comparison TrackHub.py @ 57:f9efad381948 draft

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

56:95b9d8acc235

        source_dir = os.path.dirname(file_dir)
        folder_name = os.path.basename(self.outfolder)
        source_name = os.path.basename(self.out_path)
        source = os.path.join(source_dir, folder_name, source_name)
        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)

    #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:

57:f9efad381948

        source_dir = os.path.dirname(file_dir)
        folder_name = os.path.basename(self.outfolder)
        source_name = os.path.basename(self.out_path)
        source = os.path.join(source_dir, folder_name, source_name)
        slink = source.replace('/', '_')
        slink = os.path.join('/var/www/html/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)

    #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 = "/JBrowse-1.12.1/index.html?data=%s" target="_blank" onclick="javascript:window.location.port=80">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: