Another Japan in the World

Jun Aruga's blog.

Install Miniconda3 on Fedora

Install Miniconda referring the Miniconda and Installing in silient mode.

Install

/home/root/local/miniconda3-py38-4.8.3 is installed directory in my case.

$ wget https://repo.anaconda.com/miniconda/Miniconda3-py38_4.8.3-Linux-x86_64.sh
$ sudo mkdir /home/root/local/miniconda3-py38-4.8.3
$ sudo chown jaruga:jaruga /home/root/local/miniconda3-py38-4.8.3

The installer script's options are like this. As I created the installing directory above, -u option is needed.

  • -b: batch mote.
  • -u: update
  • -p: prefix
$ bash Miniconda3-py38_4.8.3-Linux-x86_64.sh -b -u -p /home/root/local/miniconda3-py38-4.8.3
...
installation finished.

The following is the log to enable conda on the shell section like virtualenv, to enable conda setting as init. But as I do not want to modify .bashrc for that, I recommend NOT to run the following step. It's just for my note.

$ eval "$(/home/root/local/miniconda3-py38-4.8.3/bin/conda shell.bash hook)"

(base) $ command -v conda
conda

(base) $ conda init
modified      /home/jaruga/.bashrc

(base) $ conda config --set auto_activate_base false

Then add conda's bin directory to PATH with lower priority after the standard bin directories like this. Because I just want to use conda command, using specific python command set.

$ vi ~/.bashrc
...
PATH="${PATH}:/home/root/local/miniconda3-py38-4.8.3/bin"
...
export PATH

$ source ~/.bashrc
$ which conda
/home/root/local/miniconda3-py38-4.8.3/bin/conda

$ which python3
/usr/bin/python3

$ which python
/usr/bin/python

conda command

It's like this.

$ conda install -c bioconda -y mafft
$ conda install -c genomedk -y raxml-ng
$ conda list
# packages in environment at /home/root/local/miniconda3-py38-4.8.3:
#
# Name                    Version                   Build  Channel
...
mafft                     7.467                h516909a_0    bioconda
...
raxml-ng                  0.6.0                         0    genomedk
...

$ command -v mafft
/home/root/local/miniconda3-py38-4.8.3/bin/mafft

$ command -v raxml-ng
/home/root/local/miniconda3-py38-4.8.3/bin/raxml-ng

Desire for big picture - Siddhartha Mukherjee

Let's say that you are at a restaurant, you are hungry. Do you like ordering a food without seeing all the menu? Or you want to order it after seeing all the menu, checking which is the best? The second pattern connects to the desire for seeing a big picture. The desire to spend time for the most important thing.

I did read Siddhartha Mukherjee [1]'s 3 books in order by 3. => 2. => 1.

  1. The Emperor of All Maladies: A Biography of Cancer
  2. The Laws of Medicine
  3. The Gene: An Intimate History

"A Biography of Cancer" was the most impressed book. It's about the history of change. How have some people changed the things. It's not only about medical or cancer topic.

There is an interview for him in the end of the first half book Japanese edition. If I translate it to English, that is like this.

Question: You are clinical oncologist and father. How did you manage to find the time to write such as a large scaled and detailed book?

Answer: I had to create the time. What it's important is I had a reason for that. ... (snip) ... The urgent desire to tell the story enabled me to continue to write it.

The desire is what Yuval Harari also has. His expertise (the thing making the money) was crusade history. But he had to write Sapiens as his side work.

It's fortunate that Siddhartha Mukherjee and Yuval Harari are well-known in the current world.

Here is also his TED talk.

www.youtube.com

References