comparison TrackHub.py @ 53:1e4806330e51 draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit a505d6c97db9d044761b5ce92be4a39cb84eda29-dirty

52:6fec27968f86

    def createHub(self):
        self.prepareRefseq()
        for input_file in self.input_files:
            self.addTrack(input_file)
        self.indexName()
        self.makeArchive()
        self.outHtml()
        print "Success!\n"
    
    def prepareRefseq(self):
        try:
            #print os.path.join(self.tool_dir, 'prepare-refseqs.pl') + ", '--fasta', " + self.reference +", '--out', self.json])"

        subprocess.call(['generate-names.pl', '-v', '--out', self.json])
        print "finished name index \n"

    def makeArchive(self):
        shutil.make_archive(self.out_path, 'zip', self.out_path)
        data_folder = '/var/www/html/JBrowse-1.12.1/jbrowse_hub'
        try:
            if os.path.exists(data_folder):
                if os.path.isdir(data_folder):
                    shutil.rmtree(data_folder)
                else:

        except OSError as oserror:
            print "Cannot create data folder({0}): {1}".format(oserror.errno, oserror.strerror)
        shutil.copytree(self.out_path, data_folder)
        subprocess.call(['chmod', '-R', 'o+rx', '/var/www/html/JBrowse-1.12.1/jbrowse_hub'])
        shutil.rmtree(self.out_path)
    
    #TODO: this will list all zip files in the filedir and sub-dirs. worked in Galaxy but all list zip files in test-data when
    #run it locally. May need modify
    def outHtml(self):
        with open(self.outfile, 'w') as htmlfile:
            htmlstr = 'The JBrowse Hub is created: <br>'
            zipfiles = '<li><a href = "%s">Download</a></li>'
            jbrowse_hub = '<li><a href = ":80/JBrowse-1.12.1/index.html?data=jbrowse_hub/json" target="_blank">View JBrowse Hub</a></li>'
            filedir_abs = os.path.abspath(self.outfile)
            filedir = os.path.dirname(filedir_abs)
            filedir = os.path.join(filedir, self.outfolder)
            for root, dirs, files in os.walk(filedir):
                for file in files:
                    if file.endswith('.zip'):   
                        relative_directory = os.path.relpath(root, filedir)
                        relative_file_path = os.path.join(relative_directory, file)
                        htmlstr += zipfiles % relative_file_path
            htmlstr += jbrowse_hub
            htmlfile.write(htmlstr)

    def createTrackList(self):
        trackList = os.path.join(self.json, "trackList.json")
        if not os.path.exists(trackList):

53:1e4806330e51

    def createHub(self):
        self.prepareRefseq()
        for input_file in self.input_files:
            self.addTrack(input_file)
        self.indexName()
        slink = self.makeArchive()
        self.outHtml(slink)
        print "Success!\n"
    
    def prepareRefseq(self):
        try:
            #print os.path.join(self.tool_dir, 'prepare-refseqs.pl') + ", '--fasta', " + self.reference +", '--out', self.json])"

        subprocess.call(['generate-names.pl', '-v', '--out', self.json])
        print "finished name index \n"

    def makeArchive(self):
        shutil.make_archive(self.out_path, 'zip', self.out_path)
        source = os.path.abspath(self.out_path)
        slink = source.replace('/', '_')
        slink = os.path.join('/home/galaxy/galaxy/static/JBrowse-1.12.1/data', slink)
        try:
            if os.path.islink(slink):
                os.unlink(slink)
        except OSError as oserror:
            print "Cannot create symlink to the data({0}): {1}".format(oserror.errno, oserror.strerror)
        os.symlink(source, slink)
        return slink
        '''
        data_folder = '/gonramp/static/JBrowse-1.12.1/jbrowse_hub'
        try:
            if os.path.exists(data_folder):
                if os.path.isdir(data_folder):
                    shutil.rmtree(data_folder)
                else:

        except OSError as oserror:
            print "Cannot create data folder({0}): {1}".format(oserror.errno, oserror.strerror)
        shutil.copytree(self.out_path, data_folder)
        subprocess.call(['chmod', '-R', 'o+rx', '/var/www/html/JBrowse-1.12.1/jbrowse_hub'])
        shutil.rmtree(self.out_path)
        '''
    
    #TODO: this will list all zip files in the filedir and sub-dirs. worked in Galaxy but all list zip files in test-data when
    #run it locally. May need modify
    def outHtml(self, slink):
        with open(self.outfile, 'w') as htmlfile:
            htmlstr = 'The JBrowse Hub is created: <br>'
            zipfiles = '<li><a href = "%s">Download</a></li>'
            jbrowse_hub = '<li><a href = "/gonramp/static/JBrowse-1.12.1/index.html?data="%s" target="_blank">View JBrowse Hub</a></li>'
            filedir_abs = os.path.abspath(self.outfile)
            filedir = os.path.dirname(filedir_abs)
            filedir = os.path.join(filedir, self.outfolder)
            for root, dirs, files in os.walk(filedir):
                for file in files:
                    if file.endswith('.zip'):   
                        relative_directory = os.path.relpath(root, filedir)
                        relative_file_path = os.path.join(relative_directory, file)
                        htmlstr += zipfiles % relative_file_path
            htmlstr += jbrowse_hub % slink
            htmlfile.write(htmlstr)

    def createTrackList(self):
        trackList = os.path.join(self.json, "trackList.json")
        if not os.path.exists(trackList):