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  1. JABAWS
  2. JWS-131

t-coffee alignments run, but in the end fail with no results returned

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.2.0
    • Fix Version/s: 2.2.1
    • Component/s: jabaws-internal
    • Labels:
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      Description

      JABAWS appears to be looking at results.txt to find the alignment generated by T-Coffee, but the version bundled with JABAWS actually seems to write its output to input.clustalw under the current CLI configuration, where the output file is not actually specified, only the format (clustalw).

      Workaround was to patch the t_coffee.sh script so it copies the output to results.txt. Not ideal, but simpler than rebuilding JABAWS.

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            Assignee:
            smacgowan Stuart MacGowan
            Reporter:
            jprocter James Procter
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              Dates

              Created:
              Updated: