Eel pond mRNAseq tutorial

README.txt

@@ -1,6 +1,25 @@
 Documentation for the MSU Next-Gen Sequence Analysis Course, and other things,
 too.
 
+As per http://ged.msu.edu/angus/,
+
+License:
+
+This documentation and all textual/graphic site content is licensed
+under the Creative Commons - 0 License (CC0). Please feel free to
+copy, modify, distribute and perform the work, even for commercial
+purposes, all without asking permission.
+
+You can find the source code for this material under git version
+control on github at https://github.com/ngs-docs/edda. Please fork at
+your own leisure :)
+
+However, presentations (PPT/PDF) and PDFs are the property of their
+respective owners and are under the terms indicated within the
+presentation. If no terms are indicated, please do not reuse without
+specific and explicit permission - i.e. all presentations and PDFs are
+Copyright (C) their authors, all rights reserved, unless otherwise
+stated.
+
 Titus Brown
 [email protected]
-

doc/_templates/layout.html

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+  <hr>
+<font size="-1"><b>LICENSE:</b>
+This documentation and all textual/graphic site content is licensed
+under the <a href='http://creativecommons.org/publicdomain/zero/1.0/'>
+Creative Commons - 0 License
+(CC0)</a> -- <a href='https://github.com/ngs-docs/edda'>fork @
+github</a>.  Presentations (PPT/PDF) and PDFs are the property of
+their respective owners and are under the terms indicated within the
+presentation.</font>
+
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             {{ comments() }}
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doc/mrnaseq/0-download-and-save.txt

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+===========================================
+0. Downloading and Saving Your Initial Data
+===========================================
+
+The basics
+----------
+
+Amazon is happy to rent disk space to you, in addition to compute time.
+They'll rent you disk space in a few different ways, but the way that's
+most useful for us is through what's called Elastic Block Store.  This
+is essentially a hard-disk rental service.
+
+There are two basic concepts -- "volume" and "snapshot". A "volume" can
+be thought of as a pluggable-in hard drive: you create an empty volume of
+a given size, attach it to a running instance, and voila! You have extra
+hard disk space.  Volume-based hard disks have two problems, however:
+first, they cannot be used outside of the "availability zone" they've
+been created in, which means that you need to be careful to put them
+in the same zone that your instance is running in; and they can't be shared
+amongst people.
+
+Snapshots, the second concept, is the solution to transporting and
+sharing the data on volumes.  A "snapshot" is essentially a frozen
+copy of your volume; you can copy a volume into a snapshot, and a
+snapshot into a volume.
+
+Getting started
+---------------
+
+Run through :doc:`saving-data-persistently` once, to get the hang of
+the mechanics.  Essentially you create a disk; attach it; format it;
+and then copy things to and from it.
+
+Downloading and saving your data to a volume
+--------------------------------------------
+
+There are *many* different ways of getting big sequence files to and
+from Amazon.  The two that I mostly use are 'curl', which downloads
+files from a Web site URL; and 'ncftp', which is a robust FTP client
+that let's you get files from an FTP site.  Sequencing centers almost
+always make their data available in one of these two ways.
+
+.. note::
+
+   To use ncftp on your Amazon instance, you may need to install it::
+
+      apt-get -y install ncftp
+
+For example, to retrieve a file from an FTP site, you would do something
+like::
+
+   cd /mnt
+   ncftp -u <username> ftp://path/to/FTP/site
+
+use 'cd' to find the right directory, and then::
+
+   >> mget *
+
+to download the files.  Then type 'quit'.  You can also use 'curl' to
+download files one at a time from Web or FTP sites.
+
+Once you have the files, figure out their size using 'du -sk' (e.g. after the
+above, 'du -sk /mnt' will tell you how much data you have saved under /mnt),
+and go create and attach a volume (see :doc:`saving-data-persistently`).
+
+This data is now something that will *stick around* when you shut down
+your instance.  It's a good rule of thumb to do "savepoints" -- whenever
+you complete a big chunk of work, think about saving the data at that 
+point.  I've broken the mRNAseq tutorial down into chunks of work where
+you can do this -- after each Web page, basically.
+
+Some test data
+--------------
+
+To get started with multfile analysis and assembly, I've provided some
+test data.  It's on snapshot 'snap-f5a9dea7', so go create a volume from
+that and mount it as '/data' to get started.
+