lib/docopt.py

+"""Pythonic command-line interface parser that will make you smile.
+
+ * http://docopt.org
+ * Repository and issue-tracker: https://github.com/docopt/docopt
+ * Licensed under terms of MIT license (see LICENSE-MIT)
+ * Copyright (c) 2013 Vladimir Keleshev, vladimir@keleshev.com
+
+"""
+import sys
+import re
+
+
+__all__ = ['docopt']
+__version__ = '0.6.1'
+
+
+class DocoptLanguageError(Exception):
+
+    """Error in construction of usage-message by developer."""
+
+
+class DocoptExit(SystemExit):
+
+    """Exit in case user invoked program with incorrect arguments."""
+
+    usage = ''
+
+    def __init__(self, message=''):
+        SystemExit.__init__(self, (message + '\n' + self.usage).strip())
+
+
+class Pattern(object):
+
+    def __eq__(self, other):
+        return repr(self) == repr(other)
+
+    def __hash__(self):
+        return hash(repr(self))
+
+    def fix(self):
+        self.fix_identities()
+        self.fix_repeating_arguments()
+        return self
+
+    def fix_identities(self, uniq=None):
+        """Make pattern-tree tips point to same object if they are equal."""
+        if not hasattr(self, 'children'):
+            return self
+        uniq = list(set(self.flat())) if uniq is None else uniq
+        for i, child in enumerate(self.children):
+            if not hasattr(child, 'children'):
+                assert child in uniq
+                self.children[i] = uniq[uniq.index(child)]
+            else:
+                child.fix_identities(uniq)
+
+    def fix_repeating_arguments(self):
+        """Fix elements that should accumulate/increment values."""
+        either = [list(child.children) for child in transform(self).children]
+        for case in either:
+            for e in [child for child in case if case.count(child) > 1]:
+                if type(e) is Argument or type(e) is Option and e.argcount:
+                    if e.value is None:
+                        e.value = []
+                    elif type(e.value) is not list:
+                        e.value = e.value.split()
+                if type(e) is Command or type(e) is Option and e.argcount == 0:
+                    e.value = 0
+        return self
+
+
+def transform(pattern):
+    """Expand pattern into an (almost) equivalent one, but with single Either.
+
+    Example: ((-a | -b) (-c | -d)) => (-a -c | -a -d | -b -c | -b -d)
+    Quirks: [-a] => (-a), (-a...) => (-a -a)
+
+    """
+    result = []
+    groups = [[pattern]]
+    while groups:
+        children = groups.pop(0)
+        parents = [Required, Optional, OptionsShortcut, Either, OneOrMore]
+        if any(t in map(type, children) for t in parents):
+            child = [c for c in children if type(c) in parents][0]
+            children.remove(child)
+            if type(child) is Either:
+                for c in child.children:
+                    groups.append([c] + children)
+            elif type(child) is OneOrMore:
+                groups.append(child.children * 2 + children)
+            else:
+                groups.append(child.children + children)
+        else:
+            result.append(children)
+    return Either(*[Required(*e) for e in result])
+
+
+class LeafPattern(Pattern):
+
+    """Leaf/terminal node of a pattern tree."""
+
+    def __init__(self, name, value=None):
+        self.name, self.value = name, value
+
+    def __repr__(self):
+        return '%s(%r, %r)' % (self.__class__.__name__, self.name, self.value)
+
+    def flat(self, *types):
+        return [self] if not types or type(self) in types else []
+
+    def match(self, left, collected=None):
+        collected = [] if collected is None else collected
+        pos, match = self.single_match(left)
+        if match is None:
+            return False, left, collected
+        left_ = left[:pos] + left[pos + 1:]
+        same_name = [a for a in collected if a.name == self.name]
+        if type(self.value) in (int, list):
+            if type(self.value) is int:
+                increment = 1
+            else:
+                increment = ([match.value] if type(match.value) is str
+                             else match.value)
+            if not same_name:
+                match.value = increment
+                return True, left_, collected + [match]
+            same_name[0].value += increment
+            return True, left_, collected
+        return True, left_, collected + [match]
+
+
+class BranchPattern(Pattern):
+
+    """Branch/inner node of a pattern tree."""
+
+    def __init__(self, *children):
+        self.children = list(children)
+
+    def __repr__(self):
+        return '%s(%s)' % (self.__class__.__name__,
+                           ', '.join(repr(a) for a in self.children))
+
+    def flat(self, *types):
+        if type(self) in types:
+            return [self]
+        return sum([child.flat(*types) for child in self.children], [])
+
+
+class Argument(LeafPattern):
+
+    def single_match(self, left):
+        for n, pattern in enumerate(left):
+            if type(pattern) is Argument:
+                return n, Argument(self.name, pattern.value)
+        return None, None
+
+    @classmethod
+    def parse(class_, source):
+        name = re.findall('(<\S*?>)', source)[0]
+        value = re.findall('\[default: (.*)\]', source, flags=re.I)
+        return class_(name, value[0] if value else None)
+
+
+class Command(Argument):
+
+    def __init__(self, name, value=False):
+        self.name, self.value = name, value
+
+    def single_match(self, left):
+        for n, pattern in enumerate(left):
+            if type(pattern) is Argument:
+                if pattern.value == self.name:
+                    return n, Command(self.name, True)
+                else:
+                    break
+        return None, None
+
+
+class Option(LeafPattern):
+
+    def __init__(self, short=None, long=None, argcount=0, value=False):
+        assert argcount in (0, 1)
+        self.short, self.long, self.argcount = short, long, argcount
+        self.value = None if value is False and argcount else value
+
+    @classmethod
+    def parse(class_, option_description):
+        short, long, argcount, value = None, None, 0, False
+        options, _, description = option_description.strip().partition('  ')
+        options = options.replace(',', ' ').replace('=', ' ')
+        for s in options.split():
+            if s.startswith('--'):
+                long = s
+            elif s.startswith('-'):
+                short = s
+            else:
+                argcount = 1
+        if argcount:
+            matched = re.findall('\[default: (.*)\]', description, flags=re.I)
+            value = matched[0] if matched else None
+        return class_(short, long, argcount, value)
+
+    def single_match(self, left):
+        for n, pattern in enumerate(left):
+            if self.name == pattern.name:
+                return n, pattern
+        return None, None
+
+    @property
+    def name(self):
+        return self.long or self.short
+
+    def __repr__(self):
+        return 'Option(%r, %r, %r, %r)' % (self.short, self.long,
+                                           self.argcount, self.value)
+
+
+class Required(BranchPattern):
+
+    def match(self, left, collected=None):
+        collected = [] if collected is None else collected
+        l = left
+        c = collected
+        for pattern in self.children:
+            matched, l, c = pattern.match(l, c)
+            if not matched:
+                return False, left, collected
+        return True, l, c
+
+
+class Optional(BranchPattern):
+
+    def match(self, left, collected=None):
+        collected = [] if collected is None else collected
+        for pattern in self.children:
+            m, left, collected = pattern.match(left, collected)
+        return True, left, collected
+
+
+class OptionsShortcut(Optional):
+
+    """Marker/placeholder for [options] shortcut."""
+
+
+class OneOrMore(BranchPattern):
+
+    def match(self, left, collected=None):
+        assert len(self.children) == 1
+        collected = [] if collected is None else collected
+        l = left
+        c = collected
+        l_ = None
+        matched = True
+        times = 0
+        while matched:
+            # could it be that something didn't match but changed l or c?
+            matched, l, c = self.children[0].match(l, c)
+            times += 1 if matched else 0
+            if l_ == l:
+                break
+            l_ = l
+        if times >= 1:
+            return True, l, c
+        return False, left, collected
+
+
+class Either(BranchPattern):
+
+    def match(self, left, collected=None):
+        collected = [] if collected is None else collected
+        outcomes = []
+        for pattern in self.children:
+            matched, _, _ = outcome = pattern.match(left, collected)
+            if matched:
+                outcomes.append(outcome)
+        if outcomes:
+            return min(outcomes, key=lambda outcome: len(outcome[1]))
+        return False, left, collected
+
+
+class Tokens(list):
+
+    def __init__(self, source, error=DocoptExit):
+        self += source.split() if hasattr(source, 'split') else source
+        self.error = error
+
+    @staticmethod
+    def from_pattern(source):
+        source = re.sub(r'([\[\]\(\)\|]|\.\.\.)', r' \1 ', source)
+        source = [s for s in re.split('\s+|(\S*<.*?>)', source) if s]
+        return Tokens(source, error=DocoptLanguageError)
+
+    def move(self):
+        return self.pop(0) if len(self) else None
+
+    def current(self):
+        return self[0] if len(self) else None
+
+
+def parse_long(tokens, options):
+    """long ::= '--' chars [ ( ' ' | '=' ) chars ] ;"""
+    long, eq, value = tokens.move().partition('=')
+    assert long.startswith('--')
+    value = None if eq == value == '' else value
+    similar = [o for o in options if o.long == long]
+    if tokens.error is DocoptExit and similar == []:  # if no exact match
+        similar = [o for o in options if o.long and o.long.startswith(long)]
+    if len(similar) > 1:  # might be simply specified ambiguously 2+ times?
+        raise tokens.error('%s is not a unique prefix: %s?' %
+                           (long, ', '.join(o.long for o in similar)))
+    elif len(similar) < 1:
+        argcount = 1 if eq == '=' else 0
+        o = Option(None, long, argcount)
+        options.append(o)
+        if tokens.error is DocoptExit:
+            o = Option(None, long, argcount, value if argcount else True)
+    else:
+        o = Option(similar[0].short, similar[0].long,
+                   similar[0].argcount, similar[0].value)
+        if o.argcount == 0:
+            if value is not None:
+                raise tokens.error('%s must not have an argument' % o.long)
+        else:
+            if value is None:
+                if tokens.current() in [None, '--']:
+                    raise tokens.error('%s requires argument' % o.long)
+                value = tokens.move()
+        if tokens.error is DocoptExit:
+            o.value = value if value is not None else True
+    return [o]
+
+
+def parse_shorts(tokens, options):
+    """shorts ::= '-' ( chars )* [ [ ' ' ] chars ] ;"""
+    token = tokens.move()
+    assert token.startswith('-') and not token.startswith('--')
+    left = token.lstrip('-')
+    parsed = []
+    while left != '':
+        short, left = '-' + left[0], left[1:]
+        similar = [o for o in options if o.short == short]
+        if len(similar) > 1:
+            raise tokens.error('%s is specified ambiguously %d times' %
+                               (short, len(similar)))
+        elif len(similar) < 1:
+            o = Option(short, None, 0)
+            options.append(o)
+            if tokens.error is DocoptExit:
+                o = Option(short, None, 0, True)
+        else:  # why copying is necessary here?
+            o = Option(short, similar[0].long,
+                       similar[0].argcount, similar[0].value)
+            value = None
+            if o.argcount != 0:
+                if left == '':
+                    if tokens.current() in [None, '--']:
+                        raise tokens.error('%s requires argument' % short)
+                    value = tokens.move()
+                else:
+                    value = left
+                    left = ''
+            if tokens.error is DocoptExit:
+                o.value = value if value is not None else True
+        parsed.append(o)
+    return parsed
+
+
+def parse_pattern(source, options):
+    tokens = Tokens.from_pattern(source)
+    result = parse_expr(tokens, options)
+    if tokens.current() is not None:
+        raise tokens.error('unexpected ending: %r' % ' '.join(tokens))
+    return Required(*result)
+
+
+def parse_expr(tokens, options):
+    """expr ::= seq ( '|' seq )* ;"""
+    seq = parse_seq(tokens, options)
+    if tokens.current() != '|':
+        return seq
+    result = [Required(*seq)] if len(seq) > 1 else seq
+    while tokens.current() == '|':
+        tokens.move()
+        seq = parse_seq(tokens, options)
+        result += [Required(*seq)] if len(seq) > 1 else seq
+    return [Either(*result)] if len(result) > 1 else result
+
+
+def parse_seq(tokens, options):
+    """seq ::= ( atom [ '...' ] )* ;"""
+    result = []
+    while tokens.current() not in [None, ']', ')', '|']:
+        atom = parse_atom(tokens, options)
+        if tokens.current() == '...':
+            atom = [OneOrMore(*atom)]
+            tokens.move()
+        result += atom
+    return result
+
+
+def parse_atom(tokens, options):
+    """atom ::= '(' expr ')' | '[' expr ']' | 'options'
+             | long | shorts | argument | command ;
+    """
+    token = tokens.current()
+    result = []
+    if token in '([':
+        tokens.move()
+        matching, pattern = {'(': [')', Required], '[': [']', Optional]}[token]
+        result = pattern(*parse_expr(tokens, options))
+        if tokens.move() != matching:
+            raise tokens.error("unmatched '%s'" % token)
+        return [result]
+    elif token == 'options':
+        tokens.move()
+        return [OptionsShortcut()]
+    elif token.startswith('--') and token != '--':
+        return parse_long(tokens, options)
+    elif token.startswith('-') and token not in ('-', '--'):
+        return parse_shorts(tokens, options)
+    elif token.startswith('<') and token.endswith('>') or token.isupper():
+        return [Argument(tokens.move())]
+    else:
+        return [Command(tokens.move())]
+
+
+def parse_argv(tokens, options, options_first=False):
+    """Parse command-line argument vector.
+
+    If options_first:
+        argv ::= [ long | shorts ]* [ argument ]* [ '--' [ argument ]* ] ;
+    else:
+        argv ::= [ long | shorts | argument ]* [ '--' [ argument ]* ] ;
+
+    """
+    parsed = []
+    while tokens.current() is not None:
+        if tokens.current() == '--':
+            return parsed + [Argument(None, v) for v in tokens]
+        elif tokens.current().startswith('--'):
+            parsed += parse_long(tokens, options)
+        elif tokens.current().startswith('-') and tokens.current() != '-':
+            parsed += parse_shorts(tokens, options)
+        elif options_first:
+            return parsed + [Argument(None, v) for v in tokens]
+        else:
+            parsed.append(Argument(None, tokens.move()))
+    return parsed
+
+
+def parse_defaults(doc):
+    defaults = []
+    for s in parse_section('options:', doc):
+        # FIXME corner case "bla: options: --foo"
+        _, _, s = s.partition(':')  # get rid of "options:"
+        split = re.split('\n[ \t]*(-\S+?)', '\n' + s)[1:]
+        split = [s1 + s2 for s1, s2 in zip(split[::2], split[1::2])]
+        options = [Option.parse(s) for s in split if s.startswith('-')]
+        defaults += options
+    return defaults
+
+
+def parse_section(name, source):
+    pattern = re.compile('^([^\n]*' + name + '[^\n]*\n?(?:[ \t].*?(?:\n|$))*)',
+                         re.IGNORECASE | re.MULTILINE)
+    return [s.strip() for s in pattern.findall(source)]
+
+
+def formal_usage(section):
+    _, _, section = section.partition(':')  # drop "usage:"
+    pu = section.split()
+    return '( ' + ' '.join(') | (' if s == pu[0] else s for s in pu[1:]) + ' )'
+
+
+def extras(help, version, options, doc):
+    if help and any((o.name in ('-h', '--help')) and o.value for o in options):
+        print(doc.strip("\n"))
+        sys.exit()
+    if version and any(o.name == '--version' and o.value for o in options):
+        print(version)
+        sys.exit()
+
+
+class Dict(dict):
+    def __repr__(self):
+        return '{%s}' % ',\n '.join('%r: %r' % i for i in sorted(self.items()))
+
+
+def docopt(doc, argv=None, help=True, version=None, options_first=False):
+    """Parse `argv` based on command-line interface described in `doc`.
+
+    `docopt` creates your command-line interface based on its
+    description that you pass as `doc`. Such description can contain
+    --options, <positional-argument>, commands, which could be
+    [optional], (required), (mutually | exclusive) or repeated...
+
+    Parameters
+    ----------
+    doc : str
+        Description of your command-line interface.
+    argv : list of str, optional
+        Argument vector to be parsed. sys.argv[1:] is used if not
+        provided.
+    help : bool (default: True)
+        Set to False to disable automatic help on -h or --help
+        options.
+    version : any object
+        If passed, the object will be printed if --version is in
+        `argv`.
+    options_first : bool (default: False)
+        Set to True to require options precede positional arguments,
+        i.e. to forbid options and positional arguments intermix.
+
+    Returns
+    -------
+    args : dict
+        A dictionary, where keys are names of command-line elements
+        such as e.g. "--verbose" and "<path>", and values are the
+        parsed values of those elements.
+
+    Example
+    -------
+    >>> from docopt import docopt
+    >>> doc = '''
+    ... Usage:
+    ...     my_program tcp <host> <port> [--timeout=<seconds>]
+    ...     my_program serial <port> [--baud=<n>] [--timeout=<seconds>]
+    ...     my_program (-h | --help | --version)
+    ...
+    ... Options:
+    ...     -h, --help  Show this screen and exit.
+    ...     --baud=<n>  Baudrate [default: 9600]
+    ... '''
+    >>> argv = ['tcp', '127.0.0.1', '80', '--timeout', '30']
+    >>> docopt(doc, argv)
+    {'--baud': '9600',
+     '--help': False,
+     '--timeout': '30',
+     '--version': False,
+     '<host>': '127.0.0.1',
+     '<port>': '80',
+     'serial': False,
+     'tcp': True}
+
+    See also
+    --------
+    * For video introduction see http://docopt.org
+    * Full documentation is available in README.rst as well as online
+      at https://github.com/docopt/docopt#readme
+
+    """
+    argv = sys.argv[1:] if argv is None else argv
+
+    usage_sections = parse_section('usage:', doc)
+    if len(usage_sections) == 0:
+        raise DocoptLanguageError('"usage:" (case-insensitive) not found.')
+    if len(usage_sections) > 1:
+        raise DocoptLanguageError('More than one "usage:" (case-insensitive).')
+    DocoptExit.usage = usage_sections[0]
+
+    options = parse_defaults(doc)
+    pattern = parse_pattern(formal_usage(DocoptExit.usage), options)
+    # [default] syntax for argument is disabled
+    #for a in pattern.flat(Argument):
+    #    same_name = [d for d in arguments if d.name == a.name]
+    #    if same_name:
+    #        a.value = same_name[0].value
+    argv = parse_argv(Tokens(argv), list(options), options_first)
+    pattern_options = set(pattern.flat(Option))
+    for options_shortcut in pattern.flat(OptionsShortcut):
+        doc_options = parse_defaults(doc)
+        options_shortcut.children = list(set(doc_options) - pattern_options)
+        #if any_options:
+        #    options_shortcut.children += [Option(o.short, o.long, o.argcount)
+        #                    for o in argv if type(o) is Option]
+    extras(help, version, argv, doc)
+    matched, left, collected = pattern.fix().match(argv)
+    if matched and left == []:  # better error message if left?
+        return Dict((a.name, a.value) for a in (pattern.flat() + collected))
+    raise DocoptExit()

lib/ht2-stat-draw.pl

+#!/usr/bin/perl
+
+#     HTQC - a high-throughput sequencing quality control toolkit
+#
+#     This program is free software: you can redistribute it and/or modify
+#     it under the terms of the GNU General Public License as published by
+#     the Free Software Foundation, either version 3 of the License, or
+#     (at your option) any later version.
+#
+#     This program is distributed in the hope that it will be useful,
+#     but WITHOUT ANY WARRANTY; without even the implied warranty of
+#     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#     GNU General Public License for more details.
+#
+#     You should have received a copy of the GNU General Public License
+#     along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+use strict;
+use warnings;
+use File::Path;
+use File::Spec::Functions;
+use Getopt::Long;
+
+# output file name base
+my $CYC_QUAL_1       = 'cycle_quality_1';
+my $CYC_QUAL_2       = 'cycle_quality_2';
+my $CYC_QUAL_1_BOX   = 'cycle_quality_box_1';
+my $CYC_QUAL_2_BOX   = 'cycle_quality_box_2';
+my $READS_QUAL       = 'reads_quality';
+my $LANE_TILE_QUAL_1 = 'lane_tile_quality_1';
+my $LANE_TILE_QUAL_2 = 'lane_tile_quality_2';
+my $CYC_COMP_1       = 'cycle_composition_1';
+my $CYC_COMP_2       = 'cycle_composition_2';
+my $UMASK_LEN        = 'reads_length';
+my $QUAL_QQ          = 'quality_QQ';
+
+my $dir_data;
+my $WIDTH    = 600;
+my $HEIGHT   = 400;
+my $SZ_TITLE = 12;
+my $SZ_TEXT  = 9;
+my $FORMAT   = 'png';
+
+GetOptions(
+    'dir=s'        => \$dir_data,
+    'format=s'     => \$FORMAT,
+    'width=s'      => \$WIDTH,
+    'height=s'     => \$HEIGHT,
+    'title-size=s' => \$SZ_TITLE,
+    'text-size=s'  => \$SZ_TEXT,
+    'help'         => \&show_help
+);
+
+#
+# validate dir
+#
+die "data directory not specified" if !defined $dir_data;
+die "data directory not exist" if !-d $dir_data;
+
+my $file_info = catfile $dir_data, 'info.tab';
+die "info file not exist" if !-f $file_info;
+
+#
+# get info
+#
+open INFO, '<', $file_info or die "failed to open info file '$file_info': $!";
+my $PAIRED;
+my $LENGTH;
+my $QUAL_FROM;
+my $QUAL_TO;
+my $MASK;
+
+while (<INFO>) {
+    chomp;
+    my ( $key, $value ) = split /\t/;
+    if ( $key eq 'paired' ) {
+        $PAIRED = $value eq 'T' ? 1 : 0;
+    }
+    elsif ( $key eq 'length' ) {
+        $LENGTH = $value;
+    }
+    elsif ( $key eq 'quality range' ) {
+        $value =~ /^(\d+)-(\d+)$/
+          or die "failed to parse quality range: '$value'";
+        $QUAL_FROM = $1;
+        $QUAL_TO   = $2;
+    }
+    elsif ( $key eq 'mask' ) {
+        $MASK = $value eq 'T' ? 1 : 0;
+    }
+}
+
+close INFO;
+
+#
+# test the existence of gnuplot
+#
+my $HAS_GNUPLOT = 1;
+`gnuplot -V`;
+if ( $? != 0 ) {
+    print STDERR <<INFO_GNUPLOT_NOTFOUND;
+Gnuplot is not found in your system. Plot scripts are generated but are not
+rendered.
+Please install Gnuplot using the package management system of your Unix
+distribution, or visit Gnuplot website: http://sourceforge.net/projects/gnuplot
+INFO_GNUPLOT_NOTFOUND
+    $HAS_GNUPLOT = 0;
+}
+
+#
+# write gnuplot scripts
+#
+plot_cycle_quality_heatmap( $CYC_QUAL_1, 1 );
+plot_cycle_quality_heatmap( $CYC_QUAL_2, 2 ) if $PAIRED;
+
+plot_cycle_quality_box( $CYC_QUAL_1_BOX, 1 );
+plot_cycle_quality_box( $CYC_QUAL_2_BOX, 2 ) if $PAIRED;
+
+plot_reads_quality($READS_QUAL);
+
+plot_lane_tile_quality( $LANE_TILE_QUAL_1, 1 );
+plot_lane_tile_quality( $LANE_TILE_QUAL_2, 2 ) if $PAIRED;
+
+plot_cycle_composition( $CYC_COMP_1, 1 );
+plot_cycle_composition( $CYC_COMP_2, 2 ) if $PAIRED;
+
+plot_reads_length($UMASK_LEN);
+
+plot_quality_qq($QUAL_QQ) if $PAIRED;
+
+#
+# subs
+#
+
+# gnuplot scripts
+sub plot_cycle_quality_heatmap {
+    my $base = shift;
+    my $side = shift;
+
+    my $file_tab   = catfile $dir_data, $base . '.tab';
+    my $file_plot  = catfile $dir_data, $base . '.gnuplot';
+    my $file_chart = catfile $dir_data, $base . '.' . $FORMAT;
+    my $file_dat   = catfile $dir_data, $base . '.dat';
+
+    # read table
+    # write data file for gnuplot
+    open my $h_tab, '<', $file_tab
+      or die "failed to open '$file_tab' for read: $!";
+    open my $h_dat, '>', $file_dat
+      or die "failed to open '$file_dat' for write: $!";
+
+    my @qual_list;
+
+    my $line = 0;
+    while (<$h_tab>) {
+        chomp;
+        if ( $line == 0 ) {
+            ( undef, @qual_list ) = split /\t/;
+        }
+        else {
+            my ( $cyc, @values ) = split /\t/;
+            for ( my $i = 0 ; $i < @values ; $i++ ) {
+                print $h_dat join( "\t", $cyc, $qual_list[$i], $values[$i] ),
+                  "\n";
+            }
+        }
+    }
+    continue { $line++ }
+
+    close $h_tab;
+    close $h_dat;
+
+    # write script
+    my $x_min = -0.5;
+    my $x_max = $LENGTH + 0.5;
+    my $y_min = $QUAL_FROM - 0.5;
+    my $y_max = $QUAL_TO + 0.5;
+
+    open my $h_plot, '>', $file_plot or die $!;
+    print $h_plot <<HEREDOC;
+set title "Cycle Quality of Reads $side" font "*,$SZ_TITLE"
+unset key
+set terminal $FORMAT size $WIDTH,$HEIGHT
+set output "$file_chart"
+set palette rgbformulae 21,22,23
+
+set cblabel "Num reads" font "*,$SZ_TEXT"
+set cbtics font "*,$SZ_TEXT"
+
+set xrange [$x_min:$x_max]
+set yrange [$y_min:$y_max]
+set xlabel "Cycle" font "*,$SZ_TEXT"
+set ylabel "Quality" font "*,$SZ_TEXT"
+set xtics font "*,$SZ_TEXT"
+set ytics font "*,$SZ_TEXT"
+
+plot '$file_dat' using 1:2:3 with image
+
+HEREDOC
+    close $h_plot;
+
+    # run gnuplot
+    if ($HAS_GNUPLOT) {
+        system( 'gnuplot', $file_plot ) == 0 or die "gnuplot failed";
+    }
+}
+
+sub plot_cycle_quality_box {
+    my $base = shift;
+    my $side = shift;
+
+    my $file_tab   = catfile $dir_data, $base . '.tab';
+    my $file_plot  = catfile $dir_data, $base . '.gnuplot';
+    my $file_chart = catfile $dir_data, $base . '.' . $FORMAT;
+
+    # write script
+    my $x_min = -0.5;
+    my $x_max = $LENGTH + 0.5;
+    my $y_min = $QUAL_FROM - 0.5;
+    my $y_max = $QUAL_TO + 0.5;
+
+    open my $h_plot, '>', $file_plot or die $!;
+    print $h_plot <<HEREDOC;
+set title "Cycle Quality of Reads $side" font "*,$SZ_TITLE"
+unset key
+set terminal $FORMAT size $WIDTH,$HEIGHT
+set output "$file_chart"
+
+set xrange [$x_min:$x_max]
+set yrange [$y_min:$y_max]
+set xlabel "Cycle" font "*,$SZ_TEXT"
+set ylabel "Quality" font "*,$SZ_TEXT"
+set xtics font "*,$SZ_TEXT"
+set ytics font "*,$SZ_TEXT"
+
+set boxwidth 0.8 relative
+
+plot '$file_tab' using 1:3:2:6:5 with candlesticks lc rgbcolor '#00007f',\\
+     '$file_tab' using 1:7 with lines lc rgbcolor 'red'
+
+HEREDOC
+    close $h_plot;
+
+    # run gnuplot
+    if ($HAS_GNUPLOT) {
+        system( 'gnuplot', $file_plot ) == 0 or die "gnuplot failed";
+    }
+}
+
+sub plot_reads_quality {
+    my $base = shift;
+
+    my $file_tab   = catfile $dir_data, $base . '.tab';
+    my $file_plot  = catfile $dir_data, $base . '.gnuplot';
+    my $file_chart = catfile $dir_data, $base . '.' . $FORMAT;
+
+    # write script
+    open my $h_plot, '>', $file_plot or die $!;
+    print $h_plot <<HEREDOC;
+set title "Reads Quality" font "*,$SZ_TITLE"
+set terminal $FORMAT size $WIDTH,$HEIGHT
+
+set key font "*,$SZ_TEXT"
+
+set xlabel "Quality" font "*,$SZ_TEXT"
+set ylabel "Num reads" font "*,$SZ_TEXT"
+set xtics font "*,$SZ_TEXT"
+set ytics font "*,$SZ_TEXT"
+
+set output "$file_chart"
+
+HEREDOC
+
+    print $h_plot
+"plot '$file_tab' using 1:2 lc rgbcolor '#ff0000' title 'read 1 quality' with lines,\\\n";
+    print $h_plot
+"     '$file_tab' using 1:3 lc rgbcolor '#7f0000' title 'read 1 quality accum' with lines";
+
+    if ($PAIRED) {
+        print $h_plot ",\\\n";
+        print $h_plot
+"     '$file_tab' using 1:4 lc rgbcolor '#0000ff' title 'read 2 quality' with lines,\\\n";
+        print $h_plot
+"     '$file_tab' using 1:5 lc rgbcolor '#00007f' title 'read 2 quality accum' with lines\n";
+    }
+    else {
+        print $h_plot "\n";
+    }
+
+    close $h_plot;
+
+    # run gnuplot
+    if ($HAS_GNUPLOT) {
+        system( 'gnuplot', $file_plot ) == 0 or die "gnuplot failed";
+    }
+}
+
+sub plot_lane_tile_quality {
+    my $base = shift;
+    my $side = shift;
+
+    my $file_tab   = catfile $dir_data, $base . '.tab';
+    my $file_plot  = catfile $dir_data, $base . '.gnuplot';
+    my $file_chart = catfile $dir_data, $base . '.' . $FORMAT;
+    my $file_dat   = catfile $dir_data, $base . '.dat';
+
+    # read ticks
+    # create dat file
+    my @titles;
+    my @ticks_list;
+
+    open my $h_tab, '<', $file_tab
+      or die "failed to open '$file_tab' for read: $!";
+    open my $h_dat, '>', $file_dat
+      or die "failed to open '$file_dat' for write: $!";
+    my $n = 0;
+    while (<$h_tab>) {
+        chomp;
+        if ( $n == 0 ) {
+            ( undef, @titles ) = split /\t/;
+        }
+        else {
+            my ( $lane, $tile, @data ) = split /\t/;
+            push @ticks_list, "\"lane $lane tile $tile\" $n";
+            print $h_dat join( "\t", $n, @data ), "\n";
+        }
+    }
+    continue { $n++ }
+    close $h_tab;
+    close $h_dat;
+
+    my $ticks_str = join ', ', @ticks_list;
+
+    # write script
+    open my $h_plot, '>', $file_plot or die $!;
+    print $h_plot <<HEREDOC;
+set title "Lane-Tile Quality for Reads $side" font "*,$SZ_TITLE"
+set terminal $FORMAT size $WIDTH,$HEIGHT
+
+set key outside font "*,$SZ_TEXT"
+
+set xlabel "Tiles" font "*,$SZ_TEXT"
+set ylabel "Num reads" font "*,$SZ_TEXT"
+set xtics rotate 90 ($ticks_str) font "*,$SZ_TEXT"
+set ytics font "*,$SZ_TEXT"
+
+set style fill solid
+set output "$file_chart"
+plot '$file_dat' using 1:(\$5+\$4+\$3+\$2):(1) with boxes lc rgbcolor "blue" title "quality > 30", \\
+     '$file_dat' using 1:(\$4+\$3+\$2):(1) with boxes lc rgbcolor "green" title "20 < quality < 30", \\
+     '$file_dat' using 1:(\$3+\$2):(1) with boxes lc rgbcolor "red" title "10 < quality < 20", \\
+     '$file_dat' using 1:2:(1) with boxes lc rgbcolor "black" title "quality < 10"
+HEREDOC
+
+    close $h_plot;
+
+    # run gnuplot
+    if ($HAS_GNUPLOT) {
+        system( 'gnuplot', $file_plot ) == 0 or die "gnuplot failed";
+    }
+}
+
+sub plot_cycle_composition {
+    my $base = shift;
+    my $side = shift;
+
+    my $file_tab   = catfile $dir_data, $base . '.tab';
+    my $file_plot  = catfile $dir_data, $base . '.gnuplot';
+    my $file_chart = catfile $dir_data, $base . '.' . $FORMAT;
+
+    my $x_min = -0.5;
+    my $x_max = $LENGTH + 0.5;
+
+    open my $h_plot, '>', $file_plot or die $!;
+    print $h_plot <<heredoc;
+set title "Cycle Composition for Read $side" font "*,$SZ_TITLE"
+set terminal $FORMAT size $WIDTH,$HEIGHT
+set style fill solid
+
+set key outside font "*,$SZ_TEXT"
+
+set xrange [$x_min:$x_max]
+set xlabel "Cycle" font "*,$SZ_TEXT"
+set ylabel "Num reads" font "*,$SZ_TEXT"
+set xtics font "*,$SZ_TEXT"
+set ytics font "*,$SZ_TEXT"
+
+set output "$file_chart"
+heredoc
+    print $h_plot "plot";
+
+    if ($MASK) {
+        print $h_plot <<heredoc;
+'$file_tab' using 1:(\$7+\$6+\$5+\$4+\$3+\$2) with boxes lc rgbcolor "yellow" title "MASK", \\
+heredoc
+    }
+
+    print $h_plot <<heredoc;
+'$file_tab' using 1:(\$6+\$5+\$4+\$3+\$2) with boxes lc rgbcolor "grey" title "N", \\
+     '$file_tab' using 1:(\$5+\$4+\$3+\$2) with boxes lc rgbcolor "black" title "C", \\
+     '$file_tab' using 1:(\$4+\$3+\$2) with boxes lc rgbcolor "blue" title "G", \\
+     '$file_tab' using 1:(\$3+\$2) with boxes lc rgbcolor "red" title "T", \\
+     '$file_tab' using 1:2 with boxes lc rgbcolor "green" title "A"
+heredoc
+    close $h_plot;
+
+    # run gnuplot
+    if ($HAS_GNUPLOT) {
+        system( 'gnuplot', $file_plot ) == 0 or die "gnuplot failed";
+    }
+}
+
+sub plot_reads_length {
+    my $base = shift;
+
+    my $file_tab   = catfile $dir_data, $base . '.tab';
+    my $file_plot  = catfile $dir_data, $base . '.gnuplot';
+    my $file_chart = catfile $dir_data, $base . '.' . $FORMAT;
+
+    open my $h_plot, '>', $file_plot or die $!;
+    print $h_plot <<heredoc;
+set title "Reads Length" font "*,$SZ_TITLE"
+set terminal $FORMAT size $WIDTH,$HEIGHT
+
+set key font "*,$SZ_TEXT"
+
+set xlabel "Length" font "*,$SZ_TEXT"
+set ylabel "Num reads" font "*,$SZ_TEXT"
+set xtics font "*,$SZ_TEXT"
+set ytics font "*,$SZ_TEXT"
+
+set output "$file_chart"
+heredoc
+    print $h_plot
+"plot '$file_tab' using 1:2  lc rgbcolor '#ff0000' title 'read 1 length' with lines,\\\n";
+    print $h_plot
+"     '$file_tab' using 1:3  lc rgbcolor '#7f0000' title 'read 1 length accum' with lines";
+    if ($PAIRED) {
+        print $h_plot ",\\\n";
+        print $h_plot
+"     '$file_tab' using 1:4 lc rgbcolor '#0000ff' title 'read 2 length' with lines,\\\n";
+        print $h_plot
+"     '$file_tab' using 1:5 lc rgbcolor '#00007f' title 'read 2 length accum' with lines\n";
+    }
+    else {
+        print $h_plot "\n";
+    }
+    close $h_plot;
+
+    # run gnuplot
+    if ($HAS_GNUPLOT) {
+        system( 'gnuplot', $file_plot ) == 0 or die "gnuplot failed";
+    }
+}
+
+sub plot_quality_qq {
+    my $base = shift;
+
+    my $file_tab   = catfile $dir_data, $base . '.tab';
+    my $file_plot  = catfile $dir_data, $base . '.gnuplot';
+    my $file_chart = catfile $dir_data, $base . '.' . $FORMAT;
+
+    my $label_x = $QUAL_FROM + 3;
+    my $label_y = $QUAL_TO - 3;
+
+    # get pearson r value
+    open my $h_tab, '<', $file_tab
+      or die "failed to open '$file_tab' for read: $!";
+    my $tab_header = <$h_tab>;
+    chomp $tab_header;
+    $tab_header =~ /# pearson correlation: (\S+)/
+      or die "failed to parse pearson correlation from '$tab_header'";
+    my $pearson_text = $1;
+    close $h_tab;
+
+    # write gnuplot script
+    open my $h_plot, '>', $file_plot or die $!;
+    print $h_plot <<heredoc;
+set title "Read Pair Quality QQ plot" font "*,$SZ_TITLE"
+set terminal $FORMAT size $WIDTH,$HEIGHT
+set output "$file_chart"
+unset key
+
+set xrange [$QUAL_FROM:$QUAL_TO]
+set yrange [$QUAL_FROM:$QUAL_TO]
+set xtics font "*,$SZ_TEXT"
+set ytics font "*,$SZ_TEXT"
+
+set label 'r = $pearson_text' at $label_x,$label_y font "*,$SZ_TEXT"
+plot '$file_tab' with lines
+
+heredoc
+    close $h_plot;
+
+    # run gnuplot
+    if ($HAS_GNUPLOT) {
+        system( 'gnuplot', $file_plot ) == 0 or die "gnuplot failed";
+    }
+}
+
+# help document
+sub show_help {
+    print <<heredoc;
+$0 - render ht_stat outputs
+
+Usage:
+  ht_stat_draw.pl --dir STAT_DIR
+
+Options:
+--dir         the output directory of ht_stat.
+--format      picture format. [$FORMAT]
+--width       picture width. [$WIDTH]
+--height      picture height. [$HEIGHT]
+--title-size  font size for picture titles. [$SZ_TITLE]
+--text-size   font size for axis ticks, legends, etc.. [$SZ_TEXT]
+--help        show help
+heredoc
+    exit(0);
+}

lib/imp.js

-var koopa = null;
-// template
-function carousel_tmpl(selector){
-    return '<div id="${selector}" class="carousel slide" data-interval="false"><ol class="carousel-indicators"></ol><div class="carousel-inner" role="listbox"></div></div>';
-}
-
-
-
-function simple_carousel(selector){
-  return '<div class="col-sm-3 col-md-3"></div><div class="col-sm-6 col-md-6"><div id="${selector}" class="carousel slide" data-interval="false"><ol class="carousel-indicators"></ol><div class="carousel-inner" role="listbox"></div></div><a class="left carousel-control" role="button" data-slide="prev"><span class="glyphicon glyphicon-chevron-left" aria-hidden="true"></span><span class="sr-only">Previous</span></a><a class="right carousel-control" role="button" data-slide="next"><span class="glyphicon glyphicon-chevron-right" aria-hidden="true"></span><span class="sr-only">Next</span></a></div><div class="col-sm-3 col-md-3"></div>';
-}
-
-
-
-// define functions
+// format time
 String.prototype.toHHMMSS = function () {
     var sec_num = parseInt(this, 10); // don't forget the second param
     var hours   = Math.floor(sec_num / 3600);
@@ -25,6 +11,8 @@ String.prototype.toHHMMSS = function () {
     var time    = hours+'h:'+minutes+'m:'+seconds +"s";
     return time;
 }
+
+// time chart rendering
 function renderTimeChart(data, title, key, selector, total_runtime){
     var converted = [];
     for(item in data){
@@ -71,6 +59,9 @@ function renderTimeChart(data, title, key, selector, total_runtime){
     });
 }
 
+
+
+// bar chart rendrering
 function renderBarChart(data, title, key, selector, total_runtime){
     var converted = [];
     var total = 0.0;
@@ -167,83 +158,50 @@ function renderFiles(data, selector, total_runtime){
 }
 
 function renderConfiguration(data, selector){
-    var child = null, val = null, params = null;
-    var general_config = data['general'];
-    child = $("<li class='list-group-item'><ul class='list-group'><span class='label label-info'>General</span></ul></li>");
-    for(var gconf in general_config){
-        if(gconf == 'raws'){
-            val = general_config[gconf]['Metagenomics'];
-            child.append("<li class='list-group-item'><b>Metagenomics</b> : " + val + "</li>");
-            val = general_config[gconf]['Metatranscriptomics'];
-            child.append("<li class='list-group-item'><b>Metatranscriptomics</b> : " + val + "</li>");
-        } else {
-            val = general_config[gconf];
-            child.append("<li class='list-group-item'><b>" + gconf + "</b> : " + val + "</li>");
-        }
-    }
+    var child = null, val = null, params = null, p = null;
+    // rendering version information
+    child = $("<li class='list-group-item'><ul class='list-group'><span class='label label-info'>Version</span></ul></li>");
+    child.append("<li class='list-group-item'><b>" + data.IMP_VERSION + "</b></li>");
     $(selector).append(child);
-    for(item in data){
-        if(item != 'general'){
-            child = $("<li class='list-group-item'><ul class='list-group'><span class='label label-info'>" + item + "</span></ul></li>");
-            params = data[item];
-            for(p in params){
-                val = params[p];
-                child.append("<li class='list-group-item'><b>" + p + "</b> : " + val + "</li>");
+    // rendering raws
+    child = $("<li class='list-group-item'><ul class='list-group'><span class='label label-info'>Data</span></ul></li>");
+    child.append("<li class='list-group-item'><b>Metagenomics</b> : " + data.MG + "</li>");
+    child.append("<li class='list-group-item'><b>Metatranscriptomics</b> : " + data.MT + "</li>");
+    $(selector).append(child);
+
+    // rendering non-params
+    child = $("<li class='list-group-item'><ul class='list-group'><span class='label label-info'>General parameters</span></ul></li>");
+    for(var gconf in data){
+        if(gconf != 'MG' && gconf != 'MT'){
+            val = data[gconf];
+            if(typeof val !== 'object'){
+                child.append("<li class='list-group-item'><b>" + gconf + "</b> : " + val + "</li>");
             }
-            $(selector).append(child);
         }
     }
-}
+    $(selector).append(child);
 
-function renderStats(selector, path, files){
-    var fpath = null;
-    var node = $("<ul class='media-list'></ul>");
-    for(var idx in files){
-        fpath = path + '/' + files[idx];
-        node.append("<li class='media'><img class='img-responsive img-thumbnail' src='" + fpath + "'></img></li>");
-    }
-    $(selector).append(node);
-}
+    // rendering nested params
+    for(var gconf in data){
+        if(gconf != 'raws'){
+            val = data[gconf];
+            if(typeof val === 'object'){
+                child = $("<li class='list-group-item'><ul class='list-group'><span class='label label-info'>" + gconf + "</span></ul></li>");
+                for(p in val){
+                    child.append("<li class='list-group-item'><b>" + p + "</b> : " + val[p] + "</li>");
+                }
+                $(selector).append(child);
+            }
 
-function renderStatsCarousel(selector, path, files){
-    var fpath = null, dt = null, sl = null;
-    var carousel = $(carousel_tmpl(selector));
-    var slides = $(carousel).find(".carousel-inner");
-    for(var idx in files){
-        fpath = path + '/' + files[idx];
-        sl = $("<div class='item'><img class='img-responsive img-thumbnail' src='" + fpath + "'></img></div>");
-        if(idx == 0){
-            sl.addClass("active");
         }
-        slides.append(sl);
     }
-    $('#' + selector + "-wrapper").append(carousel);
-}
-
-function renderSimpleCarousel(selector, path, files){
-  var fpath = null, dt = null, sl = null;
-  var carousel = $(simple_carousel(selector));
-  var slides = $(carousel).find(".carousel-inner");
-  for(var idx in files){
-      fpath = path + '/' + files[idx];
-      sl = $("<div class='item'><img class='img-responsive img-thumbnail' src='" + fpath + "'></img></div>");
-      if(idx == 0){
-          sl.addClass("active");
-      }
-      slides.append(sl);
-  }
-  $('#' + selector + "-wrapper").append(carousel);
 }
 
-
-
-// Trigger functions
-
-
-// configuration
 if(IMP_CONFIG){
     renderConfiguration(IMP_CONFIG, '#configuration');
 }
+
+
 // runtime statistics
 if(typeof IMP_STATS !== 'undefined') {
     //renderTimeChart(IMP_STATS.rules, '% runtime per task ', 'mean-runtime', 'time-charts-mean', IMP_STATS.total_runtime);
@@ -251,115 +209,116 @@ if(typeof IMP_STATS !== 'undefined') {
     renderBarChart(IMP_STATS.rules, '% runtime per task ', 'mean-runtime', '#bar-chart', IMP_STATS.total_runtime);
 } else {
     $('#imp-stats').remove();
-    $('#imp-stats-alert').show();
-//renderTimeChart(data['rules'], 'Max runtime', 'max-runtime', 'time-charts-max');
 }
 
 
-// ht_stats
-renderStatsCarousel("carousel-mg-raw", "Preprocessing/stats/MG", [
-    "cycle_composition_2.png",
-    "cycle_quality_1.png",
-    "cycle_quality_2.png",
-    "cycle_quality_box_1.png",
-    "cycle_quality_box_2.png",
-    "lane_tile_quality_1.png",
-    "lane_tile_quality_2.png",
-    "quality_QQ.png",
-    "reads_length.png",
-    "reads_quality.png"
-]);
-
-renderStatsCarousel("carousel-mg-preprocessed", "Preprocessing/stats_after_preprocessing/MG", [
-    "cycle_composition_2.png",
-    "cycle_quality_1.png",
-    "cycle_quality_2.png",
-    "cycle_quality_box_1.png",
-    "cycle_quality_box_2.png",
-    "lane_tile_quality_1.png",
-    "lane_tile_quality_2.png",
-    "quality_QQ.png",
-    "reads_length.png",
-    "reads_quality.png"
-]);
-
-renderStatsCarousel("carousel-mt-raw", "Preprocessing/stats/MT", [
-   "cycle_composition_2.png",
-   "cycle_quality_1.png",
-   "cycle_quality_2.png",
-   "cycle_quality_box_1.png",
-   "cycle_quality_box_2.png",
-   "lane_tile_quality_1.png",
-   "lane_tile_quality_2.png",
-   "quality_QQ.png",
-   "reads_length.png",
-   "reads_quality.png"
-]);
-
-renderStatsCarousel("carousel-mt-preprocessed", "Preprocessing/stats_after_preprocessing/MT", [
-    "cycle_composition_2.png",
-    "cycle_quality_1.png",
-    "cycle_quality_2.png",
-    "cycle_quality_box_1.png",
-    "cycle_quality_box_2.png",
-    "lane_tile_quality_1.png",
-    "lane_tile_quality_2.png",
-    "quality_QQ.png",
-    "reads_length.png",
-    "reads_quality.png"
-]);
-
-renderSimpleCarousel('carousel-assembly', 'Analysis/results', [
-    'IMP-vizbin_length.png',
-    'IMP-vizbin_length_GC.png'
-]);
-
-renderSimpleCarousel('carousel-mapping', 'Analysis/results', [
-    'IMP-reads_density.png',
-    'IMP-rpkm_density.png',
-    'IMP-coverage_density.png',
-    'IMP-depth_density.png',
-    'IMP-vizbin_length_MGcov.png',
-    'IMP-vizbin_length_MTcov.png',
-    'IMP-vizbin_length_MGdepth.png',
-    'IMP-vizbin_length_MTdepth.png'
-]);
-
-renderSimpleCarousel('carousel-ration', 'Analysis/results', [
-    'IMP-vizbin_length_depthRatio.png',
-    'IMP-vizbin_length_rpkmRatio.png'
-]);
-
-renderSimpleCarousel('carousel-variant', 'Analysis/results', [
-    'IMP-var_count.png',
-    'IMP-var_density.png',
-    'IMP-vizbin_length_MGvardens.png',
-    'IMP-vizbin_length_MTvardens.png'
-]);
-
-// hide sections
-//$("section.row").hide();
-// $("section.row").prev("h2").click(function(){
-//     $(this).find(".glyphicon").toggleClass("glyphicon-plus glyphicon-minus");
-//     $(this).next("section").toggle();
-// });
-
-//carousel
-$('.left.carousel-control').click(function(){
-    $('.carousel').carousel('next');
+// BUTTONS
+$('#but-raw').on('change', function(){
+    var val = $('input[name="raw-data"]:checked').val();
+    $("#ifr-raw-stat").attr('src', val);
 });
-$('.right.carousel-control').click(function(){
-    $('.carousel').carousel('prev');
+$('#but-preprocess').on('change', function(){
+    var val = $('input[name="preprocess-data"]:checked').val();
+    $("#ifr-preprocess-stat").attr('src', val);
 });
 
-// show first tab
-$('#tabs li:first > a').tab('show');
+$('#but-annot').on('change', function(){
+    var val = $('input[name="annot-data"]:checked').val();
+    $("#ifr-kronaplot").attr('src', val);
+});
+
+
+$('#but-assembly').on('change', function(){
+    var val = $('input[name="assembly-data"]:checked').val();
+    if(val.endsWith('png')){
+        $("#assembly-wrapper").replaceWith("<div id='assembly-wrapper' class='row'><img class='img-responsive' src='" + val + "'/></div>");
+    } else {
+        $("#assembly-wrapper").replaceWith("<div id='assembly-wrapper' class='row'><iframe style='position: absolute; width: 100%;height: 100%; border: none' src='" + val + "'></iframe></div>");
+    }
+    if(val.indexOf('vizbin') > -1){
+        $('.vizbin-img').show();
+        $('.metaquast-p').hide();
+    } else {
+        $('.vizbin-img').hide();
+        $('.metaquast-p').show();
+    }
+});
+
+
+$('#but-mapping').on('change', function(){
+    var val = $('input[name="mapping-data"]:checked').val();
+    $("#mapping-wrapper").attr('src', val);
+    if(val.indexOf('vizbin') > -1){
+        $('.vizbin-img').show();
+    } else {
+        $('.vizbin-img').hide();
+    }
+});
+
+$('#but-ratio').on('change', function(){
+    var val = $('input[name="ratio-data"]:checked').val();
+    $("#ratio-wrapper").attr('src', val);
+});
+
+$('#but-variant').on('change', function(){
+    var val = $('input[name="variant-data"]:checked').val();
+    $("#variant-wrapper").attr('src', val);
+});
+
+
+
+// set last tab in cookie
+$('#tabs a[data-toggle="tab"]').on('shown.bs.tab', function (e) {
+  Cookies('tab', $(e.target).attr('href'));
+})
+// show lat iopenned tab or first one
+if(Cookies('tab')){
+    $('#tabs li > a[href=' + Cookies('tab') + ']').tab('show')
+} else {
+    $('#tabs li:first > a').tab('show');
+}
+
+// load kronaplot if people click on tab. Make a lot of errors if loaded from start.
+$('#annottab').on('show.bs.tab', function (e) {
+    if($("#MG-kronaplot").attr('src') === undefined){
+        $("#ifr-kronaplot").attr('src', 'Analysis/results/MG.gene_kegg_krona.html');
+    }
+});
+
+//load maxbin results
+$.get('Binning/MaxBin/maxbin_res.summary', function(data) {
+
+    // start the table
+    var html = '<table>';
+
+    // split into lines
+    var rows = data.split("\n");
+    var headers = false;
+    var col;
+    var colstart = '<td>';
+    var colend = '</td>';
+    // parse lines
+    rows.forEach( function getvalues(localrow) {
+        var columns = localrow.split("\t");
+        if(columns.length > 1){
+            html += "<tr>";
+            if(!headers){
+                colstart = '<th>';
+                colend = '</th>';
+                headers = true;
+            } else {
+                colstart = '<td>';
+                colend = '</td>';
+            }
+            for(var i in columns){
+                col = columns[i];
+                html += colstart + col + colend;
+            }
+            html += "</tr>";
+        }
+    })
+    html += "</table>";
+
+    $('#maxbin-results').append(html);
 
-//load html tables
-$(".table-result").each(function(idx, node) {
-  var ident = node.id;
-  //console.log(ident);
-  $("#" + ident).load("MGMT/results/" + ident + ".html", function() {
-    //console.log(ident);
-  });
 });

lib/imp.mg.html

+<!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="UTF-8">
+  <link rel="stylesheet" href="Report/lib/bootstrap.min.css">
+  <script src="Report/lib/d3.min.js"></script>
+  <script src="Report/lib/jquery-2.1.1.min.js"></script>
+  <script src="Report/lib/jquery.cookie.min.js"></script>
+  <script src="Report/data.js"></script>
+  <script src="Report/lib/bootstrap.min.js"></script>
+  <style>
+  body {
+    padding-top: 70px;
+  }
+  .bar {
+    fill: steelblue;
+  }
+
+  .axis text {
+    font: 10px sans-serif;
+  }
+
+  .axis path,
+  .axis line {
+    fill: none;
+    stroke: #000;
+    shape-rendering: crispEdges;
+  }
+
+  .img-result-container {
+    width: 350px;
+    float: left;
+  }
+
+  .table-result {
+    float: left;
+    margin: 10px;
+  }
+  .table-result table,td {
+    border: 1px solid steelblue;
+    padding: 5px;
+    text-align: center;
+  }
+
+  .imp-logo {
+      height: 150px;
+      width: 150px;
+      background: url(Report/lib/IMP_logo.png);
+      background-size: 100% 100%;
+      background-repeat: no-repeat;
+  }
+
+  .vizbin-logo {
+      width: 220px;
+  }
+
+  </style>
+</head>
+<body>
+  <div id="block-stats" class="container-fluid">
+     <div>
+         <div class="col-xs-2 col-md-2"><div class='imp-logo'></div>
+     </div>
+    <div id="tabs" role="tabpanel">
+
+          <ul id="tabnav" class="nav nav-tabs navbar-nav navbar-fixed-top navbar-inverse" role="tablist">
+            <a class="navbar-brand" href="#"> IMP <small>Integrated Meta-omic Pipeline </small></a>
+            <li><a href="#raw" aria-controls="raw" role="tab" data-toggle="tab">Raw</a></li>
+            <li><a href="#preprocess" aria-controls="preprocess" role="tab" data-toggle="tab">Preprocess</a></li>
+            <li><a href="#assembly" aria-controls="assembly" role="tab" data-toggle="tab">Assembly</a></li>
+            <li><a href="#mapping" aria-controls="mapping" role="tab" data-toggle="tab">Mapping</a></li>
+            <li><a id="annottab" href="#annotation" aria-controls="annotation" role="tab" data-toggle="tab">Annotation</a></li>
+            <li><a id="binningtab" href="#binning" aria-controls="binning" role="tab" data-toggle="tab">Binning</a></li>
+            <li><a href="#variants" aria-controls="variants" role="tab" data-toggle="tab">Variants</a></li>
+            <li><a href="#overview" aria-controls="overview" role="tab" data-toggle="tab">Workflow overview</a></li>
+            <li><a href="#configurations" aria-controls="configurations" role="tab" data-toggle="tab">Configuration</a></li>
+            <li><a href="#references" aria-controls="references" role="tab" data-toggle="tab">References</a></li>
+            <p class="navbar-text navbar-right"></p>
+          </ul>
+    </div>
+      <div id="wholecontent" class="container">
+        <div class="tab-content">
+
+
+            <!-- RAW STATISTICS -->
+            <div role="tabpanel" class="tab-pane fade" id="raw">
+              <section id="raw-section" class="row">
+                <h2><small>Raw data QC</small></h2>
+                <div id="but-raw" class="btn-group" data-toggle="buttons" name="raw-data">
+                  <label class="btn btn-primary">
+                      <input id="but-raw-mgr1" type="radio" value="Analysis/stats/mg/mg.r1.fq_fastqc.html" class="btn btn-default" name="raw-data">Metagenomic pair-1 FASTQC report
+                  </label>
+                  <label class="btn btn-primary">
+                      <input id="but-raw-mgr2" type="radio" value="Analysis/stats/mg/mg.r2.fq_fastqc.html" class="btn btn-default" name="raw-data">Metagenomic pair-2 FASTQC report
+                  </label>
+                </div>
+                <div class="row">
+                    <iframe id="ifr-raw-stat" src="Analysis/stats/mg/mg.r1.fq_fastqc.html" style="position: absolute; width: 100%;height: 100%; border: none"></iframe>
+                </div>
+              </section>
+            </div>
+
+
+          <!-- PREPROCESS STATISTICS -->
+          <div role="tabpanel" class="tab-pane fade active" id="preprocess">
+            <section id="preprocess-section" class="row">
+                <h2><small>Preprocessed data QC</small></h2>
+                <div id="but-preprocess" class="btn-group" data-toggle="buttons" name="preprocess-data">
+                  <label class="btn btn-primary">
+                      <input id="but-preprocess-mgr1" type="radio" value="Analysis/stats/mg/mg.r1_preprocessed_fastqc.html" class="btn btn-default" name="preprocess-data">Metagenomic pair-1 FASTQC report
+                  </label>
+                  <label class="btn btn-primary">
+                      <input id="but-preprocess-mgr2" type="radio" value="Analysis/stats/mg/mg.r2_preprocessed_fastqc.html" class="btn btn-default" name="preprocess-data">Metagenomic pair-2 FASTQC report
+                  </label>
+                  <label class="btn btn-primary">
+                      <input id="but-preprocess-mgse" type="radio" value="Analysis/stats/mg/mg.se_preprocessed_fastqc.html" class="btn btn-default" name="preprocess-data">Metagenomic single-end FASTQC report
+                  </label>
+                </div>
+                <div class="row">
+                    <iframe id="ifr-preprocess-stat" src="Analysis/stats/mg/mg.r1_preprocessed_fastqc.html" style="position: absolute; width: 100%;height: 100%; border: none"></iframe>
+                </div>
+            </section>
+          </div>
+
+            <!-- FILTERING -->
+            <section id="filtering-section" class="row">
+              <div class="row">
+                <div class="table-result" id="mg_read_stats"></div>
+                <div class="table-result" id="mt_read_stats"></div>
+              </div>
+            </section>
+
+          <!--  ASseMBLY -->
+          <div role="tabpanel" class="tab-pane fade" id="assembly">
+            <section id="assembly-section" class="row">
+                <h2><small>Assembly visualization, QC and taxonomic annotation</small></h2>
+                <div id="but-assembly" class="row btn-group" data-toggle="buttons" name="assembly-data">
+                    <label class="btn btn-primary active">
+                        <input id="but-assembly1" type="radio" value="Analysis/results/IMP-vizbin_length.png" class="btn btn-default" name="assembly-data" checked>VizBin + contig length
+                    </label>
+                    <label class="btn btn-primary">
+                        <input id="but-assembly2" type="radio" value="Analysis/results/IMP-vizbin_length_GC.png" class="btn btn-default" name="assembly-data">VizBin + GC %
+                    </label>
+                    <label class="btn btn-primary">
+                        <input id="but-assembly3" type="radio" value="Analysis/results/quast/summary/report.html" class="btn btn-default" name="assembly-data">MetaQUAST report
+                        <div class="metaquast-p" style="display:none">
+                            <p class="text-center lead">Sub-report made with <a href="http://bioinf.spbau.ru/metaquast">MetaQUAST</a></p>
+                        </div>
+                    </label>
+                </div>
+
+                <div class="row">
+                    <div id='assembly-wrapper' class='row'><img class='img-responsive' src='Analysis/results/IMP-vizbin_length.png'/></div>
+                </div>
+                <div class="vizbin-img row">
+                    <p class="lead text-center">
+                        In order to perform a human augmented binning of the contigs, please import the following
+                        <a href="Analysis/mg.vizbin.filtered.fa">fasta file</a> to
+                    </p>
+                </div>
+                <div class="vizbin-img row">
+                    <div style="text-align:center;">
+                        <a href="http://claczny.github.io/VizBin/"><img src='Report/lib/vizbin_logo.png'/></a>
+                    </div>
+                </div>
+
+
+
+            </section>
+          </div>
+
+          <!-- MAPPING -->
+          <div role="tabpanel" class="tab-pane fade" id="mapping">
+            <section id="mapping-section" class="row">
+                <h2><small>Read mapping visualizations</small></h2>
+                <div id="but-mapping" class="row btn-group" data-toggle="buttons" name="mapping-data">
+                    <!-- <label class="btn btn-primary active">
+                        <input id="but-mapping1" type="radio" value="Analysis/results/IMP-rpkm_density.png" class="btn btn-default" name="mapping-data" checked>RPKM density beanplot
+                    </label> -->
+                    <label class="btn btn-primary">
+                        <input id="but-mapping2" type="radio" value="Analysis/results/IMP-MG_coverage_density.png" class="btn btn-default" name="mapping-data">Coverage and depth density beanplot
+                    </label>
+                    <label class="btn btn-primary">
+                        <input id="but-mapping3" type="radio" value="Analysis/results/IMP-MG_reads_density.png" class="btn btn-default" name="mapping-data">Reads density beanplot
+                    </label>
+                    <label class="btn btn-primary">
+                        <input id="but-mapping4" type="radio" value="Analysis/results/IMP-MG_vizbin_length_cov.png" class="btn btn-default" name="mapping-data">VizBin + metagenomic coverage
+                    </label>
+                    <!-- <label class="btn btn-primary">
+                        <input id="but-mapping5" type="radio" value="Analysis/results/IMP-vizbin_length_mgcov.png" class="btn btn-default" name="mapping-data">VizBin + metatranscriptomic coverage
+                    </label> -->
+                    <label class="btn btn-primary">
+                        <input id="but-mapping6" type="radio" value="Analysis/results/IMP-MG_vizbin_length_depth.png" class="btn btn-default" name="mapping-data">VizBin + metagenomic depth of coverage
+                    </label>
+                    <!-- <label class="btn btn-primary">
+                        <input id="but-mapping7" type="radio" value="Analysis/results/IMP-vizbin_length_mgdepth.png" class="btn btn-default" name="mapping-data">VizBin + metatranscriptomic depth of coverage
+                    </label> -->
+                </div>
+                <div class="row">
+                    <img id='mapping-wrapper' class='img-responsive' src='Analysis/results/IMP-MG_reads_density.png'/>
+                </div>
+                <div class="vizbin-img row">
+                    <p class="lead text-center">
+                        In order to perform a human augmented binning of the contigs, please import the following
+                        <a href="Analysis/mg.vizbin.filtered.fa">fasta file</a> to
+                    </p>
+                </div>
+                <div class="vizbin-img row">
+                    <div style="text-align:center;">
+                        <a href="http://claczny.github.io/VizBin/"><img src='Report/lib/vizbin_logo.png'/></a>
+                    </div>
+                </div>
+          </section>
+        </div>
+
+        <!-- ANNOTATION -->
+        <div role="tabpanel" class="tab-pane fade" id="annotation">
+          <section id="annotation-section" class="row">
+              <h1><small>KEGG Ontology based Functional Krona Chart</small></h1>
+              <div id="but-annot" class="btn-group" data-toggle="buttons" name="annot-data">
+                <label class="btn btn-primary">
+                    <input id="but-annot-mg" type="radio" value="Analysis/results/mg.gene_kegg_krona.html" class="btn btn-default" name="annot-data">Metatranscriptome
+                </label>
+            </div>
+              <div class="row">
+                  <iframe id="ifr-kronaplot"  style="position: absolute; width: 80%;height: 80%; border: none"></iframe>
+              </div>
+
+          </section>
+        </div>
+        <!-- <div role="tabpanel" class="tab-pane fade" id="annotationmt">
+          <section id="annotation-section" class="row">
+              <h1>mt annotation <small>Kronaplot</small></h1>
+              <div class="row">
+                  <iframe id="mt-kronaplot" src="Analysis/results/mt.gene_kegg_krona.html" style="position: absolute; width: 80%;height: 80%; border: none"></iframe>
+              </div>
+          </section>
+        </div> -->
+
+        <!-- BINNING -->
+        <div role="tabpanel" class="tab-pane fade" id="binning">
+          <section id="binning-section" class="row">
+              <h1><small>MaxBin results</small></h1>
+
+              <div id="but-binning" class="row btn-group" data-toggle="buttons" name="binning-data">
+                  <label class="btn btn-primary active">
+                      <input id="but-binning1" type="radio" value="Binning/MaxBin/IMP-MaxBin-vizbin_length_bundance.png" class="btn btn-default" name="binning-data" checked>MaxBin bins
+                  </label>
+                  <label class="btn btn-primary">
+                      <input id="but-binning2" type="radio" value="Binning/MaxBin/IMP-MaxBin-vizbin_length_completeness_abundance.png" class="btn btn-default" name="binning-data">MaxBin bin completness
+                  </label>
+              </div>
+              <div class="row">
+                  <img id='binning-wrapper' class='img-responsive' src='Binning/MaxBin/IMP-MaxBin-vizbin_length_bundance.png'/>
+              </div>
+              <h4>
+                  MaxBin bin information
+              </h4>
+               <div id="maxbin-results" class="row"></div>
+               <p class="lead">
+                   Powered by <a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/2049-2618-2-26">MaxBin</a> and <a href="http://claczny.github.io/VizBin/">VizBin</a>.
+               </p>
+          </section>
+        </div>
+
+        <!-- VARIANTS -->
+        <div role="tabpanel" class="tab-pane fade" id="variants">
+          <section id="variants-section" class="row">
+           <h2><small>Variants </small></h2>
+           <div id="but-variant" class="row btn-group" data-toggle="buttons" name="variant-data">
+               <label class="btn btn-primary active">
+                   <input id="but-variant1" type="radio" value="Analysis/results/IMP-MG_var_count.png" class="btn btn-default" name="variant-data" checked>Variant count and density beanplot
+               </label>
+               <!-- <label class="btn btn-primary">
+                   <input id="but-variant2" type="radio" value="Analysis/results/IMP-var_density.png" class="btn btn-default" name="variant-data">Variant density beanplot
+               </label> -->
+               <label class="btn btn-primary">
+                   <input id="but-variant4" type="radio" value="Analysis/results/IMP-MG_vizbin_length_vardens.png" class="btn btn-default" name="variant-data">VizBin + metagenomic variant density
+               </label>
+           </div>
+           <div class="row">
+               <img id='variant-wrapper' class='img-responsive' src='Analysis/results/IMP-MG_var_count.png'/>
+           </div>
+           <div class="row">
+               <p class="lead vizbin-img text-center" style="display:none">
+                   In order to perform a human augmented binning of the contigs, please import the following
+                   <a href="Analysis/mg.vizbin.filtered.fa">fasta file</a> to
+               </p>
+           </div>
+           <div class="vizbin-img row" style="display:none">
+               <div style="text-align:center;">
+                   <a href="http://claczny.github.io/VizBin/"><img src='Report/lib/vizbin_logo.png'/></a>
+               </div>
+           </div>
+
+
+          </section>
+        </div>
+        <!--  IMP STATS -->
+        <div role="tabpanel" class="tab-pane fade" id="overview">
+          <section class="row">
+            <section id="impstatistics-section">
+              <h2><small>Statistics </small></h2>
+              <div id="imp-stats" class="row">
+                <div id="basic-info"></div>
+                <div id="time-charts-mean"></div>
+                <div id="bar-chart"></div>
+              </div>
+            </section>
+
+            <!--  DIAGRAMS -->
+            <span id="diagrams"></span>
+            <section id="diagrams-section">
+              <h2><small>Workflow diagram </small></h2>
+              <div id="imp-diagram" class="row">
+                <p>The workflow is also available in <a href="Report/workflow.pdf">PDF</a>.</p>
+                <img src="Report/workflow.png"/>
+              </div>
+            </section>
+          </section>
+        </div>
+        <!-- IMP CONFIG -->
+        <div role="tabpanel" class="tab-pane fade" id="configurations">
+          <section id="config-section" class="row">
+            <h2><small>Configuration </small></h2>
+            <div>
+              IMP has run with the configuration file saved at: <a href="Report/config.json">config.json</a>.
+              <ul id="configuration" class="list-group">
+              </ul>
+            </div>
+          </section>
+          <!-- IMP LOG -->
+          <span id="log"></span>
+          <section id="log-section"  class="row">
+            <h2><small>Log </small></h2>
+            <div>
+              <p>The log files register all commands that have been run by IMP.</p>
+            </div>
+            <div>
+              <p>The log are accessible in here IMP steps:
+                <ul>
+                    <li><a href="Preprocessing/Preprocessing.log">Preprocessing</a></li>
+                    <li><a href="Assembly/Assembly.log">Assembly</a></li>
+                    <li><a href="Analysis/Analysis.log">Analysis</a></li>
+                    <li><a href="Util/Util.log">Util</a></li>
+                </ul>
+            </p>
+            </div>
+          </section>
+           <section id="files-section"  class="row">
+               <h2><small>Result files </small></h2>
+               <p>All results files can be found in the <a href=".">root directory</a> of this report.</p>
+           </section>
+           <br/><br/>
+        </div>
+        <!-- REFERENCES -->
+        <div role="tabpanel" class="tab-pane fade" id="references">
+          <section id="references-section" class="row">
+            <h2><small>Please cite the pre-print article on <a href="http://biorxiv.org/">http://biorxiv.org</a>.</small></h2>
+            <div>
+                <p class="lead">
+                <strong>IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses</strong><br/>
+                <small>Shaman Narayanasamy†, Yohan Jarosz†, Emilie E.L. Muller, Cédric C. Laczny, Malte Herold1, Anne Kaysen, Anna Heintz-Buschart, Nicolás Pinel, Patrick May, and Paul Wilmes*</small>
+              </p>
+            </div>
+          </section>
+        </div>
+      </div>
+    </div>
+  </div>
+</div>
+<script src="Report/lib/imp.js"></script>
+</body>
+
+</html>

lib/imp.mg.js

+// format time
+String.prototype.toHHMMSS = function () {
+    var sec_num = parseInt(this, 10); // don't forget the second param
+    var hours   = Math.floor(sec_num / 3600);
+    var minutes = Math.floor((sec_num - (hours * 3600)) / 60);
+    var seconds = sec_num - (hours * 3600) - (minutes * 60);
+
+    if (hours   < 10) {hours   = "0"+hours;}
+    if (minutes < 10) {minutes = "0"+minutes;}
+    if (seconds < 10) {seconds = "0"+seconds;}
+    var time    = hours+'h:'+minutes+'m:'+seconds +"s";
+    return time;
+}
+
+// time chart rendering
+function renderTimeChart(data, title, key, selector, total_runtime){
+    var converted = [];
+    for(item in data){
+        converted.push({
+            label: item,
+            value: data[item][key],
+        });
+    }
+    var pie = new d3pie(selector, {
+        header: {
+            title: {
+                text: title
+            },
+            subtitle: {
+                text: (total_runtime).toString().toHHMMSS() + " total."
+            },
+            location: "pie-center",
+        },
+        data: {
+            //sortOrder: "value-asc",
+            content: converted
+        },
+        size: {
+        canvasHeight: 500,
+        canvasWidth: 500,
+        pieInnerRadius: "80%",
+        pieOuterRadius: null
+      },
+        labels: {
+            outer: {
+                format: "label",
+                hideWhenLessThanPercentage: 0,
+                pieDistance: 30
+        },
+            inner: {
+                format: "percentage",
+                hideWhenLessThanPercentage: 4
+            },
+            lines: {
+                enabled: true,
+                style: "curved",
+            }
+        }
+    });
+}
+
+
+
+// bar chart rendrering
+function renderBarChart(data, title, key, selector, total_runtime){
+    var converted = [];
+    var total = 0.0;
+    for(item in data){
+        converted.push({
+            label: item,
+            value: data[item][key],
+        });
+        total += data[item][key];
+    }
+    converted.sort(function(a, b){
+        return b.value - a.value;
+    });
+
+    function percent(value){
+        var v = (value * 100 / total).toFixed(0);
+        if(v == 0){
+            return "<1%";
+        }
+        return v + "%";
+    }
+    var margin = {top: 30, right: 50, bottom: 10, left: 400},
+    width = 960 - margin.left - margin.right,
+    height = 500 - margin.top - margin.bottom;
+
+    var x = d3.scale.linear()
+    .range([0, width])
+
+    var y = d3.scale.ordinal()
+    .rangeRoundBands([0, height], .2);
+
+    var xAxis = d3.svg.axis()
+    .scale(x)
+    .orient("top");
+
+    var svg = d3.select(selector).append("svg")
+    .attr("width", width + margin.left + margin.right)
+    .attr("height", height + margin.top + margin.bottom)
+    .append("g")
+    .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+
+    x.domain(d3.extent(converted, function(d) { return d.value; })).nice();
+    y.domain(converted.map(function(d) { return d.label; }));
+
+    var bar = svg.selectAll(".bar")
+    .data(converted)
+    .enter().append("g")
+    .attr("transform", function(d){
+        return "translate(" + x(Math.min(0, d.value)) + "," + y(d.label) + ")"});
+
+    bar.append("rect")
+    .attr("class", "bar")
+    .attr("width", function(d) { return Math.abs(x(d.value) - x(0)); })
+    .attr("height", y.rangeBand());
+
+    bar.append("text")
+    .attr("x", -6)
+    .attr("y", y.rangeBand())
+    .attr("dy", ".35em")
+    .style("text-anchor", "end")
+    .text(function(d) { return d.label; });
+
+    bar.append("text")
+    .attr("x", function(d){
+        return width + 12;
+    })
+    .attr("dy", ".35em")
+    .style("text-anchor", "end")
+    .text(function(d) { return percent(d.value); });
+
+
+    // axis
+    svg.append("g")
+    .attr("class", "x axis")
+    .call(xAxis);
+
+    svg.append("g")
+    .attr("class", "y axis")
+    .append("line")
+    .attr("x1", x(0))
+    .attr("x2", x(0))
+    .attr("y2", height);
+
+
+    function type(d) {
+        d.value = +d.value;
+        return d;
+    }
+}
+
+
+function renderFiles(data, selector, total_runtime){
+    $('#basic-info').html("IMP has run in <span class='label label-success'>" + (total_runtime).toString().toHHMMSS()+ "</span> and <span class='label label-success'>" + Object.keys(data).length + " files were generated</span>");
+}
+
+function renderConfiguration(data, selector){
+    var child = null, val = null, params = null, p = null;
+    // rendering version information
+    child = $("<li class='list-group-item'><ul class='list-group'><span class='label label-info'>Version</span></ul></li>");
+    child.append("<li class='list-group-item'><b>" + data.IMP_VERSION + "</b></li>");
+    $(selector).append(child);
+    // rendering raws
+    child = $("<li class='list-group-item'><ul class='list-group'><span class='label label-info'>Data</span></ul></li>");
+    child.append("<li class='list-group-item'><b>Metagenomics</b> : " + data.MG + "</li>");
+    child.append("<li class='list-group-item'><b>Metatranscriptomics</b> : " + data.MT + "</li>");
+    $(selector).append(child);
+
+    // rendering non-params
+    child = $("<li class='list-group-item'><ul class='list-group'><span class='label label-info'>General parameters</span></ul></li>");
+    for(var gconf in data){
+        if(gconf != 'MG' && gconf != 'MT'){
+            val = data[gconf];
+            if(typeof val !== 'object'){
+                child.append("<li class='list-group-item'><b>" + gconf + "</b> : " + val + "</li>");
+            }
+        }
+    }
+    $(selector).append(child);
+
+    // rendering nested params
+    for(var gconf in data){
+        if(gconf != 'raws'){
+            val = data[gconf];
+            if(typeof val === 'object'){
+                child = $("<li class='list-group-item'><ul class='list-group'><span class='label label-info'>" + gconf + "</span></ul></li>");
+                for(p in val){
+                    child.append("<li class='list-group-item'><b>" + p + "</b> : " + val[p] + "</li>");
+                }
+                $(selector).append(child);
+            }
+
+        }
+    }
+}
+
+if(IMP_CONFIG){
+    renderConfiguration(IMP_CONFIG, '#configuration');
+}
+
+
+// runtime statistics
+if(typeof IMP_STATS !== 'undefined') {
+    //renderTimeChart(IMP_STATS.rules, '% runtime per task ', 'mean-runtime', 'time-charts-mean', IMP_STATS.total_runtime);
+    renderFiles(IMP_STATS.files, '#files-per-samples', IMP_STATS.total_runtime);
+    renderBarChart(IMP_STATS.rules, '% runtime per task ', 'mean-runtime', '#bar-chart', IMP_STATS.total_runtime);
+} else {
+    $('#imp-stats').remove();
+}
+
+
+// BUTTONS
+$('#but-raw').on('change', function(){
+    var val = $('input[name="raw-data"]:checked').val();
+    $("#ifr-raw-stat").attr('src', val);
+});
+$('#but-preprocess').on('change', function(){
+    var val = $('input[name="preprocess-data"]:checked').val();
+    $("#ifr-preprocess-stat").attr('src', val);
+});
+
+$('#but-annot').on('change', function(){
+    var val = $('input[name="annot-data"]:checked').val();
+    $("#ifr-kronaplot").attr('src', val);
+});
+
+
+$('#but-assembly').on('change', function(){
+    var val = $('input[name="assembly-data"]:checked').val();
+    if(val.endsWith('png')){
+        $("#assembly-wrapper").replaceWith("<div id='assembly-wrapper' class='row'><img class='img-responsive' src='" + val + "'/></div>");
+    } else {
+        $("#assembly-wrapper").replaceWith("<div id='assembly-wrapper' class='row'><iframe style='position: absolute; width: 100%;height: 100%; border: none' src='" + val + "'></iframe></div>");
+    }
+    if(val.indexOf('vizbin') > -1){
+        $('.vizbin-img').show();
+        $('.metaquast-p').hide();
+    } else {
+        $('.vizbin-img').hide();
+        $('.metaquast-p').show();
+    }
+});
+
+
+$('#but-mapping').on('change', function(){
+    var val = $('input[name="mapping-data"]:checked').val();
+    $("#mapping-wrapper").attr('src', val);
+    if(val.indexOf('vizbin') > -1){
+        $('.vizbin-img').show();
+    } else {
+        $('.vizbin-img').hide();
+    }
+});
+
+$('#but-ratio').on('change', function(){
+    var val = $('input[name="ratio-data"]:checked').val();
+    $("#ratio-wrapper").attr('src', val);
+});
+
+$('#but-variant').on('change', function(){
+    var val = $('input[name="variant-data"]:checked').val();
+    $("#variant-wrapper").attr('src', val);
+});
+
+
+
+// set last tab in cookie
+$('#tabs a[data-toggle="tab"]').on('shown.bs.tab', function (e) {
+  Cookies('tab', $(e.target).attr('href'));
+})
+// show lat iopenned tab or first one
+if(Cookies('tab')){
+    $('#tabs li > a[href=' + Cookies('tab') + ']').tab('show')
+} else {
+    $('#tabs li:first > a').tab('show');
+}
+
+// load kronaplot if people click on tab. Make a lot of errors if loaded from start.
+$('#annottab').on('show.bs.tab', function (e) {
+    if($("#MG-kronaplot").attr('src') === undefined){
+        $("#ifr-kronaplot").attr('src', 'Analysis/results/mg.gene_kegg_krona.html');
+    }
+});
+
+//load maxbin results
+$.get('Binning/MaxBin/maxbin_res.summary', function(data) {
+
+    // start the table
+    var html = '<table>';
+
+    // split into lines
+    var rows = data.split("\n");
+    var headers = false;
+    var col;
+    var colstart = '<td>';
+    var colend = '</td>';
+    // parse lines
+    rows.forEach( function getvalues(localrow) {
+        var columns = localrow.split("\t");
+        if(columns.length > 1){
+            html += "<tr>";
+            if(!headers){
+                colstart = '<th>';
+                colend = '</th>';
+                headers = true;
+            } else {
+                colstart = '<td>';
+                colend = '</td>';
+            }
+            for(var i in columns){
+                col = columns[i];
+                html += colstart + col + colend;
+            }
+            html += "</tr>";
+        }
+    })
+    html += "</table>";
+
+    $('#maxbin-results').append(html);
+
+});
+
+$('#but-binning').on('change', function(){
+    var val = $('input[name="binning-data"]:checked').val();
+    $("#binning-wrapper").attr('src', val);
+});

requirements.txt

+Click
+Path.py
+requests

rules/Analysis/assembly.contig-length.rule

+rule assembly_contig_length:
+    input:
+        "Assembly/%s.assembly.merged.fa" % ASS
+    output:
+        "Analysis/%s.assembly.length.txt" % ASS,
+        "Analysis/%s.assembly.gc_content.txt" % ASS
+    shell:
+        """
+        echo "[x]  LENGTH `date +"%Y/%m/%d %H:%M:%S"`"
+        echo "Obtaining contig lengths"
+        perl {SRCDIR}/fastaNamesSizes.pl {input} > {output[0]}
+
+        echo "Obtaining GC content"
+        TMP_GC=$(mktemp --tmpdir={TMPDIR} -t "gc_out_XXXXXX.txt")
+        perl {SRCDIR}/get_GC_content.pl {input} $TMP_GC
+
+        # Th program above provides a file gc_out.txt. This command cleans the output
+        echo "Clean up output"
+        cut -f1,2 $TMP_GC | sed -e 's/>//g'> {output[1]}
+        echo "Remove intermediate files"
+        rm $TMP_GC
+        """

rules/Analysis/contig-length.rule

+rule call_contig_length:
+    input:
+        "Assembly/{type}.assembly.merged.fa"
+    output:
+        "Analysis/{type}.assembly-{type}.length.txt",
+        "Analysis/{type}.assembly-{type}.gc_content.txt",
+    shell:
+        """
+        echo "[x]  LENGTH `date +"%Y/%m/%d %H:%M:%S"`"
+        echo "Obtaining contig lengths"
+        perl {SRCDIR}/fastaNamesSizes.pl {input} > {output[0]}
+
+        echo "Obtaining GC content"
+        TMP_GC=$(mktemp --tmpdir={TMPDIR} -t "gc_out_XXXXXX.txt")
+        perl {SRCDIR}/get_GC_content.pl {input} $TMP_GC
+
+        # Th program above provides a file gc_out.txt. This command cleans the output
+        echo "Clean up output"
+        cut -f1,2 $TMP_GC | sed -e 's/>//g'> {output[1]}
+        echo "Remove intermediate files"
+        rm $TMP_GC
+        """