update README

README.md

@@ -1,4 +1,4 @@
-# EVOLINC-I 1.0
+# EVOLINC-I 1.3
 Evolinc-I is a long intergenic noncoding RNA (lincRNA) identification workflow that also facilitates genome browser visualization of identified lincRNAs and downstream differential gene expression analysis. 
 
 Evolinc-I minimally requires the following input data
@@ -23,15 +23,15 @@ Since there are several dependencies (these can be seen in [Dockerfile](https://
 
 ```
 # Pull the image from CyVerse Dockerhub
-docker pull evolinc/evolinc-i:1.1
+docker pull evolinc/evolinc-i:1.3
 
 # See the command line help for the image
-docker run evolinc/evolinc-i:1.1 -h 
+docker run evolinc/evolinc-i:1.3 -h 
 
 # Run Evolinc-I on the test data. The sample data can be found in the sample_data folder in this repo
 git clone https://github.com/Evolinc/Evolinc-I.git
 cd Evolinc-I
-docker run --rm -v $(pwd):/working-dir -w /working-dir evolinc/evolinc-i:1.1 -c Sample_cuffcompare_out.gtf -g TAIR10_chr1.fasta -r TAIR10_chr1_genes.gff -o test_out -n 4
+docker run --rm -v $(pwd):/working-dir -w /working-dir evolinc/evolinc-i:1.3 -c Sample_cuffcompare_out.gtf -g TAIR10_chr1.fasta -r TAIR10_chr1_genes.gff -o test_out -n 4
 ```
 
 ### Using CyVerse Discovery Environment
@@ -41,8 +41,7 @@ The [Evolinc-I app](https://de.cyverse.org/de/?type=apps&app-id=e980754e-8050-11
 #### Step-by-step walkthroughs
 
 Step-by-step walkthrough for running Evolinc-I on DE is available [here](https://drive.google.com/open?id=0B-ferWixi_V3cmh0QzhJeXRXSE0).
-Step-by-step walkthrough for the command-line, with directions on how to change parameters is coming soon.
-Information on how to easily create a Cuffmerge/Cuffcompare input file from 1-many SRA IDs within the DE can be found [here](https://drive.google.com/open?id=0B-ferWixi_V3NjVpdENLUXhLZjQ)
+Step-by-step walkthrough for the command-line, with directions on how to change parameters is coming soon. Information on how to easily create a Cuffmerge/Cuffcompare input file from 1-many SRA IDs within the DE can be found [here](https://drive.google.com/open?id=0B-ferWixi_V3NjVpdENLUXhLZjQ)
 
 
 # Issues
@@ -52,4 +51,6 @@ If you experience any issues with running Evolinc-I (DE app or source code or Do
 The sources in this [Github](https://github.com/Evolinc/Evolinc-I) repository, are copyright free. Thus you are allowed to use these sources in which ever way you like. Here is the full [MIT](https://choosealicense.com/licenses/mit/#) license.
 
 # Citing Evolinc-I
-Evolinc-I manuscript is currently under review but is available as a [bioRxiv](http://biorxiv.org/content/early/2017/02/20/110148) preprint.
+If you have used Evolinc-I manuscript in your research, please cite as below..
+
+*Andrew D. Nelson*, Upendra K. Devisetty*, Kyle Palos, Asher K. Haug-Baltzell, Eric Lyons, Mark A. Beilstein (2017). "Evolinc: a comparative transcriptomics and genomics pipeline for quickly identifying sequence conserved lincRNAs forfunctional analysis". Frontiers in Genetics. 1(10)*