Running in Docker container on Ostrich¶

Started Docker container with the following command:¶

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)

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%%bash
date

Check computer specs¶

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%%bash
hostname

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%%bash
lscpu

Download all Ostrea lurida files from BGI using `wget`¶

This uses the `-m` flag to recursively download all files and mirror the directory structure of the target. Additionally, it uses the `-P` flag to specify the output location of the downloaded files.¶

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%%bash
time wget -m ftp://F15FTSUSAT0327:OSTibkD@cdts-hk.genomics.cn/Ostrea_lurida/ \
- P /owl_web/O_lurida_genome_assemblies_BGI/20161201/

Noticed that the files weren't being saved in the specified directory...¶

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%%bash
ls /owl_web/O_lurida_genome_assemblies_BGI/20161201/

Instead, they were being saved in my current directory...¶

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%%bash
ls -l cdts-hk.genomics.cn/

Not going to waste time figuring out why the `-P` argument didn't work for `wget`, so just changing to desired directory and running `wget` command again...¶

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%%bash
cd /owl_web/O_lurida_genome_assemblies_BGI/20161201/

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%%bash
pwd

Well, that's weird... Try again without bash magics?¶

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cd /owl_web/O_lurida_genome_assemblies_BGI/20161201/

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%%bash
time wget -m ftp://F15FTSUSAT0327:OSTibkD@cdts-hk.genomics.cn/Ostrea_lurida/

View directory structure of downloaded files¶

Note: The following program (tree) was installed via Homebrew package manager

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%%bash
tree /owl_web/O_lurida_genome_assemblies_BGI/20161201/

Download all Panopea gererosa files from BGI using `wget`¶

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cd /owl_web/P_generosa_genome_assemblies_BGI/20161201/

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%%bash
time wget -m ftp://F15FTSUSAT0327:OSTibkD@cdts-hk.genomics.cn/Panopea_generosa

View directory structure of downloaded files¶

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%%bash
tree /owl_web/P_generosa_genome_assemblies_BGI/20161201/

In [ ]:

Running in Docker container on Ostrich¶

Started Docker container with the following command:¶

Check computer specs¶

Download all Ostrea lurida files from BGI using wget¶

This uses the -m flag to recursively download all files and mirror the directory structure of the target. Additionally, it uses the -P flag to specify the output location of the downloaded files.¶

Noticed that the files weren't being saved in the specified directory...¶

Instead, they were being saved in my current directory...¶

Not going to waste time figuring out why the -P argument didn't work for wget, so just changing to desired directory and running wget command again...¶

Well, that's weird... Try again without bash magics?¶

View directory structure of downloaded files¶

Download all Panopea gererosa files from BGI using wget¶

View directory structure of downloaded files¶

Download all Ostrea lurida files from BGI using `wget`¶

This uses the `-m` flag to recursively download all files and mirror the directory structure of the target. Additionally, it uses the `-P` flag to specify the output location of the downloaded files.¶

Not going to waste time figuring out why the `-P` argument didn't work for `wget`, so just changing to desired directory and running `wget` command again...¶

Download all Panopea gererosa files from BGI using `wget`¶