Merge branch 'master' into master

README.md

@@ -2,6 +2,7 @@
 Bacterial Epigenomics Analysis SuiTe
 
 ## Description
+
 With only a few thousand bacterial methylomes published to date, it is becoming increasingly evident that epigenetic regulation of gene expression is highly prevalent across bacterial species. Despite the exciting prospects for studying epigenetic regulation, our ability to comprehensively analyze bacterial epigenomes is limited by a bottleneck in integratively characterizing methylation events, methylation motifs, transcriptomic data, and functional genomics data. In this regard, we provided the first comprehensive comparative analysis of a large collection of epigenomes in a single bacterial species, as well as a detailed roadmap that can be used by the scientific community to leverage the current status quo of epigenetic analyses [(Oliveira et al., 2019, Nat. Microbiology)](https://www.nature.com/articles/s41564-019-0613-4). 
 
 PLEASE NOTE: BEAST includes a set of R and wrapper shell scripts that allow to reconstitute the major analyses steps of this publication. However, this pipeline requires multiple dependencies, which have to be installed prior the use of BEAST. The user has two possibilities:

Section_7/GO_CRISPRs.sh

@@ -45,6 +45,7 @@ set b = $fasta_file:r
 if (! -e $b.crispr_raw) then
 	touch $b.crispr_raw
     	echo "search crispr in $b"
+
 	java -cp $CRT_filename crt -minNR $minNR -minRL $minRL -maxRL $maxRL -minSL $minSL -maxSL $maxSL -searchWL $searchWL $fasta_file $b.crispr_raw
 endif
 

docs/usage.rst

@@ -516,8 +516,9 @@ By default, integron_finder will output 3 files under **Results_Integron_Finder_
 **integron_finder.out**: A copy of standard output;
 
 
+
 Running BEAST via Docker 
-=============
+
 For a quicker and more streamlined use of BEAST, and due to its large number of dependencies, the user may consider running it via Docker. Docker is a tool that uses OS-level virtualization, thus making it easier to run applications through capsules (containers). A step-by-step tutorial is presented below:
 
 - Install `Docker <https://www.docker.com>`_ on your computer following the instructions provided `here <https://docs.docker.com/v17.12/install/>`_.
@@ -599,4 +600,3 @@ To re-run the capsule with alternative initial starting conditions, the user jus
   78bdb7a2-6832-4167-b5e8-fd8f925e67e5 ./GO_Abundance.sh yourfile.fasta GATC 4 2 gaussian
   
   
-