day2

day2-install.rst

@@ -0,0 +1,55 @@
+=================================
+Day 2 - installation instructions
+=================================
+
+(Instructions mostly copied from :doc:`quality`!)
+
+Use ami-05384865, with a 500 GB local disk (see: :doc:`aws/boot`)
+
+Run::
+
+  sudo apt-get -y update && \
+  sudo apt-get -y install trimmomatic fastqc python-pip \
+     samtools zlib1g-dev ncurses-dev python-dev
+
+Install anaconda::
+
+  curl -O https://repo.continuum.io/archive/Anaconda3-4.2.0-Linux-x86_64.sh
+  bash Anaconda3-4.2.0-Linux-x86_64.sh
+
+Then update your environment and install khmer::
+
+  source ~/.bashrc
+
+  cd
+  git clone https://github.com/dib-lab/khmer.git
+  cd khmer
+  sudo python2 setup.py install
+
+Running Jupyter Notebook
+------------------------
+
+Let's also run a Jupyter Notebook in /mnt. First, configure it a teensy bit
+more securely, and also have it run in the background::
+
+  jupyter notebook --generate-config
+  
+  cat >>/home/ubuntu/.jupyter/jupyter_notebook_config.py <<EOF
+  c = get_config()
+  c.NotebookApp.ip = '*'
+  c.NotebookApp.open_browser = False
+  c.NotebookApp.password = u'sha1:5d813e5d59a7:b4e430cf6dbd1aad04838c6e9cf684f4d76e245c'
+  c.NotebookApp.port = 8000
+
+  EOF
+
+Now, run! ::
+
+  cd /mnt
+  jupyter notebook &
+
+You should be able to visit port 8000 on your AWS computer and see the
+Jupyter console.  (The password is 'davis'.)
+
+
+install khmer

index.rst

@@ -52,6 +52,8 @@ Tutorials:
    assemble
    prokka_tutorial
    salmon_tutorial
+
+   day2-install
 
 Technical information
 ~~~~~~~~~~~~~~~~~~~~~