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funannotate-software [2022/07/05 11:40] – aorthfunannotate-software [2023/04/20 21:21] (current) – aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 1.8.11+  * Version: 1.8.15
   * Added: August, 2021   * Added: August, 2021
-  * Updated: May, 2022+  * Updated: April, 2023
   * Link: https://github.com/nextgenusfs/funannotate   * Link: https://github.com/nextgenusfs/funannotate
  
 ===== Usage ===== ===== 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 <code>#!/usr/bin/env bash
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 #SBATCH -J funannotate #SBATCH -J funannotate
  
-# Set up environment in scratch+# Set up output directory in scratch
 WORKDIR=/var/scratch/aorth/funannotate/2022-06-09 WORKDIR=/var/scratch/aorth/funannotate/2022-06-09
  
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 singularity run \ singularity run \
             --bind "$genome:$genome","$rnaseq_ont:$rnaseq_ont","$WORKDIR:$WORKDIR" \             --bind "$genome:$genome","$rnaseq_ont:$rnaseq_ont","$WORKDIR:$WORKDIR" \
-            /export/apps/funannotate/1.8.11/funannotate.sif \+            /export/apps/funannotate/1.8.15/funannotate.sif \
             funannotate train --input "$genome" \             funannotate train --input "$genome" \
             --out "$WORKDIR" \             --out "$WORKDIR" \
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 Notes from the sysadmin during installation: 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 +$ mkdir $SINGULARITY_TMPDIR 
-$ sudo mkdir -p /export/apps/funannotate/1.8.11 +$ singularity pull /var/scratch/funannotate.sif docker://nextgenusfs/funannotate:v1.8.15 
-$ sudo /var/scratch/funannotate.sif /export/apps/funannotate/1.8.11</code>+$ sudo mkdir -p /export/apps/funannotate/1.8.15 
 +$ sudo cp /var/scratch/funannotate.sif /export/apps/funannotate/1.8.15</code>
  
 Run built-in tests: Run built-in tests:
  
 <code>singularity run \ <code>singularity run \
-            /export/apps/funannotate/1.8.11/funannotate.sif \+            /export/apps/funannotate/1.8.15/funannotate.sif \
             funannotate test -t all --cpus 10</code>             funannotate test -t all --cpus 10</code>
funannotate-software.1657021255.txt.gz · Last modified: by aorth