Merge pull request #354 from mutalyzer/docs

Documentation updates

doc/admin.rst

@@ -73,6 +73,20 @@ Examples for other assemblies can be found in `this Gist
 <https://gist.github.com/martijnvermaat/ce84945d05b4e42d3584>`_.
 
 
+Import mappings from an EBI LRG transcripts map file
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The EBI provides `FTP downloads <ftp://ftp.ebi.ac.uk/pub/databases/lrgex/>`_
+of transcript mappings for all of the LRG sequences on the latest human genome
+assembly. These can be imported with ``mutalyzer-admin``.
+
+For example, to import LRG transcript mappings for the GRCh37 assembly, run
+the following::
+
+    $ wget ftp://ftp.ebi.ac.uk/pub/databases/lrgex/list_LRGs_transcripts_GRCh37.txt -O /tmp/hg19.lrgmap.txt
+    $ mutalyzer-admin assemblies import-lrgmap -a hg19 /tmp/hg19.lrgmap.txt
+
+
 Import mappings from the UCSC Genome Browser MySQL database
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

mutalyzer/website/templates/homepage.html

@@ -118,11 +118,26 @@ nomenclature according to the
 </ul> -->
 
 <p>
-GenBank sequences are retrieved from the <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a> (<a href="http://eutils.ncbi.nlm.nih.gov/About/disclaimer.html" >Copyright and Disclaimers</a>).
+GenBank sequences are retrieved
+via <a href="http://www.ncbi.nlm.nih.gov/">NCBI Entrez</a>
+(<a href="https://www.ncbi.nlm.nih.gov/home/about/policies.shtml">Data Usage
+Policies and Disclaimers</a>).
 </p>
 
 <p>
-LRG sequences are retrieved from the <a href="http://www.lrg-sequence.org/">Locus Reference Genomic</a> FTP site (<a href="http://www.ebi.ac.uk/about/terms-of-use">EMBL-EBI Terms of Use</a>).
+LRG sequences are retrieved from
+the <a href="http://www.lrg-sequence.org/">Locus Reference Genomic</a> FTP
+site (<a href="http://www.ebi.ac.uk/about/terms-of-use">EMBL-EBI Terms of
+Use</a>).
+</p>
+
+<p>
+The <a href="http://www.ncbi.nlm.nih.gov/mapview/">NCBI Map Viewer</a> data
+and <a href="ftp://ftp.ebi.ac.uk/pub/databases/lrgex/">EBI LRG transcripts map
+files</a> are the primary sources for transcript mappings, with a selection of
+transcript mappings from
+the <a href="https://genome.ucsc.edu/goldenPath/help/mysql.html">UCSC Genome
+Browser MySQL database</a> manually added on a per-gene basis.
 </p>
 
 <script>