v.1.4.2.

tomas-fer · May 31, 2017 · 4c4c643 · 4c4c643
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diff --git a/HybPhyloMaker0a_preparedata.sh b/HybPhyloMaker0a_preparedata.sh
@@ -19,7 +19,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                     Script 0a - Download & prepare data                      *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/HybPhyloMaker0b_preparereference.sh b/HybPhyloMaker0b_preparereference.sh
@@ -18,7 +18,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                     Script 0b - Prepare pseudoreference                      *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/HybPhyloMaker0c_Rsetup_MetaCentrum.sh b/HybPhyloMaker0c_Rsetup_MetaCentrum.sh
@@ -9,7 +9,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                 Script 0c - Setup R packages on Metacentrum                  *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/HybPhyloMaker1_rawprocess.sh b/HybPhyloMaker1_rawprocess.sh
@@ -18,7 +18,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                        Script 01 - Raw data processing                       *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # * based on Weitemier et al. (2014), Applications in Plant Science 2(9): 1400042*
@@ -179,12 +179,12 @@ do
 	#Adapter and general quality trimming
 	echo "Adapter removal & quality trimming..."
 	if [[ $location == "1" ]]; then
-		java -jar /software/trimmomatic-0.32/dist/jar/trimmomatic-0.32.jar PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../NEBNext-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1
+		java -jar /software/trimmomatic-0.32/dist/jar/trimmomatic-0.32.jar PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../${adapterfile}:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1
 		#trimmomatic PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../NEBNext-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1
 	elif [[ $location == "2" ]]; then
-		java -d64 -server -XX:MaxHeapSize=10g -jar ../trimmomatic-0.33.jar PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../NEBNext-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1
+		java -d64 -server -XX:MaxHeapSize=10g -jar ../trimmomatic-0.33.jar PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../${adapterfile}:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1
 	else
-		java -jar ../trimmomatic-0.33.jar PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../NEBNext-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1
+		java -jar ../trimmomatic-0.33.jar PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../${adapterfile}:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1
 	fi	
 	#Copy trimmed reads to home
 	if [[ $location == "1" ]]; then

diff --git a/HybPhyloMaker3_generatepslx.sh b/HybPhyloMaker3_generatepslx.sh
@@ -18,7 +18,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *         Script 03 - Process consensus after mapping, make pslx files         *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # * based on Weitemier et al. (2014), Applications in Plant Science 2(9): 1400042*

diff --git a/HybPhyloMaker4_processpslx.sh b/HybPhyloMaker4_processpslx.sh
@@ -20,7 +20,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                        Script 04 - Process pslx files                        *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # * based on Weitemier et al. (2014), Applications in Plant Science 2(9): 1400042*

diff --git a/HybPhyloMaker4b_correctframe_translate.sh b/HybPhyloMaker4b_correctframe_translate.sh
@@ -8,7 +8,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *       Script 04b - Put exons to correct reading frame and translate          *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/HybPhyloMaker5_missingdataremoval.sh b/HybPhyloMaker5_missingdataremoval.sh
@@ -19,7 +19,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                      Script 05 - Missing data handling                       *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************
@@ -243,7 +243,7 @@ do
 		#Calculate percentage of missing data as integer (for evaluation in bash)
 		percentage=$(echo -e "scale=0;($count * 100) / $y" | bc)
 		echo -e "$header\t$percentageprint" >> ${file}_${MISSINGPERCENT}percN.fas
-		if [ "$percentage" -lt "$MISSINGPERCENT" ]; then
+		if [ "$percentage" -le "$MISSINGPERCENT" ]; then
 			echo "$line" >> ${file}_modif${MISSINGPERCENT}.fas
 		else
 			echo -e "Deleting $header with $percentageprint of missing data"

diff --git a/HybPhyloMaker6a2_RAxML_trees_summary.sh b/HybPhyloMaker6a2_RAxML_trees_summary.sh
@@ -19,7 +19,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                  Script 06a2 - summary of RAxML gene trees                   *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/HybPhyloMaker6a_RAxML_for_selected.sh b/HybPhyloMaker6a_RAxML_for_selected.sh
@@ -17,7 +17,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                    Script 06a - RAxML gene tree building                     *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/HybPhyloMaker6b_FastTree_for_selected.sh b/HybPhyloMaker6b_FastTree_for_selected.sh
@@ -18,7 +18,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                   Script 06b - FastTree gene tree building                   *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/HybPhyloMaker7_roottrees.sh b/HybPhyloMaker7_roottrees.sh
@@ -17,7 +17,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                          Script 07 - Root gene trees                         *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/HybPhyloMaker8a_astral.sh b/HybPhyloMaker8a_astral.sh
@@ -18,7 +18,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                       Script 08a - Astral species tree                       *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/HybPhyloMaker8b_astrid.sh b/HybPhyloMaker8b_astrid.sh
@@ -19,7 +19,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                       Script 08b - Astrid species tree                       *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/HybPhyloMaker8c_mrl.sh b/HybPhyloMaker8c_mrl.sh
@@ -18,7 +18,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                        Script 08c - MRL species tree                         *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/HybPhyloMaker8e_concatenatedFastTree.sh b/HybPhyloMaker8e_concatenatedFastTree.sh
@@ -18,7 +18,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                    Script 08e - concatenated species tree                    *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/HybPhyloMaker8f_concatenatedExaML.sh b/HybPhyloMaker8f_concatenatedExaML.sh
@@ -8,7 +8,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                     Script 08f - ExaML concatenated tree                     *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/HybPhyloMaker9_update_trees.sh b/HybPhyloMaker9_update_trees.sh
@@ -18,7 +18,7 @@
 # ********************************************************************************
 # *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
 # *                           Script 09 - Update trees                           *
-# *                                   v.1.4.1                                    *
+# *                                   v.1.4.2                                    *
 # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
 # * [email protected]                                                      *
 # ********************************************************************************

diff --git a/install_software.sh b/install_software.sh
@@ -8,7 +8,7 @@
 # Tomas Fer, 2017                                                                                                        #
 # [email protected]                                                                                                #
 # https://github.com/tomas-fer/HybPhyloMaker                                                                             #
-# v.1.4.0                                                                                                                #
+# v.1.4.2                                                                                                                #
 ##########################################################################################################################
 
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