miga-base 0.7.24.0 → 0.7.26.0

data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash

@@ -1,112 +0,0 @@
-#!/bin/bash
-
-##################### HELP
-HELP="
-Usage:
-   $0 name[ prog[ k-mers]]
-   
-   name		The name of the run.  CONFIG.name.bash must exist.
-   prog		Program to execute.  One of 'soap' or 'velvet'.  By
-   		default, it executes both.
-   k-mers	Comma-separated list of k-mers to run.  By default,
-   		it executes all the odd numbers between 21 and 63
-		(inclusive).
-   
-   See $PDIR/README.txt for more information.
-"
-##################### RUN
-# Find the directory of the pipeline
-PDIR=$(dirname $(readlink -f $0));
-# Load variables
-source "$PDIR/RUNME.bash"
-if [[ "$SCRATCH" == "" ]] ; then
-  echo "$0: Error loading $PDIR/RUNME.bash, variable SCRATCH undefined" >&2
-  exit 1
-fi
-
-# Check request
-RUNVELVET=yes
-RUNSOAP=yes
-if [[ "$2" == "velvet" ]] ; then
-  RUNSOAP=no
-elif [[ "$2" == "soap" ]] ; then
-  RUNVELVET=no
-fi
-if [[ "$3" == "" ]] ; then
-  KMERARRAY="21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63"
-else
-  KMERARRAY=$3
-fi
-if [[ "$VELVETSIM" == "" ]] ; then
-  VELVETSIM=22
-fi
-if [[ "$SOAPSIM" == "" ]] ; then
-  let SOAPSIM=130/$PPN
-fi
-
-# Run it
-RAMMULT=${RAMMULT:-1}
-echo "Jobs being launched in $SCRATCH"
-for LIB in $LIBRARIES; do
-  # Prepare info
-  echo "Running $LIB";
-  if [[ "$USECOUPLED" == "yes" ]] ; then
-    INPUT="$DATA/$LIB.CoupledReads.fa"
-  elif [[ "$USESINGLE" == "yes" ]] ; then
-    INPUT="$DATA/$LIB.SingleReads.fa"
-  else
-    echo "$0: Error: No task selected, neither USECOUPLED nor USESINGLE set to yes." >&2
-    exit 1;
-  fi
-  VARS="LIB=$LIB,PDIR=$PDIR,DATA=$DATA,USECOUPLED=$USECOUPLED,USESINGLE=$USESINGLE"
-  [[ -n $INSLEN ]] && VARS="$VARS,INSLEN=$INSLEN"
-  [[ -n $VELVETG_EXTRA ]] && VARS="$VARS,VELVETG_EXTRA=$VELVETG_EXTRA"
-  [[ -n $VELVETH_EXTRA ]] && VARS="$VARS,VELVETH_EXTRA=$VELVETH_EXTRA"
-  [[ -n $CLEANUP ]] && VARS="$VARS,CLEANUP=$CLEANUP"
-  let SIZE=$(ls -lH "$INPUT" | awk '{print $5}')/1024/1024/1024;
-  let RAMS=40+$SIZE*10*$RAMMULT;
-  let RAMV=50+$SIZE*15*$RAMMULT;
-  # Launch Velvet
-  if [[ "$RUNVELVET" == "yes" ]] ; then
-    NAME="velvet_${LIB}"
-    if [[ "$QUEUE" != "" ]]; then
-      qsub "$PDIR/velvet.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMV}gb -l "walltime=$WTIME" -q "$QUEUE" \
-          -t "$KMERARRAY%$VELVETSIM"
-    elif [[ $RAMV -gt 150 ]]; then
-      qsub "$PDIR/velvet.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMV}gb -l walltime=360:00:00 -q biohimem-6 \
-          -t "$KMERARRAY%$VELVETSIM"
-    elif [[ $SIZE -lt 6 ]]; then
-      qsub "$PDIR/velvet.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMV}gb -l walltime=12:00:00 -q iw-shared-6 \
-          -t "$KMERARRAY%$VELVETSIM"
-    elif [[ $SIZE -lt 20 ]]; then
-      qsub "$PDIR/velvet.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMV}gb -l walltime=120:00:00 -q bioforce-6 \
-          -t "$KMERARRAY%$VELVETSIM"
-    else
-      qsub "$PDIR/velvet.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMV}gb -l walltime=360:00:00 -q biocluster-6 \
-          -t "$KMERARRAY%$VELVETSIM"
-    fi
-  fi
-  # Launch SOAP
-  if [[ "$RUNSOAP" == "yes" ]] ; then
-    NAME="soap_${LIB}"
-    if [[ "$QUEUE" != "" ]]; then
-      qsub "$PDIR/soap.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMS}gb -l walltime=$WTIME -q $QUEUE -l nodes=1:ppn=$PPN \
-          -t "$KMERARRAY%$SOAPSIM"
-    elif [[ $RAMS -gt 150 ]]; then
-      qsub "$PDIR/soap.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMS}gb -l walltime=48:00:00 -q biohimem-6 \
-          -l nodes=1:ppn=$PPN -t "$KMERARRAY%$SOAPSIM"
-    else
-      qsub "$PDIR/soap.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" \
-          -l mem=${RAMS}gb -l walltime=12:00:00 -q iw-shared-6 \
-          -l nodes=1:ppn=$PPN -t "$KMERARRAY%$SOAPSIM"
-    fi
-  fi
-done
-

data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash

@@ -1,23 +0,0 @@
-#!/bin/bash
-
-##################### RUN
-# Find the directory of the pipeline
-PDIR=$(dirname $(readlink -f $0));
-# Load variables
-source "$PDIR/RUNME.bash"
-if [[ "$SCRATCH" == "" ]] ; then
-   echo "$0: Error loading $PDIR/RUNME.bash, variable SCRATCH undefined" >&2
-   exit 1
-fi
-
-# Run it
-echo "Jobs being launched in $SCRATCH"
-for LIB in $LIBRARIES; do
-   # Prepare info
-   echo "Running $LIB";
-   VARS="LIB=$LIB,PDIR=$PDIR"
-   # Launch Stats
-   NAME="N50_${LIB}"
-   qsub "$PDIR/stats.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME"
-done
-

data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash

@@ -1,44 +0,0 @@
-#!/bin/bash
-
-##################### RUN
-# Find the directory of the pipeline
-PDIR=$(dirname $(readlink -f $0));
-# Load variables
-source "$PDIR/RUNME.bash"
-if [[ "$SCRATCH" == "" ]] ; then
-   echo "$0: Error loading $PDIR/RUNME.bash, variable SCRATCH undefined" >&2
-   exit 1
-fi
-
-# Run it
-echo "Jobs being launched in $SCRATCH"
-RAMMULT=${RAMMULT:-1}
-for LIB in $LIBRARIES; do
-   # Prepare info
-   echo "Running $LIB";
-   K_VELVET=$(echo $K_VELVET | sed -e 's/ /:/g')
-   K_SOAP=$(echo $K_SOAP | sed -e 's/ /:/g')
-   if [[ "$USECOUPLED" == "yes" ]] ; then
-      INPUT="$DATA/$LIB.CoupledReads.fa"
-   elif [[ "$USESINGLE" == "yes" ]] ; then
-      INPUT="$DATA/$LIB.SingleReads.fa"
-   else
-      echo "$0: Error: No task selected, neither USECOUPLED nor USESINGLE set to yes." >&2
-      exit 1;
-   fi
-   let SIZE=30*$(ls -l "$INPUT" | awk '{print $5}')/1024/1024/1024;
-   let RAM=\(3+$SIZE\)*$RAMMULT;
-   VARS="LIB=$LIB,PDIR=$PDIR,BIN454=$BIN454,KVELVET=$K_VELVET,KSOAP=$K_SOAP"
-   # Launch Newbler
-   NAME="Newbler_${LIB}"
-   if [[ "$QUEUE" != "" ]] ; then
-      qsub "$PDIR/newbler.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" -l nodes=1:ppn=$PPN -l mem=${RAM}g -l "walltime=$WTIME" -q "$QUEUE"
-   elif [[ $RAM -gt 150 ]] ; then
-      qsub "$PDIR/newbler.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" -l nodes=1:ppn=$PPN -l mem=${RAM}g -l walltime=360:00:00 -q biohimem-6
-   elif [[ $SIZE -lt 4 ]] ; then
-      qsub "$PDIR/newbler.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" -l nodes=1:ppn=$PPN -l mem=${RAM}g -l walltime=12:00:00 -q iw-shared-6
-   else
-      qsub "$PDIR/newbler.pbs" -v "$VARS" -d "$SCRATCH" -N "$NAME" -l nodes=1:ppn=$PPN -l mem=${RAM}g -l walltime=120:00:00 -q biocluster-6
-   fi
-done
-

data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash

@@ -1,50 +0,0 @@
-#!/bin/bash
-
-##################### RUN
-# Check if it was sourced from RUNME-*.bash
-if [[ "$PDIR" == "" ]] ; then
-   echo "$0: Error: This file is not stand-alone.  Execute one of RUNME-*.bash as described in the README.txt file" >&2
-   exit 1
-fi
-
-# Find the directory of the pipeline
-CWD=$(pwd)
-PDIR=$(dirname $(readlink -f $0));
-
-# Run it
-# Actually, this script doesn't run anything.  It's meant to keep the
-# variables centralized.
-
-# Load config
-NAMES=$(ls $PDIR/CONFIG.*.bash | sed -e 's/.*CONFIG\./    * /' | sed -e 's/\.bash//');
-if [[ "$1" == "" ]] ; then
-   if [[ "$HELP" == "" ]] ; then
-      echo "
-Usage:
-   $0 name
-   
-   name		The name of the run.  CONFIG.name.bash must exist.
-   
-   See $PDIR/README.txt for more information.
-   
-   Available names are:
-$NAMES
-" >&2
-   else
-      echo "$HELP   
-   Available names are:
-$NAMES
-" >&2
-   fi
-   exit 1
-fi
-if [[ ! -e "$PDIR/CONFIG.$1.bash" ]] ; then
-   echo "$0: Error: Impossible to find $PDIR/CONFIG.$1.bash, available names are:
-$NAMES" >&2
-   exit 1
-fi
-source "$PDIR/CONFIG.$1.bash"
-
-# Create the scratch directory
-if [[ ! -d $SCRATCH ]] ; then mkdir -p $SCRATCH ; fi;
-

data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R

@@ -1,37 +0,0 @@
-
-# @author: Luis M. Rodriguez-R
-# @update: Nov-29-2012
-
-kSelector <- function(file, lib){
-   red <- rgb(0.6, 0, 0);
-   d <- read.table(file, sep=" ", h=T, fill=T);
-   d <- d[!is.na(d$N50) & !is.na(d$used), ];
-   d$reads <- max(d$reads, na.rm=T)
-   d <- d[order(d$K), ];
-   rownames(d) <- 1:nrow(d);
-   par(mar=c(5,4,4,5)+.1, cex=0.8);
-   barplot(d$reads/1e6, names=d$K, col='white', ylab='Number of reads (in millions)', xlab='K',
-      main=paste('Reads used and N50 by K-mers in the assembly of', lib));
-   barplot(d$used/1e6, col='grey', add=T);
-   par(new=T);
-   plot(1:length(d$K)-0.5, d$N50, col=red, t='b', lty=2, pch=20, cex=1, lwd=1.5,
-      xlim=c(0, length(d$K)), xaxt='n', yaxt='n', xlab='', ylab='');
-   axis(4, col.axis=red);
-   mtext('N50 (bp)', side=4, line=3, col=red);
-   # Suggest best k-mers
-   if(nrow(d) >= 3){
-      x = data.frame(K=d$K, l=(d$N50 - mean(d$N50))/sd(d$N50), u=(d$used - mean(d$used))/sd(d$used));
-      rownames(x) <- rownames(d)
-      d <- cbind(d, sel=FALSE);
-      k_s = c();
-      for(l_star in c(2, 1/2, 1)){
-         k_s_i = x$K[which.max(l_star*x$l + x$u)];
-	 k_s <- c(k_s, k_s_i);
-	 x <- x[x$K!=k_s_i, ];
-	 d$sel[d$K==k_s_i] <- TRUE;
-      }
-      abline(v=as.numeric(rownames(d)[d$sel])-0.5, col='darkgreen', lty=6);
-   }
-   return(d);
-}
-

data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs

@@ -1,68 +0,0 @@
-#!/bin/bash
-#PBS -l nodes=1:ppn=1
-#PBS -k oe
-
-# Some defaults for the parameters
-BIN454=${BIN454:-"$HOME/454/bin"};
-
-# Check mandatory variables
-if [[ "$LIB" == "" ]]; then
-   echo "Error: LIB is mandatory" >&2
-   exit 1;
-fi
-if [[ "$PDIR" == "" ]]; then
-   echo "Error: PDIR is mandatory" >&2
-   exit 1;
-fi
-if [[ "$KVELVET$KSOAP" == "" ]]; then
-   echo "Error: KVELVET and/or KSOAP are mandatory" >&2
-   exit 1;
-fi
-
-# Prepare input
-KVELVET=$(echo $KVELVET | sed -e 's/:/ /g')
-KSOAP=$(echo $KSOAP | sed -e 's/:/ /g')
-NP=$(cat "$PBS_NODEFILE" | wc -l)
-CWD=$(pwd)
-DIR="$CWD/$LIB.newbler"
-LOG="$DIR.log"
-module load perl/5.14.4
-export PATH=$PATH:$BIN454
-
-# Create project
-echo new > $DIR.proc
-nohup newAssembly $DIR > $LOG
-
-# Prepare Velvet
-if [[ "$KVELVET" != "" ]] ; then
-   echo pre-velvet > $DIR.proc
-   rm $LIB.velvet.tmp1 &>/dev/null
-   for K in $KVELVET ; do
-      perl "$PDIR/FastA.filterN.pl" "$LIB.velvet_$K/contigs.fa" >> $LIB.velvet.tmp1
-   done
-   perl "$PDIR/newbler_preparator.pl" $LIB.velvet.tmp1 $LIB.velvet.tmp2
-   cd $DIR
-   nohup addRun ../$LIB.velvet.tmp2 >> $LOG
-   cd $CWD
-fi ;
-
-# Prepare SOAP
-if [[ "$KSOAP" != "" ]] ; then
-   echo pre-soap > $DIR.proc
-   rm $LIB.soap.tmp1 &>/dev/null
-   for K in $KSOAP ; do
-      cat "$LIB.soap_$K/O.contig" >> $LIB.soap.tmp1
-   done
-   perl "$PDIR/newbler_preparator.pl" $LIB.soap.tmp1 $LIB.soap.tmp2
-   cd $DIR
-   nohup addRun ../$LIB.soap.tmp2 >> $LOG
-   cd $CWD
-fi ;
-
-# Run
-cd $DIR
-echo newbler > $DIR.proc
-nohup runProject -cpu $NP >> $LOG
-cd $CWD
-echo done > $DIR.proc
-

data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl

@@ -1,49 +0,0 @@
-#!/usr/bin/perl
-
-
-my ($in, $out) = @ARGV;
-($in and $out) or die "
-Usage: $0 input.fa output.fa
-";
-
-open IN, "<", $in  or die "Cannot read file: $in: $!\n";
-open OUT,">", $out or die "Cannot create file: $out: $!\n";
-
-%reads=();
-@reads=();
-while(<IN>){
-  chomp;
-  if(/^\>/){
-	$tag=$_;
-	$reads{$tag}='';
-	push(@reads,$tag);
-  }else{
-	$reads{$tag}.=$_;
-  }
-}
-close(IN);
-
-for(0..$#reads){
-  $tag=$reads[$_];
-  $read=$reads{$tag};
-  $l=length $read;
-  if($l<100){
-	next;
-  }else{
-	if($l<1500){
-	  print OUT "$tag\n$read\n";
-	}else{
-	  $r=int($l/1500)+1;
-	  $start=0;
-	  $i=1;
-	  while($start<$l-100){
-		$tag_new=$tag.':r'.$i;
-		$i++;
-		$read_new=substr($read,$start,1500);
-		$start+=200;
-		print OUT "$tag_new\n$read_new\n";
-	  }
-	}
-  }
-}
-close(OUT);

data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs

@@ -1,80 +0,0 @@
-#!/bin/bash
-#PBS -k oe
-
-# Some defaults for the parameters
-INSLEN=${INSLEN:-300};
-USECOUPLED=${USECOUPLED:-yes}
-USESINGLE=${USESINGLE:-no}
-CLEANUP=${CLEANUP:-yes}
-
-# Check mandatory variables
-if [[ "$LIB" == "" ]]; then
-   echo "Error: LIB is mandatory" >&2
-   exit 1;
-fi
-if [[ "$PDIR" == "" ]]; then
-   echo "Error: PDIR is mandatory" >&2
-   exit 1;
-fi
-if [[ "$DATA" == "" ]]; then
-   echo "Error: DATA is mandatory" >&2
-   exit 1;
-fi
-
-# Prepare input
-module load perl/5.14.4
-KMER=$PBS_ARRAYID
-DIR="$LIB.soap_$KMER"
-if [[ "$USECOUPLED" == "yes" ]]; then
-   MAXRDLEN=${MAXRDLEN:-$(perl $PDIR/FastA.length.pl "$DATA/$LIB.CoupledReads.fa" | head -n 200000 | awk '{if($2>MAX) MAX=$2} END{print MAX}')}
-elif [[ "$USESINGLE" == "yes" ]]; then
-   MAXRDLEN=${MAXRDLEN:-$(perl $PDIR/FastA.length.pl "$DATA/$LIB.SingleReads.fa" | head -n 200000 | awk '{if($2>MAX) MAX=$2} END{print MAX}')}
-else
-   echo "$0: Error: Nothing to do, neither USECOUPLED nor USESINGLE set to yes." >&2
-   exit 2
-fi
-NP=$(cat "$PBS_NODEFILE" | wc -l)
-
-# Config
-module load SOAP/denovo2/r240
-echo config > $DIR.proc
-echo "max_rd_len=$MAXRDLEN
-[LIB]
-reverse_seq=0
-asm_flag=3
-rank=1" > $DIR.config
-if [[ "$USECOUPLED" == "yes" ]]; then
-   echo "avg_ins=$INSLEN
-p=$DATA/$LIB.CoupledReads.fa" >> $DIR.config
-fi
-if [[ "$USESINGLE" == "yes" ]]; then
-   echo "f=$DATA/$LIB.SingleReads.fa" >> $DIR.config
-fi
-
-
-# Run
-echo pre > $DIR.proc
-if [[ -d $DIR ]] ; then rm -R $DIR ; fi
-mkdir $DIR
-echo soap > $DIR.proc
-SOAPdenovo-63mer all -s $DIR.config -p $NP -K $KMER -o $DIR/O &> $DIR.log
-if [[ -d $DIR ]] ; then
-   if [[ -s $DIR/O.contig ]] ; then
-      if [[ "$CLEANUP" != "no" ]] ; then
-	 echo cleanup > $DIR.proc
-	 rm $DIR/*edge
-	 rm $DIR/*vertex
-	 rm $DIR/*Arc*
-	 rm $DIR/*Graph*
-	 rm $DIR/*readInGap*
-      fi
-      echo done > $DIR.proc
-   else
-      echo "$0: Error: File $DIR/O.contig doesn't exist, something went wrong" >&2
-      exit 1
-   fi
-else
-   echo "$0: Error: Directory $DIR doesn't exist, something went wrong" >&2
-   exit 1
-fi
-