#21 ✓resolved
john.mccallum (at plantandfood)

less than informative info on web view

Reported by john.mccallum (at plantandfood) | May 11th, 2011 @ 02:51 AM | in v1.1

Browsing http://pgenome.crop.cri.nz/moa/data/onion/Repeats/10.RepeatScout/

info tab shows: Template simple

Execute one command, No in or output files are tracked by Moa.
Parameters

process True
default_command run
Template settings

Author Mark Fiers
Backend ruff

...................... but CL shows:

[Cfljam@pgenome 10.RepeatScout]$ moa show postcommand ~/opt/RepeatScout-1/filter-stage-1.prl output_repeats.fas > output_repeats.fas.filtered_1
precommand /home/cfljam/opt/RepeatScout-1/build_lmer_table -sequence ../01.UnfilteredGSSReads/JBVR.fasta -freq output_lmer.frequency
process /home/cfljam/opt/RepeatScout-1/RepeatScout -sequence ../01.UnfilteredGSSReads/JBVR.fasta -output output_repeats.fas -freq output_lmer.frequency
project
title detect repeats
[Cfljam@pgenome 10.RepeatScout]$

It would be nice to see template settings in browser again

Comments and changes to this ticket

  • john.mccallum (at plantandfood)

    john.mccallum (at plantandfood) May 11th, 2011 @ 09:38 PM

    THis looks like general issue with templates:

    AT http://pgenome.crop.cri.nz/moa/data/db/onion/20.Genbank_onion/30.BL...

    Template blastdb

    Parameters

    default_command run
    fasta_file
    protein F
    name blastdb
    Template settings

    Author Mark Fiers
    Backend gnumake

    BUT from CL

    [Cfljam@pgenome 15.BLASTN_repeats]$ pwd /data/moa/onion/Repeats/15.BLASTN_repeats [Cfljam@pgenome 15.BLASTN_repeats]$ moa show db /data/moa/db/onion/20.Genbank_onion/30.BLASTdb_nt/OnionNCBInt
    eval 1e-10
    gff_blasthit F
    gff_source BLAST
    input ../10.RepeatScout/output_repeats.fas.filtered_1
    nohits 50
    nothreads 2
    outgff gff/.gff
    output out/    .out
    postcommand
    precommand
    program blastn
    project repeats
    title BLASTN filtered repeats against GB onion nt

  • MF

    MF May 11th, 2011 @ 11:35 PM

    • State changed from “new” to “resolved”

    Fixed -

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lightweight workflows for bioinformatics

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