Merge branch 'master' of https://github.com/marbl/merqury

README.md

@@ -23,19 +23,30 @@ Merqury provides a set of tools for this purpose.
 Thanks to @EdHarry, a conda recipe is now available: https://anaconda.org/bioconda/merqury <br>
 On a new conda environment, run:
 ```shell
-conda install -c bioconda merqury
+conda install -c conda-forge -c bioconda merqury
 ```
 
 Or, if you have a different version of jdk installed or want to have a separate conda environnment for merqury:
 ```shell
-conda create -n merqury -c bioconda -c conda-forge merqury openjdk=11
+conda create -n merqury -c conda-forge -c bioconda merqury openjdk=11
 ```
 
 You will then need to activate the merqury environment before using it with:
 ```shell
 conda activate merqury
 ```
 
+Test running 
+```Shell
+Rscript $MERQURY/plot/plot_spectra_cn.R --help
+```
+
+In case R complains for version mismatches of the R packages, try
+```Shell
+conda update --all
+```
+It seems like R in conda isn't maintained anymore. Try to modify channel priority in `.condarc`.
+
 #### Direct installation 
 1. Get a working [Meryl](https://github.com/marbl/meryl) in your PATH
 

trio/hapmers.sh

@@ -14,8 +14,8 @@ if [[ "$#" -lt 2 ]]; then
 	echo -e "\t\tshrd.meryl\tShared k-mers"
 	echo
 	echo -e "\tOutput (when [child.meryl is given)"
-	echo -e "\t\thap1.hapmers.meryl\tHaplotype1, inherited k-mers (ex. maternal hap-mers)"
-	echo -e "\t\thap2.hapmers.meryl\tHaplotype2, inherited k-mers (ex. paternal hap-mers)"
+	echo -e "\t\thap1.hapmer.meryl\tHaplotype1, inherited k-mers (ex. maternal hap-mers)"
+	echo -e "\t\thap2.hapmer.meryl\tHaplotype2, inherited k-mers (ex. paternal hap-mers)"
 	echo -e "\t\tshrd.inherited.meryl\tShared, inherited k-mers"
 	echo
 	echo -e "\t*Build each .meryl dbs using the same k-size"