%%bash
date
system_profiler SPSoftwareDataType

"""
Explanation: Running BSMAP with different version of Genome
10k cuttoff
End of explanation
"""


bsmaploc="/Users/Shared/Apps/bsmap-2.74/"


cd /Volumes/web/halfshell/working-directory/

!ls -lh 

mkdir 16-10-29

cd 16-10-29

"""
Explanation: <img src="http://eagle.fish.washington.edu/cnidarian/skitch/Whole_genome_BSseq_December_2015_·_RobertsLab_project-olympia_oyster-genomic_Wiki_1DAD4A4D.png" alt="Whole_genome_BSseq_December_2015_·_RobertsLab_project-olympia_oyster-genomic_Wiki_1DAD4A4D.png" width=50%/>
End of explanation
"""


# Genome

cd ../data

!curl -O http://owl.fish.washington.edu/halfshell/working-directory/16-10-24/Ostrea_lurida-Scaff-10k.fa

!ls

!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/4_TGACCA_L001_R1_001.fastq.gz

!mv 4_TGACCA_L001_R1_001.fastq.gz ../16-10-17/4_TGACCA_L001_R1_001.fastq.gz

!ls ../16-10-17/*gz


pwd

for i in ("1_ATCACG","2_CGATGT","3_TTAGGC","5_ACAGTG","4_TGACCA", "6_GCCAAT", "7_CAGATC", "8_ACTTGA"):
    !{bsmaploc}bsmap \
-a ../16-10-17/{i}_L001_R1_001.fastq.gz \
-d Ostrea_lurida-Scaff-10k.fa \
-o bsmap_out_{i}.sam \
-p 8 \
2> bsmap_out_{i}.stderr

!date

!ls bsmap

!tail *err

"""
Explanation: <img src="http://eagle.fish.washington.edu/cnidarian/skitch/Whole_genome_BSseq_December_2015_·_RobertsLab_project-olympia_oyster-genomic_Wiki_1DAD4D68.png" alt="Whole_genome_BSseq_December_2015_·_RobertsLab_project-olympia_oyster-genomic_Wiki_1DAD4D68.png"/>
End of explanation
"""


