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globals.sh
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globals.sh
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# provide pathes
export CONCOCT=/work/software/CONCOCT
export DESMAN=/work/software/DESMAN
# go into conda environment
source activate concoct_env
# now global vars
pe_files="data/HOW11/trim/HOW11.pe.qc.fq.gz data/LOW6/trim/LOW6.pe.qc.fq.gz data/LOW11/trim/LOW11.pe.qc.fq.gz data/HOW6/trim/HOW6.pe.qc.fq.gz data/HOW4/trim/HOW4.pe.qc.fq.gz data/LOW8/trim/LOW8.pe.qc.fq.gz data/LOW4/trim/LOW4.pe.qc.fq.gz data/HOW8/trim/HOW8.pe.qc.fq.gz data/HOW12/trim/HOW12.pe.qc.fq.gz data/LOW7/trim/LOW7.pe.qc.fq.gz data/LOW12/trim/LOW12.pe.qc.fq.gz data/HOW7/trim/HOW7.pe.qc.fq.gz data/LOW10/trim/LOW10.pe.qc.fq.gz data/HOW5/trim/HOW5.pe.qc.fq.gz data/LOW9/trim/LOW9.pe.qc.fq.gz data/LOW5/trim/LOW5.pe.qc.fq.gz data/HOW9/trim/HOW9.pe.qc.fq.gz data/HOW10/trim/HOW10.pe.qc.fq.gz"
se_files="data/HOW11/trim/HOW11.se.qc.fq.gz data/LOW6/trim/LOW6.se.qc.fq.gz data/LOW11/trim/LOW11.se.qc.fq.gz data/HOW6/trim/HOW6.se.qc.fq.gz data/HOW4/trim/HOW4.se.qc.fq.gz data/LOW8/trim/LOW8.se.qc.fq.gz data/LOW4/trim/LOW4.se.qc.fq.gz data/HOW8/trim/HOW8.se.qc.fq.gz data/HOW12/trim/HOW12.se.qc.fq.gz data/LOW7/trim/LOW7.se.qc.fq.gz data/LOW12/trim/LOW12.se.qc.fq.gz data/HOW7/trim/HOW7.se.qc.fq.gz data/LOW10/trim/LOW10.se.qc.fq.gz data/HOW5/trim/HOW5.se.qc.fq.gz data/LOW9/trim/LOW9.se.qc.fq.gz data/LOW5/trim/LOW5.se.qc.fq.gz data/HOW9/trim/HOW9.se.qc.fq.gz data/HOW10/trim/HOW10.se.qc.fq.gz"
raw_files="./data/HOW11/8777.2.112196.AGCATC.fastq.gz ./data/HOW11/8777.2.112196.AGATAG.fastq.gz ./data/HOW11/8777.2.112196.ACTCTC.fastq.gz ./data/HOW11/8777.2.112196.AGAAGA.fastq.gz ./data/LOW6/8776.5.111705.GTGGCC.fastq.gz ./data/LOW6/8776.5.111705.GTTTCG.fastq.gz ./data/LOW6/8776.5.111705.GTGAAA.fastq.gz ./data/LOW6/8776.5.111705.CGTACG.fastq.gz ./data/LOW11/8777.1.112183.ACATCT.fastq.gz ./data/LOW11/8777.1.112183.ACCGGC.fastq.gz ./data/LOW11/8777.1.112183.ACCCAG.fastq.gz ./data/LOW11/8777.1.112183.ACGATA.fastq.gz ./data/HOW6/8776.5.111705.ACTGAT.fastq.gz ./data/HOW6/8776.5.111705.ATGAGC.fastq.gz ./data/HOW6/8776.5.111705.GGTAGC.fastq.gz ./data/HOW6/8776.5.111705.GAGTGG.fastq.gz ./data/HOW13/8777.3.112209.GAATAA.fastq.gz ./data/HOW13/8777.3.112209.GATATA.fastq.gz ./data/HOW13/8777.3.112209.GATGCT.fastq.gz ./data/HOW13/8777.3.112209.GACGGA.fastq.gz ./data/HOW4/8776.4.111692.TAGCTT.fastq.gz ./data/HOW4/8776.4.111692.GATCAG.fastq.gz ./data/HOW4/8776.4.111692.CAGATC.fastq.gz ./data/HOW4/8776.4.111692.GCCAAT.fastq.gz ./data/LOW8/8776.6.111718.CGGAAT.fastq.gz ./data/LOW8/8776.6.111718.CTAGCT.fastq.gz ./data/LOW8/8776.6.111718.CCAACA.fastq.gz ./data/LOW8/8776.6.111718.CATTTT.fastq.gz ./data/LOW13/8777.3.112209.CTGCTG.fastq.gz ./data/LOW13/8777.3.112209.CGAGAA.fastq.gz ./data/LOW13/8777.3.112209.GAAACC.fastq.gz ./data/LOW13/8777.3.112209.CCTTAG.fastq.gz ./data/LOW4/8776.4.111692.CGATGT.fastq.gz ./data/LOW4/8776.4.111692.TTAGGC.fastq.gz ./data/LOW4/8776.4.111692.ACAGTG.fastq.gz ./data/LOW4/8776.4.111692.TGACCA.fastq.gz ./data/HOW8/8776.7.111731.CTCAGA.fastq.gz ./data/HOW8/8776.7.111731.GACGAC.fastq.gz ./data/HOW8/8776.7.111731.TAATCG.fastq.gz ./data/HOW8/8776.7.111731.CTATAC.fastq.gz ./data/HOW12/8777.2.112196.ATCTAT.fastq.gz ./data/HOW12/8777.2.112196.CCCATG.fastq.gz ./data/HOW12/8777.2.112196.CCACGC.fastq.gz ./data/HOW12/8777.2.112196.CCGCAA.fastq.gz ./data/LOW7/8776.6.111718.CAACTA.fastq.gz ./data/LOW7/8776.6.111718.ATTCCT.fastq.gz ./data/LOW7/8776.6.111718.CAAAAG.fastq.gz ./data/LOW7/8776.6.111718.CACCGG.fastq.gz ./data/LOW12/8777.2.112196.ATACGG.fastq.gz ./data/LOW12/8777.2.112196.AGCGCT.fastq.gz ./data/LOW12/8777.2.112196.ATCCTA.fastq.gz ./data/LOW12/8777.2.112196.AGGCCG.fastq.gz ./data/HOW7/8776.6.111718.CATGGC.fastq.gz ./data/HOW7/8776.6.111718.CACTCA.fastq.gz ./data/HOW7/8776.6.111718.CACGAT.fastq.gz ./data/HOW7/8776.6.111718.CAGGCG.fastq.gz ./data/HOW14/8777.4.112218.TGCCAT.fastq.gz ./data/HOW14/8777.4.112218.GGCACA.fastq.gz ./data/HOW14/8777.4.112218.TGAATG.fastq.gz ./data/HOW14/8777.4.112218.GGCCTG.fastq.gz ./data/LOW10/8777.1.112183.AACTTG.fastq.gz ./data/LOW10/8777.1.112183.AACAAA.fastq.gz ./data/LOW10/8777.1.112183.AAGACT.fastq.gz ./data/LOW10/8777.1.112183.AAATGC.fastq.gz ./data/HOW5/8776.5.111705.ATGTCA.fastq.gz ./data/HOW5/8776.5.111705.GTCCGC.fastq.gz ./data/HOW5/8776.5.111705.GTAGAG.fastq.gz ./data/HOW5/8776.5.111705.CCGTCC.fastq.gz ./data/LOW9/8776.7.111731.TCCCGA.fastq.gz ./data/LOW9/8776.7.111731.TCATTC.fastq.gz ./data/LOW9/8776.7.111731.TACAGC.fastq.gz ./data/LOW9/8776.7.111731.TATAAT.fastq.gz ./data/LOW14/8777.4.112218.GCAAGG.fastq.gz ./data/LOW14/8777.4.112218.GCCTTA.fastq.gz ./data/LOW14/8777.4.112218.GCACTT.fastq.gz ./data/LOW14/8777.4.112218.GCTCCA.fastq.gz ./data/LOW5/8776.4.111692.AGTTCC.fastq.gz ./data/LOW5/8776.4.111692.CTTGTA.fastq.gz ./data/LOW5/8776.4.111692.GGCTAC.fastq.gz ./data/LOW5/8776.4.111692.AGTCAA.fastq.gz ./data/HOW9/8776.7.111731.TCGGCA.fastq.gz ./data/HOW9/8776.7.111731.AAACAT.fastq.gz ./data/HOW9/8776.7.111731.TCGAAG.fastq.gz ./data/HOW9/8776.7.111731.AAAGCA.fastq.gz ./data/HOW10/8777.1.112183.AAGGAC.fastq.gz ./data/HOW10/8777.1.112183.AAGCGA.fastq.gz ./data/HOW10/8777.1.112183.ACAAAC.fastq.gz ./data/HOW10/8777.1.112183.AATAGG.fastq.gz"