Commit b804a6b1 authored by Shaman Narayanasamy's avatar Shaman Narayanasamy
Browse files

Remove shell scripts

parent 5ec29408
#!/bin/bash -l
## Run IMP with MEGAHIT assembler on the wastewater (WW) sludge dataset
date
python3.4 IMP \
-m /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R1_001.fastq \
-m /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R2_001.fastq \
-t /mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R1_001.fastq \
-t /mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R2_001.fastq \
-o /home/snarayanasamy/Work/IMP_analysis/A02_20151202-megahit \
-c conf/bigbug_config_noHGfilter.imp.json \
-a megahit
date
#!/bin/bash -l
## Run IMP on default mode, using IDBA-UD on the wastewater (WW) sludge dataset
date
python3.4 IMP \
-m /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R1_001.fastq \
-m /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R2_001.fastq \
-t /mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R1_001.fastq \
-t /mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R2_001.fastq \
-o /home/snarayanasamy/Work/IMP_analysis/A02_20151130-idba \
-c conf/bigbug_config_noHGfilter.imp.json
date
#!/bin/bash -l
## Run IMP with MEGAHIT assembler on the human fecal (HF) dataset
date
python3.4 IMP \
-m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MG_R1.fq \
-m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MG_R2.fq \
-t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MT_R1.fq \
-t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MT_R2.fq \
-o /home/snarayanasamy/Work/IMP_analysis/X310763260_20151006-megahit \
-c conf/bigbug_config.imp.json \
-a megahit
date
#!/bin/bash -l
## Run IMP on default mode, using IDBA-UD on the human fecal (HF) dataset
date
python3.4 IMP \
-m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MG_R1.fq \
-m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MG_R2.fq \
-t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MT_R1.fq \
-t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MT_R2.fq \
-o /home/snarayanasamy/Work/IMP_analysis/X310763260_20151005-idba \
-c conf/bigbug_config.imp.json
date
#!/bin/bash -l
## Run IMP with MEGAHIT assembler on the simulated mock (SM) dataset
date
python3.4 IMP \
-m /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MG/73_species_MG_R1_fixed.fq \
-m /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MG/73_species_MG_R2_fixed.fq \
-t /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MT/73_species_all_R1.fastq \
-t /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MT/73_species_all_R2.fastq \
-o /home/snarayanasamy/Work/IMP_analysis/simulated_data_output_20151002-megahit \
-c conf/bigbug_config.imp.json \
-a megahit
date
#!/bin/bash -l
## Run IMP on default mode, using IDBA-UD on the simulated mock (SM) dataset
date
python3.4 IMP \
-m /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MG/73_species_MG_R1_fixed.fq \
-m /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MG/73_species_MG_R2_fixed.fq \
-t /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MT/73_species_all_R1.fastq \
-t /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MT/73_species_all_R2.fastq \
-o /home/snarayanasamy/Work/IMP_analysis/simulated_data_output_20151002-idba \
-c conf/bigbug_config.imp.json \
-a idba
date
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