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Pathway_cfg.txt
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Pathway_cfg.txt
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Lib == /System/Pipline/DNA/DNA_Micro/16S_pipeline/16S_pipeline_V1.10/lib
Bin == /System/Pipline/DNA/DNA_Micro/16S_pipeline/16S_pipeline_V1.10/bin
Software == /System/Pipline/DNA/DNA_Micro/16S_pipeline/16S_pipeline_V1.10/software
Database == /System/Pipline/DNA/DNA_Micro/16S_pipeline/16S_pipeline_V1.10/database
Qiime == /System/Pipline/DNA/DNA_Micro/16S_pipeline/16S_pipeline_V1.10/software/Python-2.7.3/bin
PUB == /Database/MICRO
## 0) The main module process and common contral tools:
Data_filter = perl Lib/01.BCQC/Data_filter_v1.1.pl
Data_filter1.1.1 = perl Lib/01.BCQC/Data_filter_v1.1.1.pl
Data_filter2 = perl Lib/01.BCQC/Data_filter_v1.2.pl
Data_filter3 = perl Lib/01.BCQC/Data_filter_v1.3.pl
combine_data = perl Lib/01.BCQC/lib/combine_data.pl
Frags_QC = perl Lib/02.FragsQC/Frags_QC.pl
Make_OTU = perl Lib/03.OTU/Make_OTU.pl
Diversity = perl Lib/04.Diversity/Diversity_compair.pl
get_result = perl Lib/00.Commbin/get_result.pl
super_worker = perl Lib/00.Commbin/super_worker.pl --qalter
sh_control = perl Lib/00.Commbin/sh_contral.pl
send_email = perl Lib/00.Commbin/TriggerAgent.pl
##-------------------new add----------------
SVG_Lib = Lib/00.Commbin/5.8.8
B_dir = Lib/00.Commbin/qsub
NODE_text = Lib/00.Commbin/compute-node.txt
##-------------------end add----------------
## 1) Barcode split, Flash chain and data stat
## 2) Extend data QC
Usearch = /System/software/MICRO/Usearch/usearch7.0.1001_i86linux32
Chime_16Sdb = Database/16S/gold.fa
Chime_itsdb = Database/ITS/UNITE_public_from_15.10.13.fasta
Qiime_exp = source Lib/03.OTU/lib/biom_activate.sh
Split_lib = Qiime/split_libraries_fastq.py
NG_QC = Software/qc/qc/ng_QC
LOGO = Software/qc/logo.png
## 3) Make OTU and OTU taxonomy and phylogeny
FA_num = perl Software/faID.pl
BIOM_activate = source Lib/04.Diversity/lib/biom_activate.sh
CONVERT_BIOM = Qiime/biom convert
CORE_SET_aligned = Database/16S/align_seqs/85_otus.pynast.fasta
S18_otu_tax = Database/18S/18S.taxonomy.txt
S18_refseq = Database/18S/18S.fa
ITS_refseq = Database/ITS/ITS.fa
ITS_OTU_tax = Database/ITS/ITS.taxonomy.txt
BAC_16S_refseq = Database/16S/97_bac_otus.fasta
BAC_16S_OTU_tax = Database/16S/97_bac_otu_taxonomy.txt
ARC_16S_refseq = Database/16S/97_arc_otus.fasta
ARC_16S_OTU_tax = Database/16S/97_arc_otu_taxonomy.txt
ITS_blast_db = Database/ITS/ITS.fa
ITS_blast_tax = Database/ITS/ITS.taxonomy.txt
SVG2XX = Software/svg2xxx_release/svg2xxx -t png
RDP_Classfier = Software/rdp_classifier_2.2/rdp_classifier-2.2.jar
KRONA = Lib/03.OTU/lib/Krona
MOTHUR = Software/Mothur/mothur/mothur
## 4) OTU and Tax diversity alalysis
SORT_otu_tab = Qiime/sort_otu_table.py
OTU_heatmap = Qiime/make_otu_heatmap_html.py
TAXT_summayr = Qiime/summarize_taxa.py
ALPHA_rarefaction = Qiime/alpha_rarefaction.py
TAB2JSON = perl Lib/00.Commbin/tab2json.pl
UPGAM = Qiime/jackknifed_beta_diversity.py
PCOA = Qiime/beta_diversity.py
SUMM_TAXA_TP = Qiime/summarize_taxa_through_plots.py
#Rscript = Software/R-3.1.0/bin/Rscript
#R = Software/R-3.1.0/bin/R
#R2 = Software/R-3.1.0/bin/R
Rscript = Rscript
R = R
R2 = Software/R-3.1.0/bin/R
CONVERT = /usr/bin/convert
#LEFSE = /System/Pipline/DNA/DNA_Micro/16S_pipeline/16S_pipeline_V1.10/software/lefse
LEFSE = /System/Pipline/DNA/DNA_Micro/16S_pipeline/16S_pipeline_V1.10/software/lefse/nsegata-lefse-1cd4f0f8e6cf
## 5) make html report and get result