updated docs

README.md

@@ -43,7 +43,7 @@ For a lot of virus genera it is difficult to design pan-specific primers. varVAM
 
 We, in collaboration with specialists for the respective viruses, have already designed and wet-lab evaluated primer schemes for various viral pathogens. All the input data and varVAMP outputs are freely available [here](https://github.com/jonas-fuchs/ViralPrimerSchemes). 
 
-If you design primers for a particular pathogen, we will be happy to include them in this repo and make it freely available. Just contribute via an issue or pull request!
+Moreover, varVAMP primers are now available at [primerschemes](https://labs.primalscheme.com/). varVAMP now reports primer bed files in ARTICv3 format. Feel free to contribute newly designed schemes via this [Github repository of the QuickLab](https://github.com/quick-lab/primerschemes). Use [primal-page](https://github.com/ChrisgKent/primal-page) developed by [Chris Kent](https://github.com/ChrisgKent) to generate data for compatible pull-requests.
 
 # Citing varVAMP
 

docs/installation.md

@@ -21,7 +21,8 @@ pip install setuptools varvamp
 ### CONDA:
 
 ```shell
-conda install -c bioconda varvamp
+conda create -n varvamp varvamp
+conda activate varvamp
 ```
 
 ### DOCKER:

docs/usage.md

@@ -43,6 +43,7 @@ optional arguments:
   -a , --n-ambig        	max number of ambiguous characters in a primer
   -db None, --database None     location of the BLAST db
   -th 1, --threads 1            number of threads
+  --name varVAMP                name of the scheme
   -ol 1000, --opt-length 1000   optimal length of the amplicons
   -ml 1500, --max-length 1500   max length of the amplicons
   -n inf, --report-n inf	report the top n best hits
@@ -58,6 +59,7 @@ optional arguments:
   -a , --n-ambig        	max number of ambiguous characters in a primer
   -db None, --database None     location of the BLAST db
   -th 1, --threads 1	        number of threads
+  --name varVAMP                name of the scheme
   -ol 1000, --opt-length 1000	optimal length of the amplicons
   -ml 1500, --max-length 1500	max length of the amplicons
   -o 100, --overlap 100		min overlap of the amplicons
@@ -73,6 +75,7 @@ optional arguments:
   -a , --n-ambig        	max number of ambiguous characters in a primer
   -db None, --database None     location of the BLAST db
   -th 1, --threads 1   	        number of threads
+  --name varVAMP                name of the scheme
   -pa , --pn-ambig   		max number of ambiguous characters in a probe
   -n 50, --test-n 50    	test the top n qPCR amplicons for secondary structures at the minimal primer temperature
   -d -3, --deltaG -3            minimum free energy (kcal/mol/K) cutoff at the lowest primer melting temp