Commit 4473703d authored by Penom Nom's avatar Penom Nom
Browse files

classify softwares by workflow

parent b33a79db
...@@ -49,42 +49,60 @@ tmp_directory = <path>/tmp ...@@ -49,42 +49,60 @@ tmp_directory = <path>/tmp
# where could be find binaries # where could be find binaries
[softwares] [softwares]
# uncomment and set if not in the PATH # uncomment and set if not in the PATH
#
# Global softwares
#
#blastall = /usr/bin/blastall #blastall = /usr/bin/blastall
#formatdb = /usr/bin/formatdb #formatdb = /usr/bin/formatdb
#blastn = /usr/bin/blastn #blastn = /usr/bin/blastn
#blastx = /usr/bin/blastx #blastx = /usr/bin/blastx
#makeblastdb = /usr/bin/makeblastdb #makeblastdb = /usr/bin/makeblastdb
#sfffile = /usr/bin/sfffile
#fastqc = /nosave/software/fastqc/current/fastqc
#runAssembly = /usr/bin/runAssembly
#bwa = /usr/bin/bwa #bwa = /usr/bin/bwa
#samtools = /usr/bin/samtools #samtools = /usr/bin/samtools
#ktImportBLAST = /usr/local/bin/ktImportBLAST #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 #fastq_illumina_filter = /usr/bin/fastq_illumina_filter
#CollectInsertSizeMetrics = /usr/bin/CollectInsertSizeMetrics.jar #CollectInsertSizeMetrics = /usr/bin/CollectInsertSizeMetrics.jar
#MarkDuplicates = /usr/bin/MarkDuplicates.jar #MarkDuplicates = /usr/bin/MarkDuplicates.jar
#mothur = /usr/bin/mothur #mothur = /usr/bin/mothur
#bowtie2-build = /usr/local/bin/bowtie2-build #fastx_reverse_complement = /usr/bin/fastx_reverse_complement
#tophat2 = /usr/local/bin/tophat2 #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 #geneBody_coverage.py = /usr/local/bin/geneBody_coverage.py
#infer_experiment.py = /usr/local/bin/infer_experiment.py #infer_experiment.py = /usr/local/bin/infer_experiment.py
#inner_distance.py = /usr/local/bin/inner_distance.py #inner_distance.py = /usr/local/bin/inner_distance.py
#junction_saturation.py = /usr/local/bin/junction_saturation.py #junction_saturation.py = /usr/local/bin/junction_saturation.py
#RPKM_saturation.py = /usr/local/bin/scripts/RPKM_saturation.py #RPKM_saturation.py = /usr/local/bin/scripts/RPKM_saturation.py
#junction_annotation.py = /usr/local/bin/junction_annotation.py #junction_annotation.py = /usr/local/bin/junction_annotation.py
# radseq
#ustacks = /usr/local/bin/ustacks #ustacks = /usr/local/bin/ustacks
#cstacks = /usr/local/bin/cstacks #cstacks = /usr/local/bin/cstacks
# methylseq
#trim_galore = /nosave/software/trim_galore #trim_galore = /nosave/software/trim_galore
#bismark = /nosave/software/bismark_v0.8.3/bismark #bismark = /nosave/software/bismark_v0.8.3/bismark
#bismark_genome_preparation = /nosave/software/bismark_v0.8.3/bismark_genome_preparation #bismark_genome_preparation = /nosave/software/bismark_v0.8.3/bismark_genome_preparation
#bismark_methylation_extractor = /nosave/software/bismark_v0.8.3/bismark_methylation_extractor #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 #framebot = /usr/bin/FrameBot.jar
#usearch = /usr/bin/usearch #usearch = /usr/bin/usearch
#cdhit = /usr/bin/cd-hit #cdhit = /usr/bin/cd-hit
#ktImportText = /usr/local/bin/ImportText.pl
# genome_abundance
#gaas = /usr/bin/gaas #gaas = /usr/bin/gaas
#STAR = /usr/bin/STAR
# Set cluster parameters to some components # Set cluster parameters to some components
[components] [components]
......
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