BioLockJ Release v0.9-5-beta (#83)

* Add Docker BLJ_SUP + BLJ_META env var support

* Update DatabaseModule summary

* code cleanup 

* Modify LogTransformTaxaTable to inherit from NormalizeTaxaTables to avoid code duplication

* replace $BLJ_SUP/resources/metadata/ with $BLJ_META in Config files

* Add blj_launch_gui -dev arg - if used will map $BLJ + $BLJ_SUP Docker volumes to simplify testing Docker updated in BioLockJ.jar

* Fix NormalizeTaxaTables + LogTransformTaxaTable bug - had error in Dr. Fodor's normalization formula

Author: mikesioda

.version

@@ -1 +1 @@
-v0.9.4-beta
+v0.9.5-beta

…urces/nextflow/nextflow_template_main.nf resources/aws/nextflow_template_main.nfresources/nextflow/nextflow_template_main.nf renamed to resources/aws/nextflow_template_main.nf resources/nextflow/nextflow_template_main.nf renamed to resources/aws/nextflow_template_main.nf

@@ -1,6 +1,11 @@
 # Deployment path: $BLJ/resources/config/default/docker.properties
 
+aws.profile=default
 aws.ram='8 GB'
+#aws.stack=
+#aws.s3=
+
+docker.user=biolockj
 
 exe.vsearchParams=--db /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
 

resources/config/default/docker.properties

@@ -1,6 +1,7 @@
 # Deployment path: $BLJ/resources/config/default/standard.properties
 # All available properties are listed (many commented out)
 ###################################################################
+#aws.profile=
 #aws.ram=
 #aws.stack=
 #aws.s3=

resources/config/default/standard.properties

@@ -0,0 +1,29 @@
+# Deployment path: $BLJ/resources/test/config/template/humann2Template.properties
+
+#BioModule biolockj.module.seq.SeqFileValidator
+#BioModule biolockj.module.seq.KneadData
+#BioModule biolockj.module.classifier.wgs.Humann2Classifier
+#BioModule biolockj.module.report.humann2.RemoveLowPathwayCounts
+#BioModule biolockj.module.report.humann2.RemoveScarcePathwayCounts
+#BioModule biolockj.module.report.taxa.NormalizeTaxaTables
+#BioModule biolockj.module.report.JsonReport
+#BioModule biolockj.module.report.Email
+
+cluster.jobHeader=#PBS -l nodes=1:ppn=8,mem=64GB,walltime=2:00:00
+
+input.dirPaths=/scratch/afodor_research/datasets/china/wgs
+input.ignoreFiles=Cleandata.stat 
+input.trimSuffix=.fq
+
+metadata.filePath=$BLJ_META/chinaMetadata.tsv
+
+pipeline.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
+
+r.nominalFields=ruralUrban
+r.timeout=20
+
+report.numReads=N
+report.taxonomyLevels=phylum,class,order,family,genus,species
+
+script.batchSize=4
+script.numThreads=8

resources/config/template/humann2Template.properties

@@ -19,7 +19,7 @@ input.dirPaths=/scratch/afodor_research/datasets/china/wgs
 input.ignoreFiles=Cleandata.stat 
 input.trimSuffix=.fq
 
-metadata.filePath=$BLJ_SUP/resources/metadata/chinaMetadata.tsv
+metadata.filePath=$BLJ_META/chinaMetadata.tsv
 
 pipeline.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
 

resources/config/template/kraken2Template.properties

@@ -19,7 +19,7 @@ input.dirPaths=/scratch/afodor_research/datasets/china/wgs
 input.ignoreFiles=Cleandata.stat 
 input.trimSuffix=.fq
 
-metadata.filePath=$BLJ_SUP/resources/metadata/chinaMetadata.tsv
+metadata.filePath=$BLJ_META/chinaMetadata.tsv
 
 pipeline.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
 

resources/config/template/krakenTemplate.properties

@@ -15,7 +15,7 @@ input.dirPaths=/scratch/afodor_research/datasets/china/wgs
 input.ignoreFiles=Cleandata.stat 
 input.trimSuffix=.fq
 
-metadata.filePath=$BLJ_SUP/resources/metadata/chinaMetadata.tsv
+metadata.filePath=$BLJ_META/chinaMetadata.tsv
 
 pipeline.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
 

resources/config/template/metaphlan2Template.properties

@@ -21,7 +21,7 @@ input.dirPaths=/scratch/afodor_research/datasets/china/16s/fw
 input.trimPrefix=first_
 input.trimSuffix=.fq
 
-metadata.filePath=$BLJ_SUP/resources/metadata/chinaMetadata.tsv
+metadata.filePath=$BLJ_META/chinaMetadata.tsv
 
 pipeline.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
 

resources/config/template/qiimeTemplate.properties

@@ -19,7 +19,7 @@ input.dirPaths=/scratch/afodor_research/datasets/china/16s/fw
 input.trimPrefix=first_
 input.trimSuffix=.fq
 
-metadata.filePath=$BLJ_SUP/resources/metadata/chinaMetadata.tsv
+metadata.filePath=$BLJ_META/chinaMetadata.tsv
 
 pipeline.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties