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:/gitrepos -it f99537d7e06a
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 443bc42)
%%bash
date
Wed Jan 4 15:29:29 UTC 2017
%%bash
hostname
0f2bca9c664b
%%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 -lh /owl_web/nightingales/O_lurida/
total 136G -rw-rw-rw- 1 srlab staff 584M Jan 9 2016 11_GGCTAC_L001_R1_001.fastq.gz -rw-rw-rw- 1 srlab staff 577M Jan 9 2016 12_CTTGTA_L001_R1_001.fastq.gz -rw-rw-rw- 1 srlab staff 6.6G Jan 25 2016 151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz -rw-rw-rw- 1 srlab staff 6.9G Jan 25 2016 151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz -rw-rw-rw- 1 srlab staff 6.6G Jan 25 2016 151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz -rw-rw-rw- 1 srlab staff 6.2G Jan 27 2016 151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz -rw-rw-rw- 1 srlab staff 2.4G Jan 27 2016 151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz -rw-rw-rw- 1 srlab staff 4.0G Jan 25 2016 151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz -rw-rw-rw- 1 srlab staff 2.4G Jan 25 2016 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz -rw-rw-rw- 1 srlab staff 2.8G Jan 25 2016 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz -rw-rw-rw- 1 srlab staff 1.3G Jan 25 2016 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz -rw-rw-rw- 1 srlab staff 1.5G Jan 25 2016 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz -rw-rw-rw- 1 srlab staff 2.4G Jan 25 2016 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz -rw-rw-rw- 1 srlab staff 2.8G Jan 25 2016 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz -rw-rw-rw- 1 srlab staff 1.3G Jan 25 2016 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz -rw-rw-rw- 1 srlab staff 1.5G Jan 25 2016 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz -rw-rw-rw- 1 srlab staff 2.7G Jan 25 2016 160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz -rw-rw-rw- 1 srlab staff 3.1G Jan 25 2016 160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz -rw-rw-rw- 1 srlab staff 2.6G Jan 25 2016 160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz -rw-rw-rw- 1 srlab staff 3.0G Jan 25 2016 160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz -rw-rw-rw- 1 srlab staff 503M Jan 9 2016 1_ATCACG_L001_R1_001.fastq.gz drwxrwxrwx 1 srlab staff 5.0K Nov 30 17:38 20160203_mbdseq drwxrwxrwx 1 srlab staff 6.8K Apr 29 2016 20160223_gbs -rw-rw-rw- 1 srlab staff 638M Jan 9 2016 2_CGATGT_L001_R1_001.fastq.gz drwxrwxrwx 1 srlab staff 11K Nov 12 19:47 2bRAD_Dec2015 -rw-rw-rw- 1 srlab staff 634M Jan 9 2016 3_TTAGGC_L001_R1_001.fastq.gz -rw-rw-rw- 1 srlab staff 620M Jan 9 2016 4_TGACCA_L001_R1_001.fastq.gz -rw-rw-rw- 1 srlab staff 672M Jan 9 2016 5_ACAGTG_L001_R1_001.fastq.gz -rw-rw-rw- 1 srlab staff 668M Jan 9 2016 6_GCCAAT_L001_R1_001.fastq.gz -rw-rw-rw- 1 srlab staff 549M Jan 9 2016 7_CAGATC_L001_R1_001.fastq.gz -rw-rw-rw- 1 srlab staff 765M Jan 9 2016 8_ACTTGA_L001_R1_001.fastq.gz -rwxr-xr-x 1 srlab staff 4.2K Mar 24 2016 checksums.md5 -rwxr-xr-x 1 srlab staff 1.3G Aug 14 2012 filtered_1000_GTGAAA_L004_R1.fastq.gz -rwxr-xr-x 1 srlab staff 2.6G Dec 19 2012 filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz -rwxr-xr-x 1 srlab staff 2.5G Dec 18 2012 filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz -rwxr-xr-x 1 srlab staff 1.3G Aug 14 2012 filtered_106A_Female_Mix_GATCAG_L007_R1.fastq.gz -rwxr-xr-x 1 srlab staff 3.9G Dec 18 2012 filtered_106A_Male_Mix_TAGCTT_L004_R1.fastq.gz -rwxr-xr-x 1 srlab staff 3.7G Dec 18 2012 filtered_106A_Male_Mix_TAGCTT_L004_R2.fastq.gz -rwxr-xr-x 1 srlab staff 1.9G Aug 21 2012 filtered_106A_Male_Mix_TAGCTT_L007_R1.fastq.gz -rwxr-xr-x 1 srlab staff 3.0G Dec 19 2012 filtered_108A_Female_Mix_GGCTAC_L004_R1.fastq.gz -rwxr-xr-x 1 srlab staff 2.9G Dec 19 2012 filtered_108A_Female_Mix_GGCTAC_L004_R2.fastq.gz -rwxr-xr-x 1 srlab staff 1.4G Aug 21 2012 filtered_108A_Female_Mix_GGCTAC_L007_R1.fastq.gz -rwxr-xr-x 1 srlab staff 3.7G Dec 19 2012 filtered_108A_Male_Mix_AGTCAA_L004_R1.fastq.gz -rwxr-xr-x 1 srlab staff 3.5G Dec 19 2012 filtered_108A_Male_Mix_AGTCAA_L004_R2.fastq.gz -rwxr-xr-x 1 srlab staff 1.8G Aug 21 2012 filtered_108A_Male_Mix_AGTCAA_L007_R1.fastq.gz -rwxr-xr-x 1 srlab staff 1.1G Aug 14 2012 filtered_1600_GTGGCC_L004_R1.fastq.gz -rwxr-xr-x 1 srlab staff 5.6G Jan 25 2012 filtered_2000_NoIndex_L007_R1.fastq.gz -rwxr-xr-x 1 srlab staff 1.2G Aug 14 2012 filtered_2200_GTTTCG_L004_R1.fastq.gz -rwxr-xr-x 1 srlab staff 1.1G Aug 14 2012 filtered_400_GTCCGC_L004_R1.fastq.gz -rwxr-xr-x 1 srlab staff 5.9G Jan 25 2012 filtered_400_NoIndex_L006_R1.fastq.gz -rw-rw-rw- 1 srlab staff 1.5G Dec 4 2014 lane1_NoIndex_L001_R1_001.fastq.gz -rw-rw-rw- 1 srlab staff 1.5G Dec 4 2014 lane1_NoIndex_L001_R1_002.fastq.gz -rw-rw-rw- 1 srlab staff 1.5G Dec 4 2014 lane1_NoIndex_L001_R1_003.fastq.gz -rw-rw-rw- 1 srlab staff 1.5G Dec 4 2014 lane1_NoIndex_L001_R1_004.fastq.gz -rw-rw-rw- 1 srlab staff 1.5G Dec 4 2014 lane1_NoIndex_L001_R1_005.fastq.gz -rw-rw-rw- 1 srlab staff 1.5G Dec 4 2014 lane1_NoIndex_L001_R1_006.fastq.gz -rw-rw-rw- 1 srlab staff 1.5G Dec 4 2014 lane1_NoIndex_L001_R1_007.fastq.gz -rw-rw-rw- 1 srlab staff 1.5G Dec 4 2014 lane1_NoIndex_L001_R1_008.fastq.gz -rw-rw-rw- 1 srlab staff 1.5G Dec 4 2014 lane1_NoIndex_L001_R1_009.fastq.gz -rw-rw-rw- 1 srlab staff 1.5G Dec 4 2014 lane1_NoIndex_L001_R1_010.fastq.gz -rw-rw-rw- 1 srlab staff 1.5G Dec 4 2014 lane1_NoIndex_L001_R1_011.fastq.gz -rw-rw-rw- 1 srlab staff 1.5G Dec 4 2014 lane1_NoIndex_L001_R1_012.fastq.gz -rw-rw-rw- 1 srlab staff 1.5G Dec 4 2014 lane1_NoIndex_L001_R1_013.fastq.gz -rw-rw-rw- 1 srlab staff 1.3G Dec 4 2014 lane1_NoIndex_L001_R1_014.fastq.gz -rwxr-xr-x 1 srlab staff 3.1G Jun 20 2013 m130619_081336_42134_c100525122550000001823081109281326_s1_p0.bas.h5.gz -rw-rw-rw- 1 srlab staff 3.4K Feb 9 2016 readme.md
%%bash
grep 151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz /owl_web/nightingales/O_lurida/checksums.md5
MD5 (151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz) = a503043167457337a65d51151ceb5dd0
%%bash
grep 151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz /owl_web/O_lurida_genome_assemblies_BGI/20160512/checksums.md5
grep 151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/checksums.md5
MD5 (/Volumes/web/O_lurida_genome_assemblies_BGI/20160512/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz.clean.dup.clean.gz) = a503043167457337a65d51151ceb5dd0 a503043167457337a65d51151ceb5dd0 /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz.clean.dup.clean.gz
%%bash
grep 151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz /owl_web/nightingales/O_lurida/checksums.md5
grep 151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz /owl_web/O_lurida_genome_assemblies_BGI/20160512/checksums.md5
grep 151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/checksums.md5
MD5 (151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz) = 08cfdc6fdc5a6190cb05cdcb81fa5b9c MD5 (/Volumes/web/O_lurida_genome_assemblies_BGI/20160512/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz) = 08cfdc6fdc5a6190cb05cdcb81fa5b9c 08cfdc6fdc5a6190cb05cdcb81fa5b9c /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz
%%bash
time md5sum /owl_web/nightingales/O_lurida/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz
time md5sum /owl_web/O_lurida_genome_assemblies_BGI/20160512/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz
time md5sum /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz
f10c1f143d153f364cf6be13452eea4a /owl_web/nightingales/O_lurida/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz 08cfdc6fdc5a6190cb05cdcb81fa5b9c /owl_web/O_lurida_genome_assemblies_BGI/20160512/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz 08cfdc6fdc5a6190cb05cdcb81fa5b9c /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz
real 1m39.203s user 0m0.350s sys 0m16.000s real 3m34.544s user 0m0.360s sys 0m25.510s real 3m18.641s user 0m0.370s sys 0m25.530s
%%bash
grep 151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz /owl_web/nightingales/O_lurida/checksums.md5
grep 151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz /owl_web/O_lurida_genome_assemblies_BGI/20160512/checksums.md5
grep 151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/checksums.md5
MD5 (151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz) = 8bc0d7c7a7af3954baca31a4a7fe9f2b MD5 (/Volumes/web/O_lurida_genome_assemblies_BGI/20160512/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz) = 8bc0d7c7a7af3954baca31a4a7fe9f2b 8bc0d7c7a7af3954baca31a4a7fe9f2b /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz
%%bash
time md5sum /owl_web/nightingales/O_lurida/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz
time md5sum /owl_web/O_lurida_genome_assemblies_BGI/20160512/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz
time md5sum /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz
861c8161c1e0171532a058582db3ae6d /owl_web/nightingales/O_lurida/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz 8bc0d7c7a7af3954baca31a4a7fe9f2b /owl_web/O_lurida_genome_assemblies_BGI/20160512/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz 8bc0d7c7a7af3954baca31a4a7fe9f2b /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz
real 5m45.360s user 0m0.470s sys 0m42.260s real 4m50.124s user 0m0.710s sys 0m46.230s real 5m39.771s user 0m0.750s sys 0m46.310s
%%bash
time cp /owl_web/O_lurida_genome_assemblies_BGI/20160512/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz \
/owl_web/nightingales/O_lurida/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz
real 30m31.618s user 0m0.000s sys 0m32.920s
%%bash
time md5sum /owl_web/nightingales/O_lurida/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz
time md5sum /owl_web/O_lurida_genome_assemblies_BGI/20160512/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz
time md5sum /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz
08cfdc6fdc5a6190cb05cdcb81fa5b9c /owl_web/nightingales/O_lurida/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz 08cfdc6fdc5a6190cb05cdcb81fa5b9c /owl_web/O_lurida_genome_assemblies_BGI/20160512/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz 08cfdc6fdc5a6190cb05cdcb81fa5b9c /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz
real 4m55.495s user 0m0.300s sys 0m25.810s real 2m12.678s user 0m0.370s sys 0m25.610s real 2m37.531s user 0m0.680s sys 0m25.540s
%%bash
time cp /owl_web/O_lurida_genome_assemblies_BGI/20160512/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz \
/owl_web/nightingales/O_lurida/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz
time md5sum /owl_web/nightingales/O_lurida/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz
time md5sum /owl_web/O_lurida_genome_assemblies_BGI/20160512/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz
time md5sum /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz
8bc0d7c7a7af3954baca31a4a7fe9f2b /owl_web/nightingales/O_lurida/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz 8bc0d7c7a7af3954baca31a4a7fe9f2b /owl_web/O_lurida_genome_assemblies_BGI/20160512/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz 8bc0d7c7a7af3954baca31a4a7fe9f2b /owl_web/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/clean_data/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz
real 33m16.268s user 0m0.000s sys 0m59.710s real 11m57.266s user 0m0.710s sys 0m46.420s real 4m11.480s user 0m0.550s sys 0m46.800s real 5m36.195s user 0m0.660s sys 0m46.440s