Then copy =rr_org/journal.org= file in your =~/org/= directory. This
file will be your laboratory notebook and all the notes you will
capture with =C-c c= will go automatically go in this file. The first
entry of this notebook is populated with [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][many Emacs shortcuts]] that you
entry of this notebook is populated with [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][many Emacs shortcuts]] that you
should give a try.
** Step 2: Set up Emacs configuration
Copy =rr_org/init.el= in your =~/.emacs.d/= directory.
...
...
@@ -249,7 +249,7 @@ worked.
In the video, we already have demonstrated the main features and
shortcuts of emacs/org-mode that will help you maintain a document and
benefit from literate programming. The list of features and shortcuts
is demonstrated in the [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][first entry of your labbook]].
is demonstrated in the [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][first entry of your labbook]].
** Step 5: Open and play with your journal:
In step 1, you were told to create an journal in
=~org/journal.org=. First you probably want to make sure this file is
...
...
@@ -266,7 +266,7 @@ open a terminal and run the commands =R=, =pdflatex=, and =python=, you will not
able to generate this document. When being compiled, the article downloads the
corresponding LaTeX packages so you also need to have a working =wget=
command (alternatively, it uses =curl=). Once downloaded, you may still read the
source ([[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org][article.org]]) and understand how it works though.
source ([[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org]]) and understand how it works though.
#+begin_src shell :results output :exports none
make -C replicable_article/ all ../replicable_article.tgz
...
...
@@ -275,7 +275,7 @@ make -C replicable_article/ all ../replicable_article.tgz
#+RESULTS:
Download the following [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/replicable_article.tgz][archive]], uncompress it and simply =make= to generate the
article. You should then be able to open the [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.pdf][resulting article]]. This
article. You should then be able to open the [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.pdf][resulting article]]. This
@@ -296,7 +296,7 @@ tar zxf replicable_article.tgz; cd replicable_article; make ; evince article.pdf
command line to load your personal emacs configuration.
Finally, when you'll be tired of always re-executing all the source
code when exporting, just look for the following line in [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org][article.org]]:
code when exporting, just look for the following line in [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org][article.org]]:
#+BEGIN_EXAMPLE
# #+PROPERTY: header-args :eval never-export
#+END_EXAMPLE
...
...
@@ -310,12 +310,12 @@ Learning Emacs and Org-Mode can be difficult as there is an inordinate
amount of shortcuts. Many people have thus come up with
cheat-sheats. Here is a selection in case it helps:
*** Emacs
- [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][Common and step-by-step Emacs shortcuts for our /reproducible research/ configuration]]
- [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][Common and step-by-step Emacs shortcuts for our /reproducible research/ configuration]]
- [[https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf][The official GNU emacs refcard]]
- Two graphical cheat-sheats by Sacha Chua on [[http://sachachua.com/blog/wp-content/uploads/2013/05/How-to-Learn-Emacs-v2-Large.png][how to learn Emacs]] and on
[[http://sachachua.com/blog/wp-content/uploads/2013/08/20130830-Emacs-Newbie-How-to-Learn-Emacs-Keyboard-Shortcuts.png][how to learn Emacs shortcuts]].
*** Org-mode
- [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][Common and step-by-step org-mode shortcuts for our /reproducible research/ configuration]]
- [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][Common and step-by-step org-mode shortcuts for our /reproducible research/ configuration]]
- [[https://orgmode.org/worg/orgcard.html][The official org-mode refcard]]
- [[https://orgmode.org/worg/dev/org-syntax.html][The official description of the org-mode syntax]] and a [[https://gist.github.com/hoeltgman/3825415][relatively concise description of the org-mode syntax]].
