fix conflicts

Author: SherineAwad

.gitignore

@@ -4,7 +4,6 @@
 *.egg
 *.egg-info
 dist
-build
 eggs
 parts
 bin

conf.py

@@ -68,7 +68,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ['_build','env']
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 #default_role = None

metagenomics/2-diginorm.txt

@@ -60,10 +60,6 @@ two sets of SE files (.se.qc.fq.gz.keep.abundfilt and
 .pe.qc.fq.gz.keep.abundfilt.se).  (Yes, the naming scheme does make
 sense.  Trust me.)
 
-You can now remove the ``normC20k20.kh`` file, too
-::
-
-    rm normC20k20.kh
 
 Normalize Down to C=5
 ---------------------

metagenomics/4-assemble.txt

@@ -5,7 +5,6 @@
 At last!  All that filtering and diginorming is done, and we can get
 down to the serious business of assembling.  Huzzah!
 
-Let's start with some collection of group files in ``/mnt/assembly``.
 
 .. shell start
 
@@ -76,8 +75,6 @@ and convert them all into FASTA (for IDBA)
    do
       name=$(basename $i .fq).fa
       python /usr/local/share/khmer/scripts/fastq-to-fasta.py $i > $name
-      name=$(basename $i .fq.gz).fa
-      python /usr/local/share/khmer/sandbox/fastq-to-fasta.py $i > $name
    done
 
 Setting Up the Assemblies

misc/variant.txt

@@ -1,6 +1,5 @@
 Variant calling
-###############
- 
+================ 
 
 We are using Podar dataset from ... 
 
@@ -21,7 +20,7 @@ First, we need to install the `BWA aligner
 
    cp bwa /usr/local/bin
 
-.. We also need a new version of `samtools <http://samtools.sourceforge.net/>`__::
+We also need a new version of `samtools <http://samtools.sourceforge.net/>`__::
 
    cd /root
    curl -O -L http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2
@@ -34,7 +33,7 @@ First, we need to install the `BWA aligner
    cp *.pl maq2sam-long maq2sam-short md5fa md5sum-lite wgsim /usr/local/bin/
 
 Download data
-~~~~~~~~~~~~~
+=============
 
 Download the reference genome and the resequencing reads::
 

mrnaseq/0-download-and-save.txt

@@ -44,8 +44,8 @@ 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
+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.
 
@@ -61,20 +61,20 @@ like::
    cd /mnt
    ncftp -u <username> ftp://path/to/FTP/site
 
-use 'cd' to find the right directory, and then::
+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.
+You can also use ``curl`` to download files one at a time from Web or FTP sites.
 For example, to save a file from a website, you could use::
 
    cd /mnt
    curl -O http://path/to/file/on/website
 
-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),
+Once you have the files, figure out their size using ``du -sh`` (e.g. after the
+above, ``du -sh /mnt`` will tell you how much data you have saved under /mnt),
 and go create and attach a volume (see :doc:`../amazon/index`).
 
 Any files in the '/mnt' directory will be lost when the instance is stopped or