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update README.md, conda updated #171

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58 changes: 29 additions & 29 deletions README.md
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Expand Up @@ -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 <br>
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
Expand Down Expand Up @@ -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.<br>
`source` it.

#### Through Conda
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 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`. !!
Expand Down