diff --git a/README.md b/README.md index c2f2824..79af901 100644 --- a/README.md +++ b/README.md @@ -53,9 +53,37 @@ Other dependency: * bedtools * samtools +#### Through Conda (currently deploying Meryl v1.4.1, commit 5f3f1eb) + +Thanks to @EdHarry, a conda recipe is now available: https://anaconda.org/bioconda/merqury
+On a new conda environment, run: +```shell +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 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`. ### Previous Releases -The v1.3 Merqury is compatable with Meryl v1.3, however does not support homopolymer-compressed kmers. In addition, multiple issues were fixed (e.g. use of large k-mers, better memory utilization, minor bugs in the logs etc.) since then. Therefore, we recommend to use the latest Meryl and Merqury. The Conda version below is currently deploying v1.3. +The v1.3 Merqury is compatable with Meryl v1.3, however does not support homopolymer-compressed kmers. In addition, multiple issues were fixed (e.g. use of large k-mers, better memory utilization, minor bugs in the logs etc.) since then. Therefore, we recommend to use the latest Meryl and Merqury. #### Direct installation 1. Get a working [Meryl](https://github.com/marbl/meryl) in your PATH @@ -86,34 +114,6 @@ Add the “export” part to your environment for `meryl` and `MERQURY` (~/.bash Add installation dir paths for `bedtools` and `samtools` to your environment.
`source` it. -#### Through Conda -Thanks to @EdHarry, a conda recipe is now available: https://anaconda.org/bioconda/merqury
-On a new conda environment, run: -```shell -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 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`. - ## Run * !! Merqury assumes all meryl dbs (dirs) are named with `.meryl`. !!