comparison TrackHub.py @ 52:6fec27968f86 draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 6391cdb975d14b5a7060fa1665a8a575797a0eaa-dirty

51:acedf82ea46c

        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 = '/home/galaxy/galaxy/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:

    #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 = "/static/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:

52:6fec27968f86

        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:

    #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: