diff README.md @ 1:6c92e000d684 draft

"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
author galaxy-australia
date Tue, 01 Mar 2022 02:53:05 +0000
parents 7ae9d78b06f5
children
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--- a/README.md	Fri Jan 28 04:56:29 2022 +0000
+++ b/README.md	Tue Mar 01 02:53:05 2022 +0000
@@ -3,9 +3,9 @@
 
 ## Overview
 
-Alphafold requires a customised compute environment to run. The machine needs a GPU, and access to a 2.2 Tb reference data store. 
+Alphafold requires a customised compute environment to run. The machine needs a GPU, and access to a 2.2 Tb reference data store.
 
-This document is designed to provide details on the compute environment required for Alphafold operation, and the Galaxy job destination settings to run the wrapper. 
+This document is designed to provide details on the compute environment required for Alphafold operation, and the Galaxy job destination settings to run the wrapper.
 
 For full details on Alphafold requirements, see https://github.com/deepmind/alphafold.
 
@@ -13,11 +13,11 @@
 
 ### HARDWARE
 
-The machine is recommended to have the following specs: 
+The machine is recommended to have the following specs:
 - 12 cores
 - 80 Gb RAM
 - 2.5 Tb storage
-- A fast Nvidia GPU. 
+- A fast Nvidia GPU.
 
 As a minimum, the Nvidia GPU must have 8Gb RAM. It also requires ***unified memory*** to be switched on. <br>
 Unified memory is usually enabled by default, but some HPC systems will turn it off so the GPU can be shared between multiple jobs concurrently.
@@ -31,7 +31,7 @@
 - [Singularity](https://sylabs.io/guides/3.0/user-guide/installation.html)
 - [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html)
 
-As Alphafold uses an Nvidia GPU, the NVIDIA Container Toolkit is needed. This makes the GPU available inside the running singularity container. 
+As Alphafold uses an Nvidia GPU, the NVIDIA Container Toolkit is needed. This makes the GPU available inside the running singularity container.
 
 To check that everything has been set up correctly, run the following
 
@@ -79,7 +79,7 @@
 bash scripts/download_all_data.sh /data/alphafold_databases
 ```
 
-This will install the reference data to `/data/alphafold_databases`. To check this has worked, ensure the final folder structure is as follows: 
+This will install the reference data to `/data/alphafold_databases`. To check this has worked, ensure the final folder structure is as follows:
 
 ```
 data/alphafold_databases
@@ -128,9 +128,9 @@
 
 ### JOB DESTINATION
 
-Alphafold needs a custom singularity job destination to run. 
+Alphafold needs a custom singularity job destination to run.
 The destination needs to be configured for singularity, and some
-extra singularity params need to be set as seen below. 
+extra singularity params need to be set as seen below.
 
 Specify the job runner. For example, a local runner
 
@@ -154,4 +154,4 @@
 
 ### Closing
 
-If you are experiencing technical issues, feel free to write to help@genome.edu.au. We may be able to provide comment on setting up Alphafold on your compute environment.
+If you are experiencing technical issues, feel free to write to help@genome.edu.au. We may be able to provide advice on setting up Alphafold on your compute environment.