<commit_before>#! /usr/bin/perl -w

use strict;
use CGI;
use CoGe::Accessory::Web;
use CoGe::Accessory::IRODS;
use CoGe::Accessory::Utils;
use CoGe::Core::Storage qw(get_workflow_paths get_log data_type);
use CoGe::Core::Genome qw(genomecmp);
use HTML::Template;
use JSON::XS;
use Spreadsheet::WriteExcel;
use File::Basename;
use File::Path;
use File::Slurp;
use File::Spec::Functions qw(catdir catfile);
use Sort::Versions;
use CoGe::Pipelines::CoGeSNPs;
use CoGe::Pipelines::SNP::Samtools;
use CoGe::Pipelines::SNP::Platypus;
use Data::Dumper;

use vars qw(
    $P $PAGE_TITLE $USER $LINK $coge $FORM $EMBED %FUNCTION $ERROR
    $JOB_ID $LOAD_ID $TEMPDIR $CONFIGFILE
);

$PAGE_TITLE = "ExperimentView";
$ERROR = encode_json( { error => 1 } );
$CONFIGFILE = $ENV{COGE_HOME} . '/coge.conf';

$FORM = new CGI;
( $coge, $USER, $P, $LINK ) = CoGe::Accessory::Web->init(
    cgi => $FORM,<commit_msg>Fix path to CoGe SNP pipeline<commit_after>#! /usr/bin/perl -w

use strict;
use CGI;
use CoGe::Accessory::Web;
use CoGe::Accessory::IRODS;
use CoGe::Accessory::Utils;
use CoGe::Core::Storage qw(get_workflow_paths get_log data_type);
use CoGe::Core::Genome qw(genomecmp);
use HTML::Template;
use JSON::XS;
use Spreadsheet::WriteExcel;
use File::Basename;
use File::Path;
use File::Slurp;
use File::Spec::Functions qw(catdir catfile);
use Sort::Versions;
use CoGe::Pipelines::SNP::CoGeSNPs;
use CoGe::Pipelines::SNP::Samtools;
use CoGe::Pipelines::SNP::Platypus;
use Data::Dumper;

use vars qw(
    $P $PAGE_TITLE $USER $LINK $coge $FORM $EMBED %FUNCTION $ERROR
    $JOB_ID $LOAD_ID $TEMPDIR $CONFIGFILE
);

$PAGE_TITLE = "ExperimentView";
$ERROR = encode_json( { error => 1 } );
$CONFIGFILE = $ENV{COGE_HOME} . '/coge.conf';

$FORM = new CGI;
( $coge, $USER, $P, $LINK ) = CoGe::Accessory::Web->init(
    cgi => $FORM,
{'fraction_non_alphanumeric': 0.17209045780474352, 'fraction_numerical': 0.0011031439602868175, 'mean_word_length': 6.434426229508197, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 9, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2933947', 'n_tokens_mistral': 741, 'n_tokens_neox': 718, 'n_words': 168}