[Feature request] Output final files in the output directory instead of working directory

[jolespin]

I'm working on integrating this into my VEBA pipeline (github.com/jolepsin/veba) and will be running multiple instances of this at the same time. I can't do that when the final files are output into the current working directory. Would it be possible to do the following:

• Output the final files into the output directory instead of the current working directory
• Write the pipeliner.*.cmds files to a temporary directory in the output directory instead of the current working directory

https://github.com/TransDecoder/TransDecoder/wiki#output-files-explained

[brianjohnhaas]

Hi, In your pipeline, can you just cd into the output directory where you want the results to live, and then execute the transdecoder command? ie. cd /path/to/wanted/workingdir && TransDeocder.cmd ..... ?

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On Wed, Feb 22, 2023 at 10:33 PM Josh L. Espinoza ***@***.***> wrote: I'm working on integrating this into my VEBA pipeline ( github.com/jolepsin/veba) and will be running multiple instances of this at the same time. I can't do that when the final files are output into the current working directory. Would it be possible to do the following: - Output the final files into the output directory instead of the current working directory - Write the pipeliner.*.cmds files to a temporary directory in the output directory instead of the current working directory https://github.com/TransDecoder/TransDecoder/wiki#output-files-explained — Reply to this email directly, view it on GitHub <#169>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX76WYWY46BWDLQAH6LWY3LBXANCNFSM6AAAAAAVFDJNMU> . 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>

[jolespin]

I’m running it for 100s or transcriptomes simultaneously on the grid. Each one has the same “transcript.fasta” assembly name.

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On Feb 23, 2023, at 5:51 AM, Brian Haas ***@***.***> wrote:  Hi, In your pipeline, can you just cd into the output directory where you want the results to live, and then execute the transdecoder command? ie. cd /path/to/wanted/workingdir && TransDeocder.cmd ..... ? On Wed, Feb 22, 2023 at 10:33 PM Josh L. Espinoza ***@***.***> wrote: > I'm working on integrating this into my VEBA pipeline ( > github.com/jolepsin/veba) and will be running multiple instances of this > at the same time. I can't do that when the final files are output into the > current working directory. Would it be possible to do the following: > > - Output the final files into the output directory instead of the > current working directory > - Write the pipeliner.*.cmds files to a temporary directory in the > output directory instead of the current working directory > > https://github.com/TransDecoder/TransDecoder/wiki#output-files-explained > > — > Reply to this email directly, view it on GitHub > <#169>, or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ABZRKX76WYWY46BWDLQAH6LWY3LBXANCNFSM6AAAAAAVFDJNMU> > . > 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> — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.

[brianjohnhaas]

I understand. I won't be making any changes to the code anytime soon, so I'm thinking of what you can do in the meantime. There would be a few options here, depending on how your pipeline works. One would be to just have separate working directories for each of your transcriptomes. Another would be to just rename your transcripts.fasta filename that you're starting with to match the sample identifier, such as sample_id.transcripts.fasta. Both of these would allow you to unambiguously identify outputs and avoid collisions. best, ~brian On Thu, Feb 23, 2023 at 10:27 AM Josh L. Espinoza ***@***.***> wrote:

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I’m running it for 100s or transcriptomes simultaneously on the grid. Each one has the same “transcript.fasta” assembly name. > > On Feb 23, 2023, at 5:51 AM, Brian Haas ***@***.***> wrote: > >  > Hi, > > In your pipeline, can you just cd into the output directory where you want > the results to live, and then execute the transdecoder command? > > ie. > > cd /path/to/wanted/workingdir && TransDeocder.cmd ..... > > ? > > On Wed, Feb 22, 2023 at 10:33 PM Josh L. Espinoza ***@***.***> > wrote: > > > I'm working on integrating this into my VEBA pipeline ( > > github.com/jolepsin/veba) and will be running multiple instances of this > > at the same time. I can't do that when the final files are output into the > > current working directory. Would it be possible to do the following: > > > > - Output the final files into the output directory instead of the > > current working directory > > - Write the pipeliner.*.cmds files to a temporary directory in the > > output directory instead of the current working directory > > > > https://github.com/TransDecoder/TransDecoder/wiki#output-files-explained > > > > — > > Reply to this email directly, view it on GitHub > > <#169>, or unsubscribe > > < https://github.com/notifications/unsubscribe-auth/ABZRKX76WYWY46BWDLQAH6LWY3LBXANCNFSM6AAAAAAVFDJNMU > > > . > > 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> > — > Reply to this email directly, view it on GitHub, or unsubscribe. > You are receiving this because you authored the thread. — Reply to this email directly, view it on GitHub <#169 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXZVWXIHNWWQYMVROQ3WY56XTANCNFSM6AAAAAAVFDJNMU> . You are receiving this because you commented.Message ID: ***@***.***>

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