update to docs

Author: Jon Palmer

docs/clean.rst

@@ -3,5 +3,20 @@
 
 Cleaning your Assembly
 ================================
- When working with haploid assemblies, sometimes you want to remove some repetitive contigs that are contained in other scaffolds of the assembly. If the repeats are indeed unique, then we want to keep them in the assembly. Funannotate can help "clean" up repetitive contigs in your assembly 
+ When working with haploid assemblies, sometimes you want to remove some repetitive contigs that are contained in other scaffolds of the assembly. If the repeats are indeed unique, then we want to keep them in the assembly. Funannotate can help "clean" up repetitive contigs in your assembly.  This is done using a "leave one out" methodology using Mummer (nucmer), where the the shortest contigs/scaffolds are aligned to the rest of the assembly to determine if it is repetitive. The script loops through the contigs starting with the shortest and workings its way to the N50 of the assembly, dropping contigs/scaffolds that are greater than the percent coverage of overlap (:code:`--cov`) and the percent identity of overlap (:code:`--pident`). 
+ 
+.. code-block:: none
 
+    $ funannotate clean
+    Usage:       funannotate clean <arguments>
+    version:     1.0.0
+
+    Description: The script sorts contigs by size, starting with shortest contigs it uses Mummer 
+                 to find contigs duplicated elsewhere, and then removes duplicated contigs.
+    
+    Arguments:   -i, --input    Multi-fasta genome file (Required)
+                 -o, --out      Cleaned multi-fasta output file (Required)
+                 -p, --pident   Percent identity of overlap. Default = 95
+                 -c, --cov      Percent coverage of overlap. Default = 95
+                 -m, --minlen   Minimum length of contig to keep. Default = 500
+                 --exhaustive   Test every contig. Default is to stop at N50 value.

docs/conda.rst

@@ -3,7 +3,10 @@
 
 Conda mediated Installation
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-I'd really like to build a bioconda installation package, but would need some help.  You can however install nearly all of the dependencies with conda.
+
+** This is still under construction **
+
+I'd really like to build a bioconda installation package, but would need some help.  You can however install quite a few of the dependencies with conda.
 
 .. code-block:: none
     
@@ -31,8 +34,31 @@ This will automatically install most of the dependencies.
 
     1.  Download/install GeneMark-ES/ET: (gmes_petap.pl must be in PATH)
         http://exon.gatech.edu/GeneMark/license_download.cgi
+    
+    2. Download/install Bamtools and Augustus
+    
+        If you are on linux, you can install the usual way:
+        
+        .. code-block:: none 
+        
+            #install bamtools
+            wget https://github.com/pezmaster31/bamtools/archive/v2.5.0.tar.gz && \
+            tar -zxvf v2.5.0.tar.gz && \
+            rm v2.5.0.tar.gz && mv bamtools-2.5.0 bamtools && \
+            cd bamtools && mkdir build && cd build && \
+            cmake .. && make && sudo make install && \
+            cd /usr/include && sudo ln -f -s ../local/include/bamtools/ && \
+            cd /usr/lib/ &&  sudo ln -f -s /usr/local/lib/bamtools/libbamtools.* .
+            
+            #install augustus
+            wget http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz && \
+            tar -zxvf augustus-3.2.3.tar.gz && rm augustus-3.2.3.tar.gz && \
+            mv augustus-3.2.3 augustus && cd augustus && make clean && make
+        
+        If you are on Mac, install using this version: https://github.com/nextgenusfs/augustus
+     
 
-    2.  Install python modules via PIP or conda:
+    3.  Install python modules via PIP or conda:
 
     .. code-block:: none
 
@@ -45,26 +71,38 @@ This will automatically install most of the dependencies.
         conda install -c etetoolkit ete3 ete_toolchain
 
 
-    3.  Install RepeatMasker/RepeatModler and corresponding Libraries if you have not done so already.
+    4.  Install RepeatMasker/RepeatModeler  http://www.repeatmasker.org
+    
+    
+    
+    4b. Download Repbase RepeatMasker Libraries if you have not done so already.
 
     .. code-block:: none 
       
         wget --user name --password pass http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/RepBaseRepeatMaskerEdition-20170127.tar.gz
-        tar zxvf RepBaseRepeatMaskerEdition-20170127.tar.gz -C #{HOMEBREW_PREFIX}/opt/repeatmasker/libexec
-
-        cd #{HOMEBREW_PREFIX}/opt/repeatmasker/libexec
-        ./configure <config.txt
+        tar zxvf RepBaseRepeatMaskerEdition-20170127.tar.gz -C /path/to/repeatmasker/location
+        cd /path/to/repeatmasker/location
+        ./configure
 
         #Soft-link a repeatmasker utility script into the PATH:
-        ln -s #{HOMEBREW_PREFIX}/opt/repeatmasker/util/rmOutToGFF3.pl #{HOMEBREW_PREFIX}/bin/rmOutToGFF3.pl
+        ln -s /path/to/repeatmasker/location/repeatmasker/util/rmOutToGFF3.pl /usr/local/bin/rmOutToGFF3.pl
         
-    4.  Setup funannotate databases:
+    5. Install Perl modules, i.e. with cpanminus
+    
+     .. code-block:: none
+     
+         cpanm Getopt::Long Pod::Usage File::Basename threads threads::shared \
+            Thread::Queue Carp Data::Dumper YAML Hash::Merge Logger::Simple Parallel::ForkManager \
+            DBI Text::Soundex Scalar::Util::Numeric Clone JSON LWP::UserAgent DBD::mysql
+   
+    
+    6.  Setup funannotate databases:
 
     .. code-block:: none
         
         funannotate setup -d /path/to/DB
 
-    5.  Export required ENV variables (your paths might differ slightly):
+    7.  Export required ENV variables (your paths might differ slightly):
 
     .. code-block:: none
 

docs/docker.rst

@@ -37,7 +37,7 @@ in Docker container as the databases were too large.
     RepBaseRepeatMaskerEdition-20170127.tar.gz
     signalp-4.1c.Linux.tar.Z
 
-Now you can Build the docker containiner, which will setup the remaining tools and then download and format funannotate databases.:
+Now you can Build the docker container, which will setup the remaining tools and then download and format funannotate databases.:
 
 .. code-block:: none