comparison TrackHub.py @ 60:ed17bb465bde draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 8386544cbce1efb5e9dd1f805a2099b3e214363f-dirty

59:caf649fc310b

import json
import utils


class TrackHub:
    def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path, metaData):
        self.input_files = inputFiles.tracks
        self.outfile = outputDirect
        self.outfolder = extra_files_path
        self.out_path = os.path.join(extra_files_path, genome)
        self.reference = reference
        self.tool_dir = tool_dir
        self.metaData = metaData
        self.raw = os.path.join(self.out_path, 'raw')
        self.json = os.path.join(self.out_path, 'json')
        try: 
            if os.path.exists(self.json):
                shutil.rmtree(self.json)
            os.makedirs(self.json)
        except OSError as e:

    #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 = "http://192.168.56.11/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:

60:ed17bb465bde

import json
import utils


class TrackHub:
    def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path, metaData, jbrowse_host):
        self.input_files = inputFiles.tracks
        self.outfile = outputDirect
        self.outfolder = extra_files_path
        self.out_path = os.path.join(extra_files_path, genome)
        self.reference = reference
        self.tool_dir = tool_dir
        self.metaData = metaData
        self.raw = os.path.join(self.out_path, 'raw')
        self.json = os.path.join(self.out_path, 'json')
        self.jbrowse_host = jbrowse_host
        try: 
            if os.path.exists(self.json):
                shutil.rmtree(self.json)
            os.makedirs(self.json)
        except OSError as e:

    #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>'
            url = self.jbrowse_host + "/JBrowse-1.12.1/index.html?data=%s"
            jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub</a></li>' % url
            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: