Hi Rathi!

I wrote a tophat wrapper myself- you can use it if u want, the files are attached. you need to adapt the BOWTIE_INDEXES path in the toohatwrapper.py and the bowtie path. if these variables are already set then you can just remove the lines between "#path settings" and "#path settings end". And you must include the tophat.xml in the tool-conf.xml in the main galaxy folder - in a section of your choice.

Let me know if u find any errors-

greetings

mat

Rathi Thiagarajan schrieb:

Hello there,

I was really pleased to see that you have the NGS toolbox within Galaxy. I was wondering if there are any plans to include TopHat (http://tophat.cbcb.umd.edu/)and/or Cufflinks (http://cufflinks.cbcb.umd.edu/) into the toolbox as this would be really beneficial.

Also do you have tools to convert fastq format to SAM?

Thanking you in advance.

Cheers, Rathi

#! /usr/bin/python

import optparse, os, sys, tempfile

def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) sys.exit()

def moveToTarget(target,filePath,log_report): # if os.path.isfile(filePath): cmd = "mv %s %s" % (filePath,target) try: os.system(cmd) except: print "Error moving files to galaxy "

def copyToTarget(targetStream,filePath,log_report): try: source = open(filePath,"r") handle = open(targetStream,"w") for line in source: handle.write(line) #handle.write('\n') source.close() handle.close() except IOError: log_report += "Target file " + filePath + "does not exist- probably Tophat createt no output."

def __main__(): #Parse Command Line parser = optparse.OptionParser() parser.add_option('-i', '--min-intron-length', dest='min_intron', help='Min. intron length') parser.add_option('-I', '--max-intron-length', dest='max_intron', help='Max. intron length') parser.add_option('-G', '--annotation', dest='gff3_file', help='none/filename') parser.add_option('', '--no-gff-juncs', dest='no_gff_juncs', help='Dont report GFF junctions (yes/no)') parser.add_option('', '--no-novel-juncs', dest='no_novel_juncs', help='Only report new junctions (yes/no)') parser.add_option('', '--bowtie_index', dest='bowtie_index', help='Bowtie index name') parser.add_option('', '--source-left', dest='source_left', help='source file (left if paired end)') parser.add_option('', '--source-right', dest='source_right', help='source file (right paired end reads)') parser.add_option('', '--coverage', dest='coverage', help='coverage') parser.add_option('', '--junctions', dest='junctions', help='junctions') parser.add_option('', '--expr_file', dest='expr_file', help='expr_file') parser.add_option('', '--accepted_hits', dest='accepted_hits', help='hits') parser.add_option('', '--report', dest='report', help='report') parser.add_option('', '--solexa1.3-quals', dest='solexa13', help='use solexa 1.3 pipeline (yes/no)') parser.add_option('', '--log_report', dest='log_report', help='log report') parser.add_option('', '--mate-inner-dist', dest='mate_inner_dist', help='report') parser.add_option('', '--paired-end', dest='paired_end', help='use paired end reads (yes/no)') parser.add_option('', '--file-format', dest='file_format', help='(fasta/fastqsolexa/fastqsanger)')

(options, args) = parser.parse_args()

solexa13_cmd="" if options.solexa13 == "yes": solexa13_cmd="--solexa1.3-quals"

no_novel_cmd="" if options.no_novel_juncs == "yes": no_novel_cmd="--no-novel-juncs"

no_gff_cmd="" if options.no_gff_juncs == "yes": no_gff_cmd="--no-gff-juncs"

gff3_cmd = "" if options.gff3_file != 'none': gff3_cmd = "-G %s " % options.gff3_file

# make temp directory for result files tmp_dir = tempfile.gettempdir() #print tmp_dir

new_files_left=[] new_files_right=[] files_right=[] files_left=[]

# ========= path settings

os.putenv('BOWTIE_INDEXES','/data/galaxy/indexes/')

path = os.environ['PATH'] path += ':/usr/local/bowtie/' os.putenv('PATH',path)

# ========= path settings end

try: if options.paired_end == "yes": if len(options.source_right) != len(options.source_left): print "Error, must be an equivalent number of left/right read files" return

files_right = options.source_right.split(',') files_right.pop(-1)

files_left = options.source_left.split(',') files_left.pop(-1)

tmpFileName=""

for i in files_left: tmpFileName=i.rstrip('.dat') tmpFileName = tmpFileName + "_1." + options.file_format moveToTarget(i,tmpFileName,options.log_report) new_files_left.append(tmpFileName)

for i in files_right: tmpFileName=i.rstrip('.dat') tmpFileName = tmpFileName + "_2." + options.file_format moveToTarget(i,tmpFileName,options.log_report) new_files_right.append(tmpFileName)

print 'LEFT %s'%new_files_left

print 'RIGHT %s'%new_files_right

tophat_cmd = 'tophat -p 4 -i %s -I %s -r %s -o %s %s %s %s %s %s %s %s' % (options.min_intron, options.max_intron,options.mate_inner_dist,tmp_dir,solexa13_cmd,no_novel_cmd,no_gff_cmd,gff3_cmd,options.bowtie_index,','.join(new_files_left),','.join(new_files_right)) os.system(tophat_cmd) os.wait()

#print 'CMD %s'%tophat_cmd

#copy files back for i in new_files_left: for j in files_left: moveToTarget(i,j,log_report) for i in new_files_right: for j in files_right: moveToTarget(i,j,log_report)

else: files_left = options.source_left.split(',') files_left.pop(-1) if len(files_left) == 1: file_list = files_left[0] else: file_list = ','.join(files_left)

tophat_cmd = 'tophat -p 4 -i %s -I %s -r %s -o %s %s %s %s %s %s %s' % (options.min_intron, options.max_intron,options.mate_inner_dist,tmp_dir,solexa13_cmd,no_novel_cmd,no_gff_cmd,gff3_cmd,options.bowtie_index,file_list)

os.system(tophat_cmd) os.wait()

#print tophat_cmd

except Exception, erf: options.log_report += 'Error creating temp directory for indexing purposes\n'

filePath = tmp_dir + "/coverage.wig" moveToTarget(options.coverage,filePath,options.log_report)

filePath = tmp_dir + "/junctions.bed" moveToTarget(options.junctions,filePath,options.log_report)

filePath = tmp_dir + "/tophat_output.gff3.expr" moveToTarget(options.expr_file,filePath,options.log_report)

filePath = tmp_dir + "/accepted_hits.sam" moveToTarget(options.accepted_hits,filePath,options.log_report)

if options.paired_end == "yes":

for i in new_files_right: moveToTarget(i,files_right,options.log_report);

for i in new_files_left: moveToTarget(i,files_left,options.log_report); #if os.path.exists(tmp_dir): #os.rmdir(tmp_dir)

if __name__=="__main__": __main__()