Differences

This shows you the differences between two versions of the page.

--- funannotate-software [2022/07/05 11:40] – aorth
+++ funannotate-software [2022/07/05 11:43] – aorth
@@ Line 6: / Line 6: @@
   * Version: 1.8.11
   * Added: August, 2021
-  * Updated: May, 2022
+  * Updated: June, 2022
   * Link: https://github.com/nextgenusfs/funannotate
 ===== Usage =====
-See versions that are available:
+Funannotate is installed in a dedicated "container" environment using [[https://docs.sylabs.io/guides/latest/user-guide/|Singularity]] (similar to Docker, but more suited to HPC environments) so you need to run it a bit differently than other software. Here is an example SLURM batch script, ''funannotate.sbatch'':
-<code>$ module avail funannotate</code>
-Load a particular version into your environment and run it:
-<code>$ module load funannotate/1.8.11
-$ funannotate --help</code>
-Note: funannotate is installed in a dedicated "container" environment using Singularity so you need to run it a bit differently than other software. Here is an example SLURM batch script, ''funannotate.sbatch'':
 <code>#!/usr/bin/env bash
@@ Line 26: / Line 18: @@
 #SBATCH -J funannotate
-# Set up environment in scratch
+# Set up output directory in scratch
 WORKDIR=/var/scratch/aorth/funannotate/2022-06-09
@@ Line 53: / Line 45: @@
 Notes from the sysadmin during installation:
-<code>export SINGULARITY_TMPDIR=/var/scratch/aorth
+<code>$ export SINGULARITY_TMPDIR=/var/scratch/aorth
 $ singularity pull /var/scratch/funannotate.sif docker://nextgenusfs/funannotate:v1.8.11
 $ sudo mkdir -p /export/apps/funannotate/1.8.11