Update of 'News' section, bug fix for the tools table, added new depe…

…ndencies to 'install' section
deeptools · Nov 6, 2017 · 45ceea8 · 45ceea8
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diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -1,8 +1,28 @@
 News and Developments
 =====================
 
-Release 1.7.2
+Release 1.8
 -----------
+
+**October 25, 2017**
+
+This release is adding new features and fixes many bugs:
+
+ * hicBuildMatrix: Added multicore support, new parameters --threads and --inputBufferSize
+ * hicFindTADs:
+  * One call instead of two: hicFindTADs TAD_score and hicFindTADs find_TADs merged to hicFindTADs.
+  * New multiple correction method supported: False discovery rate. Call it with --correctForMultipleTesting fdr and --threshold 0.05.
+ * Update of the tutorial: mES-HiC analysis.
+ * Additional test cases and docstrings to improve the software quality
+ * Fixed a bug occurring with bigwig files with frequent NaN values which resulted in only NaN averages
+ * hicPlotTADs: Support for plotting points
+ * Moved galaxy wrappers to https://github.com/galaxyproject/tools-iuc
+ * Fixed multiple bugs with saving matrices
+ * hicCorrelate: Changes direction of dendograms to left
+
+Release 1.7.2
+-------------
+
 **April 3, 2017**
 
  * Added option to plot bigwig files as a line hicPlotTADs

diff --git a/docs/content/installation.rst b/docs/content/installation.rst
@@ -17,6 +17,8 @@ Requirements
 * pytables >= 3.3.0
 * pandas >= 0.20.2
 * pybigwig >= 0.3.4
+* six >= 1.10.0
+* jinja2 >= 2.9.6
 
 Command line installation using ``conda``
 -----------------------------------------

diff --git a/docs/content/list-of-tools.rst b/docs/content/list-of-tools.rst
@@ -30,7 +30,7 @@ HiCExplorer tools
    +--------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
    |:ref:`hicPlotDistVsCounts`      | visualization    | hicMatrix object                  | log log plot of Hi-C contacts per distance  | Quality control                                                                   |
    +--------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
-   |:ref:`hicExport`                | data integration | multiple Hi-C file formats         | Hi-C matices/outputs in several formats      | Export matrix to different formats                                                |
+   |:ref:`hicExport`                | data integration | multiple Hi-C file formats        | Hi-C matices/outputs in several formats     | Export matrix to different formats                                                |
    +--------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
    |:ref:`hicInfo`                  | information      | one or more hicMatrix objects     | Screen info                                 | Prints information about  matrices, like size, maximum, minimux, bin size, etc.   |
    +--------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+