BioLockJ requires Java 1.8+ and a Unix-like operating system such as Darwin/macOS, see Notes about environments.
BioLockJ is a pipeline manager, designed to integrate and manage external tools. These external tools are not packaged into the BioLockJ program. BioLockJ must run in an environment where these other tools have been installed OR run through docker using docker images that have the tools installed. The core program, and all modules packaged with it, have corresponding docker images.
- 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.