Merge pull request #352 from ajodeh-juma/gis-branch

add gis.md documentation

docs/gis.md

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+# nf-core/configs: GIS Aquila Configuration
+
+All nf-core pipelines have been successfully configured for use on the cluster of the GIS (Genome Institute of Singapore (Aquila)).
+
+To use, run the pipeline with `-profile gis`. This will download and launch the [`gis.config`](../conf/gis.config) which has been pre-configured with a setup suitable for the GIS Aquila cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
+
+## How to use on GIS core
+
+Before running the pipeline you will need to load Nextflow using the environment module system on GIS Aquila. You can do this by issuing the commands below:
+
+```bash
+# Login to a compute node
+srun --pty bash
+
+## Load Nextflow and Singularity environment modules
+module purge
+source /mnt/projects/rpd/rc/init.2017-04
+module load miniconda3
+
+
+# Run a nextflow pipeline with dependencies bundled in a conda environment
+set +u
+source activate nfcore-rnaseq-1.0dev
+set -u
+
+# Run a downloaded/git-cloned nextflow workflow from
+nextflow run \\
+nf-core/workflow \\
+-resume \\
+-profile gis \\
+--email my-email@example.org  \\
+-c my-specific.config
+...
+
+
+# Or use the nf-core client
+nextflow run nf-core/rnaseq ...
+
+```
+
+## Databanks
+
+A local copy of several genomes are available in `/mnt/projects/rpd/genomes.testing/S3_igenomes/` directory.
+
+> NB: You will need an account to use the HPC cluster on GIS in order to run the pipeline. If in doubt contact IT or go to [Andreas Wilm](https://github.com/andreas-wilm)