metawrap

docs/remote_repositories.md

@@ -114,6 +114,44 @@ Type "help", "copyright", "credits" or "license" for more information.
 >>>
 ```
 
+### metaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
+
+Here is an example how to use the metaWRAP pipeline with via the docker container - [installation instructions](https://github.com/bxlab/metaWRAP#docker-installation).
+
+```
+$ docker pull quay.io/biocontainers/metawrap:1.2--1
+```
+In this particular case it is as easy as:
+
+```
+$ singularity pull docker://quay.io/biocontainers/metawrap:1.2--1
+
+INFO: Converting OCI blobs to SIF format
+INFO: Starting build...
+Getting image source signatures
+...
+```
+
+One can start the container and use it interactively.
+
+```
+$ ./metawrap_1.2--1.sif
+WARNING: Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
+
+Singularity> metawrap --version
+metaWRAP v=1.2
+```
+
+but to run the tool from the command line (as you would use it in scripts) we need to add the call for the tool from Singularity.
+
+Original commad in the cript: 
+$ **metawrap** binning -o Lanna-straw_initial_binning_concoct -t 20 -a /proj/test/megahit_ass_Lanna-straw/final.contigs.fa --concoct --run-checkm /proj/test/Lanna-straw_reads_trimmed/*.fastq
+
+The command now calls the tool from the Singularity container: 
+$ ==singularity exec metawrap_1.2--1.sif== **metawrap** binning -o Lanna-straw_initial_binning_concoct -t 20 -a /proj/test/megahit_ass_Lanna-straw/final.contigs.fa --concoct --run-checkm /proj/test/Lanna-straw_reads_trimmed/*.fastq
+
+
+
 !!! info "Pulling Singularity container from online or local library/repository"
  - **library://** to build from the [Container Library](https:// cloud.sylabs.io/library) 
  ` library://sylabs-jms/testing/lolcow`
@@ -122,4 +160,5 @@ Type "help", "copyright", "credits" or "license" for more information.
  - **shub://** to build from [Singularity Hub](https:// singularityhub.com/)
  - path to a existing container on your local machine
  - path to a directory to build from a sandbox
- - path to a Singularity definition file
+ - path to a Singularity definition file
+