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Binaries missing with conda install #208

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Binaries missing with conda install#208

Description

@fgvieira
fgvieira
opened on Apr 7, 2026

When installing through conda, I get:

/usr/bin/bash: TransDecoder.LongOrfs: command not found

Looking into the bin/ folder, the two symlinks are broken:

bin/TransDecoder.LongOrfs -> ../opt/transdecoder/TransDecoder.LongOrfs
bin/TransDecoder.Predict -> ../opt/transdecoder/TransDecoder.Predict

And in opt/transdecoder:

total 592K
-rw-r--r--. 1 user users  14K Apr  7 09:07 build_env_setup.sh
-rw-r--r--. 1 user users 6.6K Mar 28 06:35 Changelog.txt
-rwxr-xr-x. 1 user users  617 Mar 28 06:35 conda_build.sh
drwxr-xr-x. 2 user users  152 Apr  7 09:12 Docker
-rw-r--r--. 1 user users 1.5K Mar 28 06:35 LICENSE.txt
-rw-r--r--. 1 user users  218 Mar 28 06:35 Makefile
-rw-r--r--. 1 user users 1.1K Mar 28 06:35 metadata_conda_debug.yaml
-rw-r--r--. 1 user users  120 Mar 28 06:35 notes
drwxr-xr-x. 2 user users  441 Apr  7 09:12 PerlLib
-rw-r--r--. 1 user users  278 Mar 28 06:35 README.md
drwxr-xr-x. 7 user users  264 Apr  7 09:12 sample_data
drwxr-xr-x. 2 user users  347 Apr  7 09:12 __testing
-rwxr-xr-x. 1 user users  13K Mar 28 06:35 TransDecoder
drwxr-xr-x. 6 user users 1.3K Apr  7 09:12 util

Activity

  1. evatosco commented on Jun 12, 2026

    @evatosco
    evatosco
    on Jun 12, 2026

    Hi there, thanks for the report!

    Same over here.
    Here's a quick workaround (for now) for noobies and for one of those days when you just cannot think:

    (replace miniconda3 by what you use -- conda or whatever, and my_env with the name of your environment)

      cd ~/miniconda3/envs/my_env/bin/
  ln -s ../opt/transdecoder/TransDecoder transdecoder

  rm TransDecoder.LongOrfs # for cleanup
  rm TransDecoder.Predict # for cleanup

  exec bash && conda activate my_env # to reload the terminal
  # Now you can run it with "transdecoder".

    Apparently, there is a single binary now that automatically runs the LongOrfs and the Predict functions by default in that order, as far as I have understood (source).

    Hope it helps!

  2. fgvieira commented on Jun 12, 2026

    @fgvieira
    fgvieira
    on Jun 12, 2026
    Author

    Does that mean that it is no longer possible to run each command separately?

  3. evatosco commented on Jun 12, 2026

    @evatosco
    evatosco
    on Jun 12, 2026

    I honestly do not know, but I think the main binary changed in newer versions to be easier to use.

    However, I found the separated binaries (TransDecoder.LongOrfs and TransDecoder.Predict) in this path:
    ~/miniconda3/envs/my_env/opt/transdecoder/util/
    I do not know the detail, whether these work the same as the main binary, or they are old and now legacy binaries. I guess that is something the developer is to answer.

    Hope it helps!

  4. brianjohnhaas commented on Jun 12, 2026

    @brianjohnhaas
    brianjohnhaas
    on Jun 12, 2026 via email
    Contributor

  5. fgvieira commented on Jun 12, 2026

    @fgvieira
    fgvieira
    on Jun 12, 2026
    Author

    Ok, just to be sure on the recommended way to run transdecoder. Does it make sense (under any circumstance) to run each step separately? If so, then it would be nice to also have TransDecoder.LongOrfs and TransDecoder.Predict in $PATH. Or, on the contrary, is this behavior deprecated (or not recomended)?

  6. brianjohnhaas commented on Jun 12, 2026

    @brianjohnhaas
    brianjohnhaas
    on Jun 12, 2026 via email
    Contributor

  7. fgvieira commented on Jun 16, 2026

    @fgvieira
    fgvieira
    on Jun 16, 2026
    Author

    Thanks for the clarifications, but the binaries are still missing.

    @evatosco solutions works since the binaries seem to be under opt/transdecoder but, if these binaries are the ones intended for use, shouldn't they be added to $PATH by the conda recipe?

  8. evatosco commented on Jun 17, 2026

    @evatosco
    evatosco
    on Jun 17, 2026

    Thanks for the clarifications, but the binaries are still missing.

    @evatosco solutions works since the binaries seem to be under opt/transdecoder but, if these binaries are the ones intended for use, shouldn't they be added to $PATH by the conda recipe?

    Hi,

    I imagine that the idea was to use the updated and merged transdecoder binary at /opt/transdecoder/TransDecoder , that is probably why there is no mention of the separate packages anymore.

  9. fgvieira commented on Jun 17, 2026

    @fgvieira
    fgvieira
    on Jun 17, 2026
    Author

    But that binary is not in $PATH and, therefore, not accessible when the conda environment is loaded.

  10. mike2vandy commented on Sep 20, 2026

    @mike2vandy
    mike2vandy
    on Sep 20, 2026

    Having no working binaries in the conda env is kind of a problem. I need my conda env to be reproducible and workable for others testing my workflows. Can this problem be updated and / or fixed semi-quickly? Whether or not its TransDecoder or TransDecoder.LongestOrf whatever I don't care, if I install the conda env, I just need it to work on activation and not require a workaround. Ya know? Or has this been fixed and I don't know about it?

  11. titodamiani
    added a commit that references this issue on Oct 15, 2026

    Ask for build 1 or later of TransDecoder 6.0.0

    030c0df
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