| Previous changeset 3:3db16e8335e1 (2012-06-21) Next changeset 5:eb55013e0f28 (2012-06-24) |
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Commit message:
Added sequence gap remover and Trimming Reads. |
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modified:
ucsb_phylogenetics/phylobayes/pb.xml ucsb_phylogenetics/phylomatic/phylomatic.xml |
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added:
ucsb_phylogenetics/gap-rem/gap-rem.xml ucsb_phylogenetics/gap-rem/gap_rem_README.txt ucsb_phylogenetics/gap-rem/seqfill.pl ucsb_phylogenetics/trimmingreads/TrimmingReads.pl ucsb_phylogenetics/trimmingreads/TrimmingReads.xml ucsb_phylogenetics/trimmingreads/TrimmingReads_README.txt |
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removed:
ucsb_phylogenetics/phylobayes/phylobayes_wrapper.tar.bz2 |
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| diff -r 3db16e8335e1 -r 5b23f3eb3f09 ucsb_phylogenetics/gap-rem/gap-rem.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsb_phylogenetics/gap-rem/gap-rem.xml Sun Jun 24 16:02:29 2012 -0400 |
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| @@ -0,0 +1,29 @@ +<tool id="gap-rem" name="Sequence Gap Remover" version="1.0.1"> + <description>Removes gap in sequences</description> + <command interpreter="perl">seqfill.pl $file $question_mark $hyphen $N $usePart $pfile</command> + <inputs> + <param format="phylipnon" name="file" type="data" label="File" /> + <param type ="boolean" name="usePart" truevalue="true" falsevalue="false" label="Also use Partition File -- if unchecked, it will be ignored." /> + <param format="txt" name="pfile" type="data" label="Partition file" /> + <param type="boolean" name="question_mark" truevalue="true" falsevalue="false" label="'?' signifies gap" /> + <param type="boolean" name="hyphen" truevalue="true" falsevalue="false" label="'-' signifies gap" /> + <param type="boolean" name="N" truevalue="true" falsevalue="false" label="'N' signifies gap"/> + </inputs> + + <outputs> + <data from_work_dir="out.phy" format="phylipnon" name="out1" /> + <data from_work_dir="partOut.txt" format="txt" name="out2" /> + </outputs> + + <help> + http://labs.eemb.ucsb.edu/oakley/todd/ + + Sequence Gap Remover + + Takes an input phylip file and removes any specified gap characters that exist in the same + columns of containing sequences. + + Output will be a text file. + </help> + +</tool> |
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| diff -r 3db16e8335e1 -r 5b23f3eb3f09 ucsb_phylogenetics/gap-rem/gap_rem_README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsb_phylogenetics/gap-rem/gap_rem_README.txt Sun Jun 24 16:02:29 2012 -0400 |
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| @@ -0,0 +1,30 @@ +Sequence Gap Remover + http://labs.eemb.ucsb.edu/oakley/todd/ + + Sequence Gap Remover + + Takes an input phylip file and removes any specified gap characters that exist in the same + columns of containing sequences. + + Output will be a text file. + +Original Perl and Galaxy script implemented by: Roger Ngo and Todd H. Oakley, UCSB + +Sequence Gap Remover will remove any common gaps within a sequence in a phylip file. + +The package includes: + +* gap-rem.xml - the Galaxy tool +* seqfill.pl - the Perl script +* gap_rem_README.txt - the documentation file + +To install, copy the seqfill.pl and gap-rem.xml to a folder in the /galaxy-dist/tools/ +directory and add the XML file to tool_conf.xml. + +Restart the Galaxy instance with: + +./run.sh --stop-daemon + +and then + +./run.sh --reload --daemon \ No newline at end of file |
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| diff -r 3db16e8335e1 -r 5b23f3eb3f09 ucsb_phylogenetics/gap-rem/seqfill.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsb_phylogenetics/gap-rem/seqfill.pl Sun Jun 24 16:02:29 2012 -0400 |
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| @@ -0,0 +1,147 @@ +#!/usr/bin/perl + +# Sequence Gap Remover + +# Todd H. Oakley and Roger Ngo, UCSB + +# 2012 + +# Removes gaps in sequences from a phylip file. + +my $file = $ARGV[0]; +my $q_mark = $ARGV[1]; +my $hyphen = $ARGV[2]; +my $N = $ARGV[3]; +my $usePartFile = $ARGV[4]; +my $partFile = $ARGV[5]; + +my $out = "out.phylipnon"; # output file + +open(FILE, $file); + my @speciesNames; + my @sequenceLines; + + my @currentLineContent; + + my $i = 0; + while($currentLine = <FILE>) { + chomp($currentLine); + @currentLineContent = split(/\t/, $currentLine); + $speciesNames[$i] = $currentLineContent[0]; + $sequenceLines[$i] = $currentLineContent[1]; + $i++; + } + + my $dataInfo = $speciesNames[1]; # gets num of species and sequence length + my @numbers = split(/ /, $dataInfo); + + my $numberOfSpecies = $numbers[0]; + my $sequenceLength = $numbers[1]; + +close(FILE); + +open(OUT, '>'.$out); + my @columnData; # this will have $sequenceLength elements + for($j = 0; $j < $numberOfSpecies+2; $j++) { + for($k = 0; $k < $sequenceLength; $k++) { + $currChar = substr($sequenceLines[$j], $k, 1); + $columnData[$k] = $columnData[$k].$currChar; + } + } + + # mark locations that will be removed + my @flagMap; + for($i = 0; $i < $sequenceLength; $i++) { + $flagMap[$i] = 0; + } + my $index = 0; + foreach $el(@columnData) { + my $tot = 0; + my $q_mark_occur = 0; + my $hyphen_occur = 0; + my $N_occur = 0; + + if($q_mark eq "true") { + $q_mark_occur = ($el =~ tr/?//); + } + if($hyphen eq "true") { + $hyphen_occur = ($el =~ tr/-//); + } + if($N eq "true") { + $N_occur = ($el =~ tr/N//); + } + + $tot = $q_mark_occur + $hyphen_occur + $N_occur; + if($tot == $numberOfSpecies) { + $flagMap[$index] = 1; + } + $index++; + } + + my $newSequenceLength = $sequenceLength; + foreach $el(@flagMap) { + if($el == 1) { + $newSequenceLength--; + } + } + + print OUT $speciesNames[0]."\n"; + print OUT $numberOfSpecies." ".$newSequenceLength."\n"; + for($i = 2; $i < $numberOfSpecies+3; $i++) { + print OUT $speciesNames[$i]."\t"; + for($j = 0; $j < $sequenceLength; $j++) { + if($flagMap[$j] == 0) { + my $character = substr($sequenceLines[$i], $j, 1); + print OUT $character; + } + } + print OUT "\n"; + } + +close(OUT); + +my $partOut = "partOut.txt"; + +if($usePartFile eq "true") { + # update the partition file + open(PART, $partFile); + my @data; + my @ranges; + my @names; + $i = 0; + while($currentLine = <PART>) { + @data = split(/=/, $currentLine); + $names[$i] = $data[0]; + $ranges[$i] = $data[1]; + $i++; + } + close(PART); + + my $firstFlag = 1; + open(PARTOUT, '>'.$partOut); + $j = 0; + my $newLower; + foreach $el(@ranges) { + print PARTOUT $names[$j]." = "; + @lowerUpper = split(/-/, $el); + if($firstFlag == 1) { + $newLower = $lowerUpper[0]; + $firstFlag = 0; + } + my $currUpper = $lowerUpper[1]; + my $newUpper = $currUpper; + + + + for($i = $currLower; $i < $currUpper; $i++) { + if($flagMap[$i] == 1) { + $newUpper--; + } + } + + print PARTOUT $newLower." - ".$newUpper."\n"; + $newLower = $newUpper + 1; + $j++; + } + close(PARTOUT); +} |
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| diff -r 3db16e8335e1 -r 5b23f3eb3f09 ucsb_phylogenetics/phylobayes/pb.xml --- a/ucsb_phylogenetics/phylobayes/pb.xml Thu Jun 21 17:48:46 2012 -0400 +++ b/ucsb_phylogenetics/phylobayes/pb.xml Sun Jun 24 16:02:29 2012 -0400 |
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| @@ -1,5 +1,8 @@ -<tool id="phylobayes" name="Phylobayes"> +<tool id="phylobayes" name="Phylobayes" version="1.0.1"> <description>Runs phylobayes</description> + <requirements> + <requirement type="binary">Phylobayes 3.3b</requirement> + </requirements> <command interpreter="perl">pb.pl $filename $nchain $cycles $discrepancies $effectivesize $burnin $sampleInterval</command> <inputs> <param name="filename" type="data" format="txt" label="Input file (ali)" /> |
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| diff -r 3db16e8335e1 -r 5b23f3eb3f09 ucsb_phylogenetics/phylobayes/phylobayes_wrapper.tar.bz2 |
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| Binary file ucsb_phylogenetics/phylobayes/phylobayes_wrapper.tar.bz2 has changed |
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| diff -r 3db16e8335e1 -r 5b23f3eb3f09 ucsb_phylogenetics/phylomatic/phylomatic.xml --- a/ucsb_phylogenetics/phylomatic/phylomatic.xml Thu Jun 21 17:48:46 2012 -0400 +++ b/ucsb_phylogenetics/phylomatic/phylomatic.xml Sun Jun 24 16:02:29 2012 -0400 |
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| @@ -1,5 +1,8 @@ -<tool id="phylomatic" name="Phylomatic"> +<tool id="phylomatic" name="Phylomatic" version="1.0.1"> <description>Run Phylomatic</description> + <requirements> + <requirement type="binary">Phylocom Phylomatic</requirement> + </requirements> <command interpreter="perl">./phylomatic.pl $input1 $input2</command> <inputs> <param name="input1" type="data" format="txt" label="Phylogenetic Tree" /> |
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| diff -r 3db16e8335e1 -r 5b23f3eb3f09 ucsb_phylogenetics/trimmingreads/TrimmingReads.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsb_phylogenetics/trimmingreads/TrimmingReads.pl Sun Jun 24 16:02:29 2012 -0400 |
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| b'@@ -0,0 +1,310 @@\n+#! /usr/bin/perl\n+\n+use strict;\n+use warnings;\n+use Getopt::Long;\n+use File::Basename;\n+use List::Util qw(sum min max);\n+\n+my $seqFormat = "a";\t\t# 1: Sanger; 2: Solexa; 3: Illumina 1.3+; 4: Illumina 1.5+;\n+my $subVal;\n+\n+# Parameter variables\n+my $file;\n+my $helpAsked;\n+my $rTrimBases = 0;\n+my $lTrimBases = 0;\n+my $qCutOff = 0;\n+my $lenCutOff = -1;\n+my $outFile = "";\n+my $isQualTrimming = 1;\n+\n+GetOptions(\n+\t\t\t"i=s" => \\$file,\n+\t\t\t"h|help" => \\$helpAsked,\n+\t\t\t"l|leftTrimBases=i" => \\$lTrimBases,\n+\t\t\t"o|outputFile=s" => \\$outFile,\n+\t\t\t"r|rightTrimBases=i" => \\$rTrimBases,\n+\t\t\t"q|qualCutOff=i" => \\$qCutOff,\n+\t\t\t"n|lenCutOff=i" => \\$lenCutOff,\n+\t\t );\n+if(defined($helpAsked)) {\n+\tprtUsage();\n+\texit;\n+}\n+if(!defined($file)) {\n+\tprtError("No input files are provided");\n+}\n+\n+my ($fileName, $filePath) = fileparse($file);\n+$outFile = $file . "_trimmed" if($outFile eq "");\n+\n+open(I, "$file") or die "Can not open file $file\\n";\n+open(O, ">$outFile") or die "Can not create file $outFile\\n";\n+my $tmpLine = <I>;\n+close(I);\n+if($tmpLine =~ /^@/) {\n+\tprint "Input read/sequence format: FASTQ\\n";\n+\tif($lTrimBases == 0 && $rTrimBases == 0 && $qCutOff == 0 && $lenCutOff == -1) {\n+\t\tprint "Trimming parameters are not set.\\nNothing to do.\\nExiting...\\n";\n+\t\tunlink($outFile);\n+\t\texit;\n+\t}\n+\tprint "Checking FASTQ variant: File $file...\\n";\n+\tmy $nLines = checkFastQFormat($file, 1);\n+\tif($seqFormat == 1) {\n+\t\t$subVal = 33;\n+\t\tprint "Input FASTQ file format: Sanger\\n";\n+\t}\n+\tif($seqFormat == 2) {\n+\t\t$subVal = 64;\n+\t\tprint "Input FASTQ file format: Solexa\\n";\n+\t}\n+\tif($seqFormat == 3) {\n+\t\t$subVal = 64;\n+\t\tprint "Input FASTQ file format: Illumina 1.3+\\n";\n+\t}\n+\tif($seqFormat == 4) {\n+\t\t$subVal = 64;\n+\t\tprint "Input FASTQ file format: Illumina 1.5+\\n";\n+\t}\n+\tif($seqFormat == 5) {\n+\t\t$subVal = 33;\n+\t\tprint "Input FASTQ file format: Illumina 1.8+\\n";\n+\t}\n+\tif($lTrimBases != 0 || $rTrimBases != 0) {\n+\t\tprint "Trimming $lTrimBases bases from left end and $rTrimBases bases from right end";\n+\t\t$isQualTrimming = 0;\n+\t}\n+\telse {\n+\t\tprint "Trimming based on PHRED quality score (< $qCutOff)";\n+\t}\n+\tprint " followed by length filtering (< $lenCutOff bp)\\n";\n+\n+\topen(I, "$file") or die "Can not open file $file\\n";\t\n+\tmy $c = 0;\n+\tmy $currId1 = "";\n+\tmy $currId2 = "";\n+\tmy $currSeq = "";\n+\tmy $currQual = "";\n+\t\n+\t\n+\twhile(my $line = <I>) {\n+\t\tchomp $line;\n+ $c++;\n+ if($c == 5) {\n+ $c = 1;\n+ }\n+ if($c == 1) {\n+ \t$currId1 = $line;\n+ }\n+ if($c == 3) {\n+ \t$currId2 = $line;\n+ }\n+ if($isQualTrimming == 0) {\n+\t if($c == 2) {\n+\t \t$currSeq = trimSeq($line);\n+\t }\n+\t elsif($c == 4) {\n+\t \t$currQual = trimSeq($line);\n+\t \tprint O "$currId1\\n$currSeq\\n$currId2\\n$currQual\\n" if(length $currSeq >= $lenCutOff);\n+\t }\n+ }\n+ else {\n+\t if($c == 4) {\n+\t\t\t\t$currQual = trimSeq4Qual($line);\n+\t\t\t\tif(defined($currQual)) {\n+\t\t\t\t\tmy $len = length $currQual;\n+\t\t\t\t\t$currSeq =~ /^(.{$len})/;\n+\t\t\t\t\t$currSeq = $1;\n+\t\t \tprint O "$currId1\\n$currSeq\\n$currId2\\n$currQual\\n" if(length $currSeq >= $lenCutOff);\n+\t\t\t\t}\n+\t }\n+\t elsif($c == 2) {\n+\t \t$currSeq = $line;\n+\t }\n+ }\n+\t}\n+\tprint "Trimmed file is generated: $outFile\\n";\n+}\n+else {\n+\tprint "Input read/sequence format: FASTA\\n";\n+\tif($qCutOff != 0) {\n+\t\tprint "Warning: Quality trimming can not be performed for FASTA files\\n";\n+\t\t$qCutOff = 0;\n+\t}\n+\tif($lTrimBases == 0 && $rTrimBases == 0 && $lenCutOff == -1) {\n+\t\tprint "Trimming parameters are not set.\\nNothing to do.\\nExiting...\\n";\n+\t\tunlink($outFile);\n+\t\texit;\n+\t}\n+\tprint "Trimming $lTrimBases bases from left end and $rTrimBases bases from right end followed by length filtering (< $lenCutOff bp)\\n";\n+\topen(I, "$file") or die "Can not open file $file\\n";\n+\tmy $prevFastaSeqId = "";\n+\tmy $fastaSeqId = "";\n+\tmy $fastaSeq = "";\n+\t\n+\twhile(my $line = <I>) {\n+\t\tchomp $line;\n+\t\tif($line =~ /^>/'..b'\n+ $newSeq .= substr($seq, $i, $ch) . "\\n";\n+ }\n+ chomp($newSeq); # To remove \\n at the end of the whole sequence..\n+ return $newSeq;\n+}\n+\n+sub prtHelp {\n+\tprint "\\n$0 options:\\n\\n";\n+\tprint "### Input reads/sequences (FASTQ/FASTA) (Required)\\n";\n+\tprint " -i <Read/Sequence file>\\n";\n+\tprint " File containing reads/sequences in either FASTQ or FASTA format\\n";\n+\tprint "\\n";\n+\tprint "### Other options [Optional]\\n";\n+\tprint " -h | -help\\n";\n+\tprint " Prints this help\\n";\n+\tprint "--------------------------------- Trimming Options ---------------------------------\\n";\n+\tprint " -l | -leftTrimBases <Integer>\\n";\n+\tprint " Number of bases to be trimmed from left end (5\' end)\\n";\n+\tprint " default: 0\\n";\n+\tprint " -r | -rightTrimBases <Integer>\\n";\n+\tprint " Number of bases to be trimmed from right end (3\' end)\\n";\n+\tprint " default: 0\\n";\n+\tprint " -q | -qualCutOff <Integer> (Only for FASTQ files)\\n";\n+\tprint " Cut-off PHRED quality score for trimming reads from right end (3\' end)\\n";\n+\tprint " For eg.: -q 20, will trim bases having PHRED quality score less than 20 at 3\' end of the read\\n";\n+\tprint " Note: Quality trimming can be performed only if -l and -r are not used\\n";\n+\tprint " default: 0 (i.e. quality trimming is OFF)\\n";\n+\tprint " -n | -lenCutOff <Integer>\\n";\n+\tprint " Read length cut-off\\n";\n+\tprint " Reads shorter than given length will be discarded\\n";\n+\tprint " default: -1 (i.e. length filtering is OFF)\\n";\n+\tprint "--------------------------------- Output Options ---------------------------------\\n";\n+\tprint " -o | -outputFile <Output file name>\\n";\n+\tprint " Output will be stored in the given file\\n";\n+\tprint " default: By default, output file will be stored where the input file is\\n";\n+\tprint "\\n";\n+}\n+\n+sub prtError {\n+\tmy $msg = $_[0];\n+\tprint STDERR "+======================================================================+\\n";\n+\tprintf STDERR "|%-70s|\\n", " Error:";\n+\tprintf STDERR "|%-70s|\\n", " $msg";\n+\tprint STDERR "+======================================================================+\\n";\n+\tprtUsage();\n+\texit;\n+}\n+\n+sub prtUsage {\n+\tprint "\\nUsage: perl $0 <options>\\n";\n+\tprtHelp();\n+}\n+\n+sub checkFastQFormat {\t\t\t\t# Takes FASTQ file as an input and if the format is incorrect it will print error and exit, otherwise it will return the number of lines in the file.\n+\tmy $file = $_[0];\n+\tmy $isVariantIdntfcntOn = $_[1];\n+\tmy $lines = 0;\n+\topen(F, "<$file") or die "Can not open file $file\\n";\n+\tmy $counter = 0;\n+\tmy $minVal = 1000;\n+\tmy $maxVal = 0;\n+\twhile(my $line = <F>) {\n+\t\t$lines++;\n+\t\t$counter++;\n+\t\tnext if($line =~ /^\\n$/);\n+\t\tif($counter == 1 && $line !~ /^\\@/) {\n+\t\t\tprtErrorExit("Invalid FASTQ file format.\\n\\t\\tFile: $file");\n+\t\t}\n+\t\tif($counter == 3 && $line !~ /^\\+/) {\n+\t\t\tprtErrorExit("Invalid FASTQ file format.\\n\\t\\tFile: $file");\n+\t\t}\n+\t\tif($counter == 4 && $lines < 1000000) {\n+\t\t\tchomp $line;\n+\t\t\tmy @ASCII = unpack("C*", $line);\n+\t\t\t$minVal = min(min(@ASCII), $minVal);\n+\t\t\t$maxVal = max(max(@ASCII), $maxVal);\n+\t\t}\n+\t\tif($counter == 4) {\n+\t\t\t$counter = 0;\n+\t\t}\n+\t}\n+\tclose(F);\n+\tmy $tseqFormat = 0;\n+\tif($minVal >= 33 && $minVal <= 73 && $maxVal >= 33 && $maxVal <= 73) {\n+\t\t$tseqFormat = 1;\n+\t}\n+\telsif($minVal >= 66 && $minVal <= 105 && $maxVal >= 66 && $maxVal <= 105) {\n+\t\t$tseqFormat = 4;\t\t\t# Illumina 1.5+\n+\t}\n+\telsif($minVal >= 64 && $minVal <= 105 && $maxVal >= 64 && $maxVal <= 105) {\n+\t\t$tseqFormat = 3;\t\t\t# Illumina 1.3+\n+\t}\n+\telsif($minVal >= 59 && $minVal <= 105 && $maxVal >= 59 && $maxVal <= 105) {\n+\t\t$tseqFormat = 2;\t\t\t# Solexa\n+\t}\n+\telsif($minVal >= 33 && $minVal <= 74 && $maxVal >= 33 && $maxVal <= 74) {\n+\t\t$tseqFormat = 5;\t\t\t# Illumina 1.8+\n+\t}\n+\tif($isVariantIdntfcntOn) {\n+\t\t$seqFormat = $tseqFormat;\n+\t}\n+\telse {\n+\t\tif($tseqFormat != $seqFormat) {\n+\t\t\tprint STDERR "Warning: It seems the specified variant of FASTQ doesn\'t match the quality values in input FASTQ files.\\n";\n+\t\t}\n+\t}\n+\treturn $lines;\n+}\n+\n' |
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| diff -r 3db16e8335e1 -r 5b23f3eb3f09 ucsb_phylogenetics/trimmingreads/TrimmingReads.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsb_phylogenetics/trimmingreads/TrimmingReads.xml Sun Jun 24 16:02:29 2012 -0400 |
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| @@ -0,0 +1,33 @@ +<tool id="trimming_reads" name="TrimmingReads"> + <description>Runs TrimmingReads</description> + <command interpreter="perl">TrimmingReads.pl -i $input -l $l_int -o out.fastq -r $r_int -q $q_int -n $len_int</command> + <inputs> + <param name="input" label="Input file" type="data" format="fastq"/> + <param name="l_int" label="Left Trim Bases" type="integer" value="0" /> + <param name="r_int" label="Right Trim Bases" type="integer" value="0" /> + <param name="q_int" label="Qual Cut Off" type="integer" value="0"/> + <param name="len_int" label="Length Cut Off" type="integer" value="0"/> + </inputs> + <outputs> + <data from_work_dir="out.fastq" format="fastq" /> + </outputs> + + <help> + + Trimming Reads is a part of the NGS QC Toolkit. + + This tool trims the reads/sequences and their quality scores (in case of FASTQ file) in two ways. + First, it trims fixed (user-specified) number of bases from 5� and/or 3� end of the reads and corresponding qualities from the input FASTQ file. + Second, it trims low quality bases from 3� end of the read using user-defined threshold value of quality score. + Input to this tool is either FASTQ or FASTA format file. + Options are provided to specify the number of bases to be trimmed and the quality threshold for quality based trimming. + (http://59.163.192.90:8080/ngsqctoolkit/NGSQCToolkitv2.2.3_manual.pdf) + + http://59.163.192.90:8080/ngsqctoolkit/ + + http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030619 + Patel RK, Jain M (2012). NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS ONE, 7(2): e30619. + + Left Trim + </help> +</tool> |
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| diff -r 3db16e8335e1 -r 5b23f3eb3f09 ucsb_phylogenetics/trimmingreads/TrimmingReads_README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsb_phylogenetics/trimmingreads/TrimmingReads_README.txt Sun Jun 24 16:02:29 2012 -0400 |
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| @@ -0,0 +1,29 @@ +Trimming Reads is a part of NGS QC Toolkit. + +Original script written by: Mukesh Jain, and Ravi Patel + +Galaxy tool wrapper written by: Roger Ngo and Todd H. Oakley, UCSB + +Required files included in this package: + +* TrimmingReads.xml - Galaxy tool file for the Perl script +* TrimmingReads_README.txt - Documentation file + +Dependencies: + +TrimmingReads.pl from the NGS QC Toolkit is required to be installed +in the Galaxy user account. + +Installation and Configuration Instructions: + +1. Copy TrimmingReads.xml to a folder in /galaxy-dist/tools/ +2. Add the XML tool to tool_conf.xml in /galaxy-dist/ +3. Add the TrimmingReads.pl to your path variable in .bashrc +4. Type: source .bashrc +5. Restart Galaxy using: + +./run.sh --stop-reload + +and then + +./run.sh --reload --daemon |