECTORY - MY_PIRANHA_PATH="$(echo ${SCRIPT_PATH}/../piranha | sed 's/bin\/\.\.\///g')"; + MY_PIRANHA_PATH="$(echo ${SCRIPT_PATH}/../piranha.sh | sed 's/bin\/\.\.\///g')"; echo "INFO | $(date) | piranha path: $MY_PIRANHA_PATH" echo "#!/bin/sh diff --git a/bin/alignAlleles b/bin/alignAlleles index 1b0a5fd1..553d9841 100755 --- a/bin/alignAlleles +++ b/bin/alignAlleles @@ -6,10 +6,10 @@ # | # # # # File: alignAlleles.sh # - VERSION="v1.0.3" # + VERSION="v1.0.4" # # Author: Justin C. Bagley # # Date: Created by Justin Bagley on Fri, Apr 17 13:59:38 CDT 2020. # -# Last update: December 1, 2020 # +# Last update: December 16, 2020 # # Copyright (c) 2020 Justin C. Bagley. All rights reserved. # # Please report bugs to . # # # @@ -137,7 +137,7 @@ alignAlleles () { ########################################################################################## echo "INFO | $(date) |----------------------------------------------------------------" | tee -a "$MY_LOGFILE_SWITCH" -echo "INFO | $(date) | alignAlleles, v1.0.3 December 2020 " | tee -a "$MY_LOGFILE_SWITCH" +echo "INFO | $(date) | alignAlleles, v1.0.4 December 2020 " | tee -a "$MY_LOGFILE_SWITCH" echo "INFO | $(date) | Copyright (c) 2020 Justin C. Bagley. All rights reserved. " | tee -a "$MY_LOGFILE_SWITCH" echo "INFO | $(date) |----------------------------------------------------------------" | tee -a "$MY_LOGFILE_SWITCH" @@ -597,7 +597,7 @@ count=1 cd ./FASTAsummary/ ; echo "INFO | $(date) | Current dir: $PWD" | tee -a "$MY_INPUT_DIR""$MY_LOGFILE_SWITCH" - MY_PIRANHA_PATH="$(echo ${SCRIPT_PATH}/../piranha | sed 's/bin\/\.\.\///g')"; + MY_PIRANHA_PATH="$(echo ${SCRIPT_PATH}/../piranha.sh | sed 's/bin\/\.\.\///g')"; echo "INFO | $(date) | piranha path: $MY_PIRANHA_PATH" | tee -a "$MY_INPUT_DIR""$MY_LOGFILE_SWITCH" echo "#!/bin/sh