docker run - p 8888:8888 -v /Users/sam/data/:/data -v /Users/sam/owl_home/:/owl_home -v /Users/sam/owl_web/:owl_web -v /Users/sam/gitrepos/LabDocs/jupyter_nbs/sam/:/jupyter_nbs -it 0ba43904567e
The command allows access to Jupyter Notebook over port 8888 and makes my Jupyter Notebook GitHub repo and my data files on Owl/home and Owl/web accessible to the Docker container.
Once the container was started, started Jupyter Notebook with the following command inside the Docker container:
jupyter notebook
This is configured in the Docker container to launch a Jupyter Notebook without a browser on port 8888.
The Docker container is running on an image created from this Dockerfile (Git commit 65ab831)
%%bash
date
Thu Nov 17 22:30:49 UTC 2016
%%bash
hostname
65e23f54bcc9
%%bash
lscpu
Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 8 On-line CPU(s) list: 0-7 Thread(s) per core: 1 Core(s) per socket: 8 Socket(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 26 Model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz Stepping: 5 CPU MHz: 2260.998 BogoMIPS: 4521.99 Hypervisor vendor: KVM Virtualization type: full L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 8192K
%%bash
ls -l /root/owl_web/Athaliana/20160715_pyrad_outfiles
total 1908968 -rw-rw-rw- 1 srlab staff 260547113 Aug 16 15:46 oly_gbs_pyrad.alleles -rw-rw-rw- 1 srlab staff 239419515 Aug 16 15:46 oly_gbs_pyrad.excluded_loci -rw-rw-rw- 1 srlab staff 126920538 Aug 16 15:46 oly_gbs_pyrad.gphocs -rw-rw-rw- 1 srlab staff 133378169 Aug 16 15:46 oly_gbs_pyrad.loci -rw-rw-rw- 1 srlab staff 86991 Aug 16 15:47 oly_gbs_pyrad.migrate -rw-rw-rw- 1 srlab staff 571222263 Aug 16 15:47 oly_gbs_pyrad.nex -rw-rw-rw- 1 srlab staff 463115051 Aug 16 15:47 oly_gbs_pyrad.phy -rw-rw-rw- 1 srlab staff 1266466 Aug 16 15:46 oly_gbs_pyrad.phy.partitions -rw-rw-rw- 1 srlab staff 26795940 Aug 16 15:46 oly_gbs_pyrad.snps -rw-rw-rw- 1 srlab staff 11519817 Aug 16 15:46 oly_gbs_pyrad.snps.geno -rwxrwxrwx 1 srlab staff 13474538 Aug 16 22:20 oly_gbs_pyrad.str -rw-rw-rw- 1 srlab staff 30531 Aug 16 15:46 oly_gbs_pyrad.treemix.gz -rw-rw-rw- 1 srlab staff 2417961 Aug 16 15:46 oly_gbs_pyrad.unlinked_snps -rw-rw-rw- 1 srlab staff 2441102 Aug 16 15:46 oly_gbs_pyrad.usnps.geno -rw-rw-rw- 1 srlab staff 50527186 Aug 16 15:46 oly_gbs_pyrad.vcf -rw-rw-rw- 1 srlab staff 0 Aug 16 15:51 oly_gbs_pyrad.vcf.fai -rw-rw-rw- 1 srlab staff 50527182 Aug 16 16:01 oly_gbs_pyrad_no_spaces.vcf -rw-rw-rw- 1 srlab staff 1056041 Aug 16 16:24 oly_gbs_pyrad_no_spaces.vcf.idx
%%bash
mkdir /root/data/20161117_oly_gbs_vcf_analysis
%%bash
time cp -avr /root/owl_web/Athaliana/20160715_pyrad_outfiles/oly_gbs_pyrad.vcf /root/data/20161117_oly_gbs_vcf_analysis/
'/root/owl_web/Athaliana/20160715_pyrad_outfiles/oly_gbs_pyrad.vcf' -> '/root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf'
real 0m2.747s user 0m0.000s sys 0m0.410s
%%bash
head -12 /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf
##fileformat=VCFv4.1 ##fileDate=20160725 ##source=pyRAD.v.3.0.66 ##reference=common_allele_at_each_locus ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1HL_10A.assembled 1HL_11A.assembled 1HL_12A.assembled 1HL_13A.assembled 1HL_14A.assembled 1HL_15A.assembled 1HL_16A.assembled 1HL_17A.assembled 1HL_19A.assembled 1HL_1A.assembled 1HL_20A.assembled 1HL_21A.assembled 1HL_22A.assembled 1HL_23A.assembled 1HL_24A.assembled 1HL_25A.assembled 1HL_26A.assembled 1HL_27A.assembled 1HL_28A.assembled 1HL_29A.assembled 1HL_2A.assembled 1HL_31A.assembled 1HL_33A.assembled 1HL_34A.assembled 1HL_35A.assembled 1HL_3A.assembled 1HL_4A.assembled 1HL_5A.assembled 1HL_6A.assembled 1HL_7A.assembled 1HL_8A.assembled 1HL_9A.assembled 1NF_10A.assembled 1NF_11A.assembled 1NF_12A.assembled 1NF_13A.assembled 1NF_14A.assembled 1NF_15A.assembled 1NF_16A.assembled 1NF_17A.assembled 1NF_18A.assembled 1NF_19A.assembled 1NF_1A.assembled 1NF_20A.assembled 1NF_21A.assembled 1NF_22A.assembled 1NF_23A.assembled 1NF_24A.assembled 1NF_25A.assembled 1NF_26A.assembled 1NF_27A.assembled 1NF_28A.assembled 1NF_29A.assembled 1NF_2A.assembled 1NF_30A.assembled 1NF_31A.assembled 1NF_32A.assembled 1NF_33A.assembled 1NF_4A.assembled 1NF_5A.assembled 1NF_6A.assembled 1NF_7A.assembled 1NF_8A.assembled 1NF_9A.assembled 1SN_10A.assembled 1SN_11A.assembled 1SN_12A.assembled 1SN_13A.assembled 1SN_14A.assembled 1SN_15A.assembled 1SN_16A.assembled 1SN_17A.assembled 1SN_18A.assembled 1SN_19A.assembled 1SN_1A.assembled 1SN_20A.assembled 1SN_21A.assembled 1SN_22A.assembled 1SN_23A.assembled 1SN_24A.assembled 1SN_25A.assembled 1SN_26A.assembled 1SN_27A.assembled 1SN_28A.assembled 1SN_29A.assembled 1SN_2A.assembled 1SN_30A.assembled 1SN_31A.assembled 1SN_32A.assembled 1SN_3A.assembled 1SN_4A.assembled 1SN_5A.assembled 1SN_6A.assembled 1SN_7A.assembled 1SN_8A.assembled 1SN_9A.assembled
%%bash
head -12 /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf | wc -l
12
$(awk 'NR == 12 {print $0}' - This uses awk to process only the 12th line (NR == 12) of the file and prints all the fields ({print $0}) on that line.¶if [[ "$i" =~ 1HL.* ]] then echo "$i" >> /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop - A set of if/elif statements that evaluate each field from the awk command and determines if they match a pattern ([[ "$i" =~ 1HL.* ]]. If they match that pattern, the value currently stored in $i is written to the appropriate population file.¶%%bash
time for i in $(awk 'NR == 12 {print $0}' /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf)
do
if [[ "$i" =~ 1HL.* ]]
then echo "$i" >> /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop
elif [[ "$i" =~ 1NF.* ]]
then echo "$i" >> /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop
elif [[ "$i" =~ 1SN.* ]]
then echo "$i" >> /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop
fi
done
real 0m2.496s user 0m0.050s sys 0m0.900s
%%bash
cat /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop
1HL_10A.assembled 1HL_11A.assembled 1HL_12A.assembled 1HL_13A.assembled 1HL_14A.assembled 1HL_15A.assembled 1HL_16A.assembled 1HL_17A.assembled 1HL_19A.assembled 1HL_1A.assembled 1HL_20A.assembled 1HL_21A.assembled 1HL_22A.assembled 1HL_23A.assembled 1HL_24A.assembled 1HL_25A.assembled 1HL_26A.assembled 1HL_27A.assembled 1HL_28A.assembled 1HL_29A.assembled 1HL_2A.assembled 1HL_31A.assembled 1HL_33A.assembled 1HL_34A.assembled 1HL_35A.assembled 1HL_3A.assembled 1HL_4A.assembled 1HL_5A.assembled 1HL_6A.assembled 1HL_7A.assembled 1HL_8A.assembled 1HL_9A.assembled
%%bash
cat /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop
1NF_10A.assembled 1NF_11A.assembled 1NF_12A.assembled 1NF_13A.assembled 1NF_14A.assembled 1NF_15A.assembled 1NF_16A.assembled 1NF_17A.assembled 1NF_18A.assembled 1NF_19A.assembled 1NF_1A.assembled 1NF_20A.assembled 1NF_21A.assembled 1NF_22A.assembled 1NF_23A.assembled 1NF_24A.assembled 1NF_25A.assembled 1NF_26A.assembled 1NF_27A.assembled 1NF_28A.assembled 1NF_29A.assembled 1NF_2A.assembled 1NF_30A.assembled 1NF_31A.assembled 1NF_32A.assembled 1NF_33A.assembled 1NF_4A.assembled 1NF_5A.assembled 1NF_6A.assembled 1NF_7A.assembled 1NF_8A.assembled 1NF_9A.assembled
%%bash
cat /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop
1SN_10A.assembled 1SN_11A.assembled 1SN_12A.assembled 1SN_13A.assembled 1SN_14A.assembled 1SN_15A.assembled 1SN_16A.assembled 1SN_17A.assembled 1SN_18A.assembled 1SN_19A.assembled 1SN_1A.assembled 1SN_20A.assembled 1SN_21A.assembled 1SN_22A.assembled 1SN_23A.assembled 1SN_24A.assembled 1SN_25A.assembled 1SN_26A.assembled 1SN_27A.assembled 1SN_28A.assembled 1SN_29A.assembled 1SN_2A.assembled 1SN_30A.assembled 1SN_31A.assembled 1SN_32A.assembled 1SN_3A.assembled 1SN_4A.assembled 1SN_5A.assembled 1SN_6A.assembled 1SN_7A.assembled 1SN_8A.assembled 1SN_9A.assembled
%%bash
for i in /root/data/20161117_oly_gbs_vcf_analysis/*.pop
do
wc -l "$i"
done
32 /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop 32 /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop 32 /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop
%%bash
which vcftools
/usr/local/bin/vcftools
%%bash
time vcftools --vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf \
--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop \
--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop
mv out.weir.fst /root/data/20161117_oly_gbs_vcf_analysis/1HL_NF.fst
VCFtools - 0.1.14 (C) Adam Auton and Anthony Marcketta 2009 Parameters as interpreted: --vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf --weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop --weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop --keep /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop --keep /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop Eighth Header entry should be INFO: INFO Keeping individuals in 'keep' list After filtering, kept 64 out of 96 Individuals Outputting Weir and Cockerham Fst estimates. Weir and Cockerham mean Fst estimate: 0.0029054 Weir and Cockerham weighted Fst estimate: 0.14582 After filtering, kept 120130 out of a possible 120130 Sites Run Time = 25.00 seconds real 0m24.933s user 0m0.760s sys 0m13.630s
%%bash
time vcftools --vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf \
--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop \
--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop
mv out.weir.fst /root/data/20161117_oly_gbs_vcf_analysis/1HL_SN.fst
VCFtools - 0.1.14 (C) Adam Auton and Anthony Marcketta 2009 Parameters as interpreted: --vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf --weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop --weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop --keep /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop --keep /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop Eighth Header entry should be INFO: INFO Keeping individuals in 'keep' list After filtering, kept 64 out of 96 Individuals Outputting Weir and Cockerham Fst estimates. Weir and Cockerham mean Fst estimate: 0.018513 Weir and Cockerham weighted Fst estimate: 0.18011 After filtering, kept 120130 out of a possible 120130 Sites Run Time = 24.00 seconds real 0m24.362s user 0m0.800s sys 0m13.780s
%%bash
time vcftools --vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf \
--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop \
--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop
mv out.weir.fst /root/data/20161117_oly_gbs_vcf_analysis/1NF_1SN.fst
VCFtools - 0.1.14 (C) Adam Auton and Anthony Marcketta 2009 Parameters as interpreted: --vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf --weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop --weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop --keep /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop --keep /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop Eighth Header entry should be INFO: INFO Keeping individuals in 'keep' list After filtering, kept 64 out of 96 Individuals Outputting Weir and Cockerham Fst estimates. Weir and Cockerham mean Fst estimate: -0.010855 Weir and Cockerham weighted Fst estimate: 0.10355 After filtering, kept 120130 out of a possible 120130 Sites Run Time = 27.00 seconds real 0m26.961s user 0m1.890s sys 0m12.430s
%%bash
time vcftools --vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf \
--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop \
--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop \
--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop
mv out.weir.fst /root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst
VCFtools - 0.1.14 (C) Adam Auton and Anthony Marcketta 2009 Parameters as interpreted: --vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf --weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop --weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop --weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop --keep /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop --keep /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop --keep /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop Eighth Header entry should be INFO: INFO Keeping individuals in 'keep' list After filtering, kept 96 out of 96 Individuals Outputting Weir and Cockerham Fst estimates. Weir and Cockerham mean Fst estimate: 0.048516 Weir and Cockerham weighted Fst estimate: 0.13739 After filtering, kept 120130 out of a possible 120130 Sites Run Time = 25.00 seconds real 0m24.840s user 0m1.080s sys 0m13.720s