ngs-docs · ctb · Jul 15, 2013 · Jul 31, 2013 · Aug 1, 2013 · Aug 7, 2013
diff --git a/README.txt b/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]
-
diff --git a/doc/2012-oslo-metagenomics/a-fake-metagenome.txt b/doc/2012-oslo-metagenomics/a-fake-metagenome.txt
@@ -1,6 +1,12 @@
 A fake metagenome
 =================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 Let's start by playing with a little fake metagenome. ::
 
   %% mkdir ~/metag/

diff --git a/doc/2012-oslo-metagenomics/a-real-genome.txt b/doc/2012-oslo-metagenomics/a-real-genome.txt
@@ -1,6 +1,12 @@
 Assembling a real genome
 ========================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 Normalize to 20::
 
    %% cd ~/metag

diff --git a/doc/2012-oslo-metagenomics/index.txt b/doc/2012-oslo-metagenomics/index.txt
@@ -2,6 +2,12 @@
 A Short Metagenomics Workshop in Oslo (Dec 2012)
 ================================================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 Hipchat room: https://www.hipchat.com/gSoSjn5lP
 
 Other links:

diff --git a/doc/2012-oslo-metagenomics/installing.txt b/doc/2012-oslo-metagenomics/installing.txt
@@ -1,6 +1,13 @@
 Installing the necessary software on the cod servers
 ====================================================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
+
 This should all run on cod3::
 
    %% ssh [email protected]

diff --git a/doc/2012-oslo-metagenomics/preparing-data.txt b/doc/2012-oslo-metagenomics/preparing-data.txt
@@ -2,6 +2,12 @@
 Preparing data from raw
 =======================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 I grabbed the PhiX, DH10B, and MG1655 data sets from `Illumina's
 public data repo
 <http://www.illumina.com/systems/miseq/scientific_data.ilmn>`__.

diff --git a/doc/2013-04-assembly-workshop/assembly-with-a5.txt b/doc/2013-04-assembly-workshop/assembly-with-a5.txt
@@ -1,6 +1,12 @@
 Assembling microbial genomes with A5
 ====================================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 Let's try using a different assembly pipeline -- the A5 pipeline, from
 `An Integrated Pipeline for de Novo Assembly of Microbial Genomes
 <http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0042304>`__.

diff --git a/doc/2013-04-assembly-workshop/assembly-with-velvet.txt b/doc/2013-04-assembly-workshop/assembly-with-velvet.txt
@@ -1,6 +1,12 @@
 Assembling sequences with Velvet
 ================================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 Start at the EC2 command line prompt -- ::
 
    cd /mnt

diff --git a/doc/2013-04-assembly-workshop/getting-data.txt b/doc/2013-04-assembly-workshop/getting-data.txt
@@ -1,6 +1,12 @@
 Getting the data
 ================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 Start at your EC2 prompt, then type ::
 
    cd /mnt

diff --git a/doc/2013-04-assembly-workshop/index.txt b/doc/2013-04-assembly-workshop/index.txt
@@ -1,6 +1,12 @@
 2013 MSU Assembly Workshop
 ==========================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 Tracy Teal <[email protected]>
 
 Titus Brown <[email protected]>

diff --git a/doc/2013-04-assembly-workshop/installing-software.txt b/doc/2013-04-assembly-workshop/installing-software.txt
@@ -1,6 +1,12 @@
 Packages to install
 ===================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 These command should work on the default `StarCluster <http://star.mit.edu/cluster/>`__ AMI, ami-999d49f0.
 These have already been pre-installed on the course AMI, ami-d6e581bf.
 

diff --git a/doc/2013-04-assembly-workshop/mapping-reads.txt b/doc/2013-04-assembly-workshop/mapping-reads.txt
@@ -1,6 +1,12 @@
 Mapping reads to a reference
 ----------------------------
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 Create a new directory to do the mapping in::
 
    cd /mnt

diff --git a/doc/2013-04-assembly-workshop/running-blast.txt b/doc/2013-04-assembly-workshop/running-blast.txt
@@ -1,6 +1,12 @@
 Installing and running BLAST
 ============================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 Everyone wants to BLAST!  How do we do it?
 
 First, install NCBI BLAST::

diff --git a/doc/2013-04-assembly-workshop/trimming-and-quality-evaluation.txt b/doc/2013-04-assembly-workshop/trimming-and-quality-evaluation.txt
@@ -1,6 +1,12 @@
 Trimming and quality evaluation of your sequences
 =================================================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 Start at the EC2 login prompt.  Then, ::
 
   cd /mnt

diff --git a/doc/2013-caltech-cemi.txt b/doc/2013-caltech-cemi.txt
@@ -0,0 +1,10 @@
+2013 Caltech workshop: Center for Environmental Microbial Interactions
+======================================================================
+
+Titus Brown and Chris Welcher ran this workshop from Sep 17, 2013 to
+Sep 20, 2013 at Caltech.  The workshop was focused on microbial data sets.
+
+The materials are available here:
+
+    http://2013-caltech-workshop.readthedocs.org
+
diff --git a/doc/2013-hmp-assembly-webinar/exploring-stamps-data.txt b/doc/2013-hmp-assembly-webinar/exploring-stamps-data.txt
@@ -1,6 +1,12 @@
 Exploring a simple simulated data set
 =====================================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 Let's take a look at some k-mer abundance distributions, and the effects
 of various activities on them.
 

diff --git a/doc/2013-hmp-assembly-webinar/index.txt b/doc/2013-hmp-assembly-webinar/index.txt
@@ -1,6 +1,12 @@
 2013 HMP Assembly Webinar -- electronic materials
 =================================================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 :author: Titus Brown <[email protected]>
 :date: May 6th, 2013
 

diff --git a/doc/2013-hmp-assembly-webinar/installing-assemblers.txt b/doc/2013-hmp-assembly-webinar/installing-assemblers.txt
@@ -1,6 +1,12 @@
 Installing assemblers (and other necessary software)
 ====================================================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 The first thing we need to do to make use of our Amazon machine is
 to install a bunch of assemblers.
 

diff --git a/doc/2013-hmp-assembly-webinar/playing-with-assemblers.txt b/doc/2013-hmp-assembly-webinar/playing-with-assemblers.txt
@@ -1,6 +1,12 @@
 Playing with metagenome assemblers
 ==================================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 :author: C. Titus Brown
 :date: May 7, 2013
 

diff --git a/doc/2013-hmp-assembly-webinar/working-with-real-volumes-of-data.txt b/doc/2013-hmp-assembly-webinar/working-with-real-volumes-of-data.txt
@@ -1,6 +1,12 @@
 Preparing the data you just used - filtering, normalizing, partitiong
 =====================================================================
 
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
 :author: C. Titus Brown
 :date: May 7, 2013
 

diff --git a/doc/2013-msu-zero-entry.txt b/doc/2013-msu-zero-entry.txt
@@ -0,0 +1,11 @@
+2013 MSU "Zero-Entry" workshop: Computational Science for Biologists
+====================================================================
+
+Titus Brown, Tracy Teal, and Jory Schossau ran this workshop on Sep 23
+and Sep 25, 2013, at Michigan State University.  The workshop was
+focused on an introduction to computational science, the shell, the
+cloud, and IPython Notebook.
+
+The materials are here::
+
+   http://2013-msu-zero-entry.readthedocs.org
diff --git a/doc/2013-stamps/1-quality.txt b/doc/2013-stamps/1-quality.txt
@@ -0,0 +1,17 @@
+=========================================
+1. Adapter trimming and quality filtering
+=========================================
+
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
+Configure your environment::
+
+   echo 'export PYTHONPATH=$PYTHONPATH:/class/stamps-software/share/khmer/python' >> ~/.bash_login
+   echo 'export PYTHONPATH=$PYTHONPATH:/class/stamps-software/share/khmer/python' >> ~/.bashrc
+   echo 'export PATH=/class/stamps-software/bin:$PATH' >> ~/.bashrc
+   echo 'export PATH=/class/stamps-software/bin:$PATH' >> ~/.bash_login
+
diff --git a/doc/2013-stamps/1-setup.txt b/doc/2013-stamps/1-setup.txt
@@ -0,0 +1,33 @@
+========
+1. Setup
+========
+
+.. Warning:: These documents are not maintained and their instructions may be
+	out of date. However the GED Lab does maintain the `khmer protocols
+	<http://khmer-protocols.readthedocs.org/>`__ which may cover similar
+	topics. See also the `installation instructions for the current version
+	of the khmer project <https://khmer.readthedocs.org/en/latest/install.html>`__. 
+
+Configure your environment::
+
+   echo 'export PYTHONPATH=$PYTHONPATH:/class/stamps-software/share/khmer/python' >> ~/.bash_login
+   echo 'export PYTHONPATH=$PYTHONPATH:/class/stamps-software/share/khmer/python' >> ~/.bashrc
+   echo 'export PATH=/class/stamps-software/bin:$PATH' >> ~/.bashrc
+   echo 'export PATH=/class/stamps-software/bin:$PATH' >> ~/.bash_login
+
+   source ~/.bashrc
+
+Create a virtual environment and activate it::
+
+   python -m virtualenv ~/env
+   . ~/env/bin/activate
+
+Install screed in your virtual environment::
+
+   pip install git+https://github.com/ged-lab/screed.git
+
+Also see:  :doc:`../mrnaseq/using-screen`.
+
+----
+
+Next: :doc:`2-quality`.