Run Automatically

#Automatically Cnidaria can be run completely automatically using the Make system.

-1- Put Cnidaria in your path: source enable.sh

-2- Copy the data/Makefile to your folder of interest.

cp data/Makefile <MY ANALYSIS FOLDER> && cd <MY ANALYSIS FOLDER>

-3- Create a data folder mkdir data

-4- Create a output folder mkdir out

-5- Create one folder to each of your sample. the name of the sample will be the name of the sample in the tree. be wise.

mkdir data/sample1 && cp <YOUR ORIGINAL DATA FOLDER 1>/*.fastq.gz data/sample1/
mkdir data/sample2 && cp <YOUR ORIGINAL DATA FOLDER 2>/*.fastq.gz data/sample2/

• The extensions allowed are .fq.gz .fastq.gz .fastq .fasta.gz .fa.gz .fasta .fa

-6- run make help to find which parameters can be set

make help
AVAILABLE COMMANDS: all, clean, print, help, json, maker, jfs


DATA_BASE             ?=data  - base path for input
OUT_BASE              ?=out   - base path for output
OUT_FOLDER            ?=test  - project name
NUM_SAMPLE_ROWS       ?=40000 - number of rows to sample if sampling, must be multiple of 4
SAMPLEDATA            ?=0     - sample the data

CNIDARIA_NUM_PIECES   ?=1     - number of pieces for cnidaria to multithread
CNIDARIA_DOIMAGE      ?=      - Export images (needs X11)
CNIDARIA_GENDB        ?=      - create full database [slow]
CNIDARIA_EXTRA_FILES  ?=      - add extra files to cnidaria

JELLY_KMER_SIZE       ?=21    - kmer size
JELLY_HASH_SIZE       ?=1G    - hash size
JELLY_LOWER_COUNT_FA  ?=1     - lower count for fastA files
JELLY_LOWER_COUNT_FQ  ?=2     - lower count for fastQ files
JELLY_THREADS         ?=5     - number of threads
JELLY_COUNTER_LEN     ?=7     - counter len
JELLY_OUT_COUNTER_LEN ?=1     - out counter len
JELLY_NUM_FILES       ?=300   - number of disk files

So, to set the k-mer to 17, run:

JELLY_KMER_SIZE=17 make

To change the k-mer to 17, run cnidaria multithreaded with 2 threads and generating images:

CNIDARIA_NUM_PIECES=2 JELLY_KMER_SIZE=17 CNIDARIA_DOIMAGE=1 make

to see the parameters as they will be used:

make print
USING PIGZ /usr/bin/pigz
JELLY_KMER_SIZE       21
JELLY_HASH_SIZE       1G
JELLY_LOWER_COUNT_FA  1
JELLY_LOWER_COUNT_FQ  2
JELLY_THREADS         5
JELLY_COUNTER_LEN     7
JELLY_OUT_COUNTER_LEN 1
JELLY_NUM_FILES       300

CNIDARIA_NUM_PIECES   1
CNIDARIA_EXTRA_FILES
CNIDARIA_NOIMAGE      false
CNIDARIA_NOIMAGE      false

CURR_DIR              /home/cnidaria/cnidaria/test
DATA_BASE             data
DATA_FOLDER           /home/cnidaria/cnidaria/test/data
FILE_LIST             /home/cnidaria/cnidaria/test/test_filelist.csv
DEF_FILE              /home/cnidaria/cnidaria/test/test_def.csv
OUT_MAKE              /home/cnidaria/cnidaria/test/out/test/Makefile
OUT_BASE              out
OUT_FILE              /home/cnidaria/cnidaria/test/out/test/test/test.json
OUT_DIR               /home/cnidaria/cnidaria/test/out/test
OUT_FOLDER            test
JELLYFISH             /home/cnidaria/cnidaria/src/libs/Jellyfish/bin//jellyfish

INFOLDERS
/home/cnidaria/cnidaria/test/data/Aspergillus_fumigatus
/home/cnidaria/cnidaria/test/data/Aspergillus_nidulans
/home/cnidaria/cnidaria/test/data/Aspergillus_niger
/home/cnidaria/cnidaria/test/data/Aspergillus_oryzae
/home/cnidaria/cnidaria/test/data/Candida_dubliniensis
/home/cnidaria/cnidaria/test/data/Candida_glabrata
/home/cnidaria/cnidaria/test/data/Cryptococcus_gattii
/home/cnidaria/cnidaria/test/data/Cryptococcus_neoformans
/home/cnidaria/cnidaria/test/data/Kluyveromyces_lactis
/home/cnidaria/cnidaria/test/data/Neurospora_crassa
/home/cnidaria/cnidaria/test/data/Saccharomyces_cerevisiae
/home/cnidaria/cnidaria/test/data/Schizosaccharomyces_pombe
/home/cnidaria/cnidaria/test/data/Yarrowia_lipolytica
/home/cnidaria/cnidaria/test/data/Zygosaccharomyces_rouxii

INJF
/home/cnidaria/cnidaria/test/data/Aspergillus_fumigatus/21.jf
/home/cnidaria/cnidaria/test/data/Aspergillus_nidulans/21.jf
/home/cnidaria/cnidaria/test/data/Aspergillus_niger/21.jf
/home/cnidaria/cnidaria/test/data/Aspergillus_oryzae/21.jf
/home/cnidaria/cnidaria/test/data/Candida_dubliniensis/21.jf
/home/cnidaria/cnidaria/test/data/Candida_glabrata/21.jf
/home/cnidaria/cnidaria/test/data/Cryptococcus_gattii/21.jf
/home/cnidaria/cnidaria/test/data/Cryptococcus_neoformans/21.jf
/home/cnidaria/cnidaria/test/data/Kluyveromyces_lactis/21.jf
/home/cnidaria/cnidaria/test/data/Neurospora_crassa/21.jf
/home/cnidaria/cnidaria/test/data/Saccharomyces_cerevisiae/21.jf
/home/cnidaria/cnidaria/test/data/Schizosaccharomyces_pombe/21.jf
/home/cnidaria/cnidaria/test/data/Yarrowia_lipolytica/21.jf
/home/cnidaria/cnidaria/test/data/Zygosaccharomyces_rouxii/21.jf

INCNE

-7- Run make

make