classify softwares by workflow

application.properties

@@ -49,42 +49,60 @@ tmp_directory = <path>/tmp
 # where could be find binaries
 [softwares]
 # uncomment and set if not in the PATH
+#
+# Global softwares
+#
 #blastall = /usr/bin/blastall
 #formatdb = /usr/bin/formatdb
 #blastn = /usr/bin/blastn
 #blastx = /usr/bin/blastx
 #makeblastdb = /usr/bin/makeblastdb
-#sfffile = /usr/bin/sfffile
-#fastqc = /nosave/software/fastqc/current/fastqc
-#runAssembly = /usr/bin/runAssembly
 #bwa = /usr/bin/bwa
 #samtools = /usr/bin/samtools
 #ktImportBLAST = /usr/local/bin/ktImportBLAST
-#ktImportText = /usr/local/bin/ImportText.pl
+#fastqc = /nosave/software/fastqc/current/fastqc
 #fastq_illumina_filter = /usr/bin/fastq_illumina_filter
 #CollectInsertSizeMetrics = /usr/bin/CollectInsertSizeMetrics.jar
 #MarkDuplicates = /usr/bin/MarkDuplicates.jar
 #mothur = /usr/bin/mothur
-#bowtie2-build = /usr/local/bin/bowtie2-build
-#tophat2 = /usr/local/bin/tophat2
+#fastx_reverse_complement = /usr/bin/fastx_reverse_complement
+#STAR = /usr/bin/STAR
+
+#
+# workflow specific
+#
+
+# r454_qc
+#sfffile = /usr/bin/sfffile
+#runAssembly = /usr/bin/runAssembly
+
+# illumina_rnaseq
 #geneBody_coverage.py = /usr/local/bin/geneBody_coverage.py
 #infer_experiment.py = /usr/local/bin/infer_experiment.py
 #inner_distance.py = /usr/local/bin/inner_distance.py
 #junction_saturation.py = /usr/local/bin/junction_saturation.py
 #RPKM_saturation.py = /usr/local/bin/scripts/RPKM_saturation.py
 #junction_annotation.py = /usr/local/bin/junction_annotation.py
+
+
+# radseq
 #ustacks = /usr/local/bin/ustacks
 #cstacks = /usr/local/bin/cstacks
+
+# methylseq
 #trim_galore = /nosave/software/trim_galore
 #bismark = /nosave/software/bismark_v0.8.3/bismark
 #bismark_genome_preparation = /nosave/software/bismark_v0.8.3/bismark_genome_preparation
 #bismark_methylation_extractor = /nosave/software/bismark_v0.8.3/bismark_methylation_extractor
-#fastx_reverse_complement = /usr/bin/fastx_reverse_complement
+
+# gene_diversity
 #framebot = /usr/bin/FrameBot.jar
 #usearch = /usr/bin/usearch
 #cdhit = /usr/bin/cd-hit
+#ktImportText = /usr/local/bin/ImportText.pl
+
+# genome_abundance
 #gaas = /usr/bin/gaas
-#STAR = /usr/bin/STAR
 
 # Set cluster parameters to some components
 [components]