<commit_before>{
    "global_tmp_dir": "$SNIC_TMP",
    "bowtie2_rules": {
        "load_env": "module load bioinfo-tools bowtie2/2.2.6 samtools/1.1",
        "platform": "Illumina",
        "mapping_params": {
            "default": "",
            "local": "--local",
            "local_very_sensitive": "--very-sensitive-local"
        }
    },
    "samtools_rules": {
        "load_env": "module load bioinfo-tools samtools/1.3 BEDTools/2.21.0 picard/1.118",
        "picard_jars": "/sw/apps/bioinfo/picard/1.118/milou",
        "threads_for_sorting": "16"
    },
    "mapping_report_rules": {},
    "kallisto_rules": {
        "load_env": "module load bioinfo-tools kallisto/0.43.0",
        "inputtable_script":  "toolbox/scripts/kallisto_concoct/input_table.py"
    },
    "gattaca_rules": {
        "load_env": "module load gcc/4.9.4 && export PATH=/proj/b2017017/bin:$PATH"
    },
    "khmer_rules": {
        "load_env": "module load bioinfo-tools khmer/2.1.1 && export PATH=/proj/b2017017/bin:$PATH",
        "inputtable_script":  "toolbox/scripts/khmer_concoct/input_table.py"
    },
    "metabat_rules": {
        "load_default_env": "source activate binning_checkm && module load bioinfo-tools hmmer",
        "binning_params": {
            "default": {
                "load_env": "module load bioinfo-tools MetaBat",
                "commandline_params": "--minContig 1500"
            },
            "maxEdge500": {
                "load_env": "module load bioinfo-tools MetaBat",
                "commandline_params": "--minContig 1500 --maxEdge 500"
            },
        },
        "quant_commandline_params": {
            "default": "--cvExt",
            "kallisto": "--cvExt",
            "default_jgi": ""<commit_msg>Load kallisto as module on rackham<commit_after>{
    "global_tmp_dir": "$SNIC_TMP",
    "bowtie2_rules": {
        "load_env": "module load bioinfo-tools bowtie2/2.2.6 samtools/1.1",
        "platform": "Illumina",
        "mapping_params": {
            "default": "",
            "local": "--local",
            "local_very_sensitive": "--very-sensitive-local"
        }
    },
    "samtools_rules": {
        "load_env": "module load bioinfo-tools samtools/1.3 BEDTools/2.21.0 picard/1.118",
        "picard_jars": "/sw/apps/bioinfo/picard/1.118/milou",
        "threads_for_sorting": "16"
    },
    "mapping_report_rules": {},
    "kallisto_rules": {
        "load_env": "module load bioinfo-tools",
        "inputtable_script":  "toolbox/scripts/kallisto_concoct/input_table.py"
    },
    "gattaca_rules": {
        "load_env": "module load gcc/4.9.4 && export PATH=/proj/b2017017/bin:$PATH"
    },
    "khmer_rules": {
        "load_env": "module load bioinfo-tools khmer/2.1.1 && export PATH=/proj/b2017017/bin:$PATH",
        "inputtable_script":  "toolbox/scripts/khmer_concoct/input_table.py"
    },
    "metabat_rules": {
        "load_default_env": "source activate binning_checkm && module load bioinfo-tools hmmer",
        "binning_params": {
            "default": {
                "load_env": "module load bioinfo-tools MetaBat",
                "commandline_params": "--minContig 1500"
            },
            "maxEdge500": {
                "load_env": "module load bioinfo-tools MetaBat",
                "commandline_params": "--minContig 1500 --maxEdge 500"
            },
        },
        "quant_commandline_params": {
            "default": "--cvExt",
            "kallisto": "--cvExt",
            "default_jgi": ""
{'fraction_non_alphanumeric': 0.15545376467220154, 'fraction_numerical': 0.033781849413111936, 'mean_word_length': 2.1821493624772312, 'pattern_counts': {'":': 68, '<': 3, '<?xml version=': 0, '>': 3, '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': '2127826', 'n_tokens_mistral': 1251, 'n_tokens_neox': 1153, 'n_words': 188}