Transdecoder Docker doesnt work

[yannic-chen]

after pulling the dockerized version, I cannot get transdecoder to run.

The command:
sudo docker run --rm -vpwd:pwd trinityrnaseq/transdecoder TransDecoder.LongOrfs -t trinity_out_dir.Trinity.fasta -O ~/test/
doesnt run the analysis, but returns me the information/readme on how to use transdecoder, akin to --help functions.

the --version command does indeed returns the version. I found out that regardless on what string you input after the -t, the result is the same. If nothing is written after -t it returns error Error, don't understand options: -t at /usr/local/bin/TransDecoder.LongOrfs line 121.

[brianjohnhaas]

Hi, Try giving the full path to the Trinity fasta file. It's probably not finding it given that the Docker instance isn't running in your current working directory.

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On Wed, Sep 6, 2023 at 4:02 AM Dimora ***@***.***> wrote: after pulling the dockerized version, I cannot get transdecoder to run. The command: sudo docker run --rm -vpwd:pwd trinityrnaseq/transdecoder TransDecoder.LongOrfs -t trinity_out_dir.Trinity.fasta -O ~/test/ doesnt run the analysis, but returns me the information/readme on how to use transdecoder, akin to --help functions. the --version command does indeed returns the version. I found out that regardless on what string you input after the -t, the result is the same. If nothing is written after -t it returns error Error, don't understand options: -t at /usr/local/bin/TransDecoder.LongOrfs line 121. — Reply to this email directly, view it on GitHub <#182>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX73FRZYTI7OURDAVMLXZAU2DANCNFSM6AAAAAA4M5EAGQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>