Dependencies

BioLockJ requires Java 1.8+ and a Unix-like operating system such as Darwin/macOS.

• Dependencies are required by modules listed in the BioModule Function column.
• Users DO NOT NEED TO INSTALL dependencies if not interested in the listed modules.
  • For example, if you intend to classify 16S samples with RDP and WGS samples with Kraken, do not install:
    Bowtie2, GNU Awk, GNU Gzip, MetaPhlAn2, Python, QIIME 1, or Vsearch.

#	Program	Version	BioModule Function	Link
1	Bowtie2	2.3.2	Metaphlan2Classifier: Build reference indexes	download
2	GNU Awk	4.0.2	AwkFastaConverter: Convert Fastq to Fasta BuildQiimeMapping: Format metadata as QIIME mapping QiimeClosedRefClassifier: Build batch mapping files	download
3	GNU Gzip	1.5	AwkFastaConverter: Decompress .gz files Gunzipper: Decompress .gz files	download
4	Kraken	0.10.5-beta	KrakenClassifier: Report WGS taxonomic summary	download
5	MetaPhlAn2	2.0	Metaphlan2Classifier: Report WGS taxonomic summary (WGS)	download
6	Python	2.7.12	BuildQiimeMapping: Run validate_mapping_file.py MergeQiimeOtuTables: Run merge_otu_tables.py QiimeClosedRefClassifier: Run pick_closed_reference_otus.py QiimeDeNovoClassifier: Run pick_de_novo_otus.py QiimeOpenRefClassifier: Run pick_open_reference_otus.py QiimeClassifier: Run add_alpha_to_mapping_file.py, add_qiime_labels.py, alpha_diversity.py, filter_otus_from_otu_table.py, print_qiime_config.py, and summarize_taxa.py Metaphlan2Classifier: Run metaphlan2.py	download
7	PEAR	0.9.8	Paired-End reAd merger PearMergeReads Merge paired Fastq files since some classifiers (RDP & QIIME) will not accept paired reads.	download
8	QIIME 1	1.9.1	Quantitative Insights Into Microbial Ecology BuildQiimeMapping: Validate QIIME mapping MergeQiimeOtuTables: Merge otu_table.biom files QiimeClosedRefClassifier: Pick OTUs by reference QiimeDeNovoClassifier: Pick OTUs by clustering QiimeOpenRefClassifier: Pick OTUs by reference and clustering QiimeClassifier: Report 16S taxonomic summary	download
9	R	3.5.0	R_CalculateStats: Statistical modeling R_PlotPvalHistograms: Plot p-value histograms for each reportable metadata field R_PlotOtus: Build OTU-metadata boxplots and scatterplots R_PlotMds: Plot by top MDS axis R_PlotEffectSize: Build barplot of effect magnetude by OTU/taxa	download
10	R-coin	1.2	COnditional Inference procedures in a permutatioN test framework R_CalculateStats: Compute exact Wilcox_test p-values	download
11	R-ggpubr	0.1.8	R_PlotPvalHistograms: Set color palette R_PlotMds: Set color palette R_PlotEffectSize: Set color palette	download
12	R-Kendall	2.2	R_CalculateStats: Compute rank correlation p-values for continuous data types	download
13	R-properties	0.0-9	R_Module: Reads in the MASTER Configuration properties file from the pipeline root directory	download
14	R-stringr	1.2.0	R_Module: For string manipulation for handling Configuration properties	download
15	R-vegan	2.5-2	R_PlotMds: Ordination methods, diversity analysis and other functions for ecologists.	download
16	RDP	2.12	Ribosomal Database Project RdpClassifier: Report 16S taxonomic summary	download
17	Vsearch	2.4.3	QiimeDeNovoClassifier: Chimera detection QiimeOpenRefClassifier: Chimera detection	download

Version Dependencies

• The Version column contains the version tested during BioLockJ development, but other versions can often be substituted.
• Major releases (such as Python 2 vs. Python 3) contain API changes that will not integrate with the current BioLockJ code.
• Application APIs often change over time, so not all versions are supported. For example, Bowtie2 did not add the large index functionality until version 2.3.2.