Software Carpentry Boot Camp, setup

Setup instructions for the Software Carpentry Boot Camp at Woods Hole Oceanographic Institution from 14-15 Nov. I’m really looking forward to this Boot Camp and setting up something similar at HBOI.

I already have the Linux command terminal, a text editor, and Python IDLE. The workshop will be using Python version 2.7. While I use Python IDLE version 3.3, I’m unsure of whether this will be ok. I’ve heard this before, that people still use Python version 2 for things, and I don’t understand why. I will have to ask tomorrow. Python version 3.3 is the latest. There are syntax differences between the two versions, e.g. print foo vs. print(foo).

I did have to install git.  I’m a little fuzzy on the concept of git, which I’m looking forward to learning more about tomorrow. This fuzziness is even despite my own github account. Github is, coincidentally, the subject of a blog post this week on Molecular Ecologist.

flcellogrl@flcellogrl:~$ sudo apt-get install git-core
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  libcurl3-nss libnspr4-dev libnss3-dev libssl-dev libssl-doc
  linux-headers-3.8.0-19 linux-headers-3.8.0-19-generic
  linux-image-3.8.0-19-generic linux-image-extra-3.8.0-19-generic
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
  git git-man liberror-perl
Suggested packages:
  git-daemon-run git-daemon-sysvinit git-doc git-el git-arch git-cvs git-svn
  git-email git-gui gitk gitweb
The following NEW packages will be installed:
  git git-core git-man liberror-perl
0 upgraded, 4 newly installed, 0 to remove and 12 not upgraded.
Need to get 7,417 kB of archives.
After this operation, 17.3 MB of additional disk space will be used.
Do you want to continue [Y/n]? y
Get:1 http://us.archive.ubuntu.com/ubuntu/ raring/main liberror-perl all 0.17-1 [23.8 kB]
Get:2 http://us.archive.ubuntu.com/ubuntu/ raring/main git-man all 1:1.8.1.2-1 [653 kB]
Get:3 http://us.archive.ubuntu.com/ubuntu/ raring/main git i386 1:1.8.1.2-1 [6,739 kB]
Get:4 http://us.archive.ubuntu.com/ubuntu/ raring/main git-core all 1:1.8.1.2-1 [1,392 B]
Fetched 7,417 kB in 5min 13s (23.7 kB/s)                                       
Selecting previously unselected package liberror-perl.
(Reading database ... 438507 files and directories currently installed.)
Unpacking liberror-perl (from .../liberror-perl_0.17-1_all.deb) ...
Selecting previously unselected package git-man.
Unpacking git-man (from .../git-man_1%3a1.8.1.2-1_all.deb) ...
Selecting previously unselected package git.
Unpacking git (from .../git_1%3a1.8.1.2-1_i386.deb) ...
Selecting previously unselected package git-core.
Unpacking git-core (from .../git-core_1%3a1.8.1.2-1_all.deb) ...
Processing triggers for man-db ...
Setting up liberror-perl (0.17-1) ...
Setting up git-man (1:1.8.1.2-1) ...
Setting up git (1:1.8.1.2-1) ...
Setting up git-core (1:1.8.1.2-1) ...

As a side note, I think that the Software Carpentry concept and team are incredibly  cool. This is a non-profit organization comprised of a multidisciplinary team of instructors (University professors, graduate students, software professionals) who are involved with software at various levels. The aim is to train post-graduate scientists in computing skills to get us to where we need to be: programming and using advanced computing tools in our research to help with big data needs. I would love to be a part of this as an instructor someday, if I can ever get my skills to a level where they should be!

I was reading their blog, and some of their developers posted an interesting report from a project they’re working on with PLOS Computational Biology and partners at Mozilla looking into code published in scientific literature.

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About Lisa Cohen

PhD student at UC Davis.
This entry was posted in Linux, Python, software, Software Carpentry, Ubuntu. Bookmark the permalink.

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