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Installation
1. Download & unpack the tarball: biolock_v1_0.tar.gz
> tar -zxvf biolock_v1_0.tar.gz
(https://github.com/msioda/BioLockJ/blob/master/resources/img/release_contents_v1.0.png "biolock_v1_0.tar.gz contents")
3. Install the software Dependencies required by the modules you wish to include in your pipeline.
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The install script updates the $USER bash profile to call blj_config
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The installation script completes immediately since only 1 line is added to your bash profile.
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See Commands for a full description of blj_config
> ./install > Saved backup: /users/msioda/.bash_profile~ > Saved profile: /users/msioda/.bash_profile > BioLockJ installation complete!
BioLockJ: data-wrangling done right.
Getting Started
Dependencies
Installation
Configuration
Commands
Example Pipeline
Failure Recovery
Validation
Building Modules
API
FAQ
Sequence Processing Modules
AwkFastaConverter
Gunzipper
KneadDataSanitizer
Multiplexer
PearMergeReads
RarefySeqs
SeqFileValidator
TrimPrimers
Classifier Modules
for whole genome sequences
Humann2Classifier
KrakenClassifier
Kraken2Classifier
Metaphlan2Classifier
for 16S sequences
QiimeClosedRefClassifier
QiimeDeNovoClassifier
QiimeOpenRefClassifier
RdpClassifier
Report Modules
general
Email
JsonReport
for otu tables
CompileOtuCounts
RarefyOtuCounts
RemoveLowOtuCounts
RemoveScarceOtuCounts
for taxa tables
AddMetadataToOtuTables
BuildTaxaTables
LogTransformTaxaTables
NormalizeTaxaTables
for pathway tables
AddMetadataToPathwayTables
RemoveLowPathwayCounts
RemoveScarcePathwayCounts
for statistics and visualization
R_CalculateStats
R_PlotEffectSize
R_PlotMds
R_PlotOtus
R_PlotPvalHistograms