Dependencies - RCChan5/BioLockJ GitHub Wiki
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.