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Annogesic on Biowulf & Helix

ANNOgesic is a modular, command-line tool that can integrated different types of RNA-Seq data like dRNA-Seq or RNA-Seq generated after transcript fragmentation and generates high quality genome annotations. It can detect gene, CDS/tRNA/rRNA, TSS and processing sites, transcripts, terminator, Untranslated region (UTR) as well as small RNA (sRNA), small open reading frame (sORF), circular RNA, CRISPR related RNAs, riboswitch and RNA-thermometer. It can also perform RNA-RNA and protein-protein interaction predictions. Furthermore, it groups genes into operon and sub-operons and reveal promotor motifs. It can also allocate GO term and subcellular localization to genes. Several of ANNOgesic features are new implementation while others are performed and improved by third-party tools and for some of them adaptive parameter-optimizations were included. Additionally, numerous visualization and statistitcs help the user quickly evaluated feature predictions resulting from an ANNOgesic analysis. The pipeline is modular and was heavily tested with several RNA-Seq data set from bacterial as well as archaeal samples.

 

Running on Helix

helix$ module load annogesic
helix$ usage: annogesic [-h] [--version]
{create,get_input_files,get_target_fasta,annotation_transfer,tsspredator,optimize_tsspredator,color_png,terminator,transcript_assembly,utr,srna,sorf,promoter,operon,circrna,go_term,srna_target,snp,ppi_network,subcellular_localization,riboswitch_thermometer,crispr,merge_features,screenshot}
[.....]

  

Running a single batch job on Biowulf

Set up a batch script along the following lines.

#!/bin/bash 

cd /data/$USER/mydir
module load annogesic

annogesic command

Submit to the batch system with:

sbatch myscript


Running a swarm of batch jobs on Biowulf

Set up a swarm command file (eg /data/$USER/cmdfile). Here is a sample file:

cd /data/$USER/mydir1; annogesic command
cd /data/$USER/mydir2; annogesic command
cd /data/$USER/mydir3; annogesic command [...]

Submit this job with

swarm -f cmdfile --module annogesic

Running an interactive job on Biowulf

Users may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.

[user@biowulf]$ sinteractive  
      salloc.exe: Granted job allocation 1528

[user@pxxx]$ module load annogesic

[user@pxxx]$ cd /data/$USER/run1

[user@pxxx]$ annogesic command
[user@p4] exit [user@biowulf]$

Documentation

https://pypi.python.org/pypi/ANNOgesic