Implements #39

lentendu · Sep 14, 2018 · d36a4f6 · d36a4f6
1 parent f915196
commit d36a4f6
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Showing 34 changed files with 573 additions and 12 deletions.
diff --git a/auxiliary_scripts/update_FUNGuild.sh b/auxiliary_scripts/update_FUNGuild.sh
@@ -1,5 +1,23 @@
 #!/bin/bash
 
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 if [ -z "$1" ]
 then
 	echo "usage: ${0##*/} TARGET_DIRECTORY"

diff --git a/auxiliary_scripts/update_PR2.sh b/auxiliary_scripts/update_PR2.sh
@@ -1,5 +1,23 @@
 #!/bin/bash
 
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 if [ -z "$1" ] || [ -z "$2" ]
 then
 	echo "usage: ${0##*/} VERSION TARGET_DIRECTORY"

diff --git a/auxiliary_scripts/update_UNITE.sh b/auxiliary_scripts/update_UNITE.sh
@@ -1,5 +1,23 @@
 #!/bin/bash
 
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 if [ -z "$1" ] || [ -z "$2" ] || [ -z "$3" ]
 then
 	echo "usage: ${0##*/} RELEASE_DATE MOTHUR_DOI TARGET_DIRECTORY [UTAX_DOI]"

diff --git a/auxiliary_scripts/update_silva.sh b/auxiliary_scripts/update_silva.sh
@@ -1,5 +1,23 @@
 #!/bin/bash
 
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 if [ -z "$1" ] || [ -z "$2" ]
 then
 	echo "usage: ${0##*/} VERSION TARGET_DIRECTORY"

diff --git a/bin/barcode_mismatch_check.sh b/bin/barcode_mismatch_check.sh
@@ -1,13 +1,29 @@
 #!/bin/bash
 
-# author: Guillaume Lentendu (guillaume.lentendu@ufz.de)
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
 
-	if [ -z "$1" ]; then 
-		echo usage: $0 MOTHUR-oligo-file
-		echo "Determine the allowed amount of mismatches (only indels checked) to use for demultiplexing a 454 library (from 0 to 2)"
-		exit
+if [ -z "$1" ]; then 
+	echo usage: $0 MOTHUR-oligo-file
+	echo "Determine the allowed amount of mismatches (only indels checked) to use for demultiplexing a 454 library (from 0 to 2)"
+	exit
 
-	fi
+fi
 
 OLIGO=$1 ; shift
 BAR=(`awk '$1~"barcode"{print $2}' $OLIGO | sed 's/\(.\)/\1#/g;s/#$//' | tr "\n" " " | sed 's/$/\n/'`)

diff --git a/bin/check_barcodes.sh b/bin/check_barcodes.sh
@@ -1,5 +1,23 @@
 #!/bin/bash
 
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 LIB_ALL=($@)
 
 echo "Library Raw_reads_count Raw_reads_with_forward_primer Raw_reads_with_one_of_the_provided_barcode Provided_barcode_count Found_barcodes_with_forward_primer_in_library Average_read_count_per_provided_barcodes Unused_provided_barcode(s) Unused_barcode(s)_with_forward_primer_in_library" | tr " " "," | tr "_" " "

diff --git a/bin/make_doc.sh b/bin/make_doc.sh
@@ -1,5 +1,23 @@
 #!/bin/bash
 
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 ## Documentation
 declare -a TITLE=("Input data" "Pipeline execution" "Benchmarking" "Demultiplexing" "Quality check" "High quality reads processing" "Outputs" "References" "Raw reads extraction")
 

diff --git a/bin/twofasta b/bin/twofasta
@@ -1,6 +1,4 @@
 #!/bin/bash
 
-# author: Guillaume Lentendu (guillaume.lentendu@ufz.de)
-
 fasta=$@
 sed '/>/G' $fasta |  sed -e :a -e '$!N;/>/!s/\n//;ta' -e 'P;D'
diff --git a/src/454_demulti.step b/src/454_demulti.step
@@ -1,3 +1,21 @@
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 # Define Variables
 while read var val; do unset $var ; if [[ $val == "(["* ]]; then declare -A $var="`echo $val | sed 's/].\"/]=\"/g'`" ; else declare $var="$val" ; fi ; done < config/env.txt
 . $BIN/check_previous_step

diff --git a/src/454_opt.step b/src/454_opt.step
@@ -1,3 +1,21 @@
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 # Define Variables
 while read var val; do unset $var ; if [[ $val == "(["* ]]; then declare -A $var="`echo $val | sed 's/].\"/]=\"/g'`" ; else declare $var="$val" ; fi ; done < config/env.txt
 . $BIN/check_previous_step

diff --git a/src/454_quality.step b/src/454_quality.step
@@ -1,3 +1,21 @@
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 # Define Variables
 while read var val; do unset $var ; if [[ $val == "(["* ]]; then declare -A $var="`echo $val | sed 's/].\"/]=\"/g'`" ; else declare $var="$val" ; fi ; done < config/env.txt
 . $BIN/check_previous_step

diff --git a/src/454_raw_stat.step b/src/454_raw_stat.step
@@ -1,3 +1,21 @@
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 # Define Variables
 while read var val; do unset $var ; if [[ $val == "(["* ]]; then declare -A $var="`echo $val | sed 's/].\"/]=\"/g'`" ; else declare $var="$val" ; fi ; done < config/env.txt
 . $BIN/check_previous_step

diff --git a/src/454_sff.step b/src/454_sff.step
@@ -1,3 +1,21 @@
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 # Define Variables
 while read var val; do unset $var ; if [[ $val == "(["* ]]; then declare -A $var="`echo $val | sed 's/].\"/]=\"/g'`" ; else declare $var="$val" ; fi ; done < config/env.txt
 . $BIN/check_previous_step

diff --git a/src/Illumina_demulti.step b/src/Illumina_demulti.step
@@ -1,3 +1,21 @@
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 # Define Variables
 while read var val; do unset $var ; if [[ $val == "(["* ]]; then declare -A $var="`echo $val | sed 's/].\"/]=\"/g'`" ; else declare $var="$val" ; fi ; done < config/env.txt
 . $BIN/check_previous_step

diff --git a/src/Illumina_fastq.step b/src/Illumina_fastq.step
@@ -1,3 +1,21 @@
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 # Define Variables
 while read var val; do unset $var ; if [[ $val == "(["* ]]; then declare -A $var="`echo $val | sed 's/].\"/]=\"/g'`" ; else declare $var="$val" ; fi ; done < config/env.txt
 . $BIN/check_previous_step

diff --git a/src/Illumina_opt.step b/src/Illumina_opt.step
@@ -1,3 +1,21 @@
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 # Define Variables
 while read var val; do unset $var ; if [[ $val == "(["* ]]; then declare -A $var="`echo $val | sed 's/].\"/]=\"/g'`" ; else declare $var="$val" ; fi ; done < config/env.txt
 . $BIN/check_previous_step

diff --git a/src/Illumina_pair_end.step b/src/Illumina_pair_end.step
@@ -1,3 +1,21 @@
+# 
+# DeltaMP, a flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
+# Copyright (C) 2018 Guillaume Lentendu, Christina Weißbecker, Anna Heintz-Buschart, Tesfaye Wubet
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 
+
 # Define Variables
 while read var val; do unset $var ; if [[ $val == "(["* ]]; then declare -A $var="`echo $val | sed 's/].\"/]=\"/g'`" ; else declare $var="$val" ; fi ; done < config/env.txt
 . $BIN/check_previous_step