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blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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Transrate broken and unsupported? #230

Closed Shellfishgene closed 5 years ago

Shellfishgene commented 5 years ago

Hi, I just tried to use this for a project before I realized there are a number of bugs (nicely listed in issue https://github.com/blahah/transrate/issues/201), and apparently no support any more for some years now. Maybe it would be nice to put a warning on the webpage and in the main readme that Transrate is currently only semi-useable and not supported anymore, so people don't waste time trying to use it befor running into those issues.

macmanes commented 5 years ago

I'll just note that there is a working version of TransRate packaged in the Oyster River Transcriptome assembler. Install via docker: https://oyster-river-protocol.readthedocs.io/en/latest/docker_install.html

Shellfishgene commented 5 years ago

Thanks, unfortunately I can't use Docker on our cluster but I'll have a look.

macmanes commented 5 years ago

You can use https://oyster-river-protocol.readthedocs.io/en/latest/aws_setup.html for manual install, but it’s fairly finicky on some systems.

Matt

Matthew MacManes, Ph.D. University of New Hampshire | Associate Professor of Genome Enabled Biology Department of Molecular, Cellular, & Biomedical Sciences Durham, NH 03824 Phone: 603-862-4052tel://Phone:%20603-862-4052 | Web: genomebio.orghttp://genomebio.org/ Office: 434 Gregg Hall | Laboratory: 437 Gregg Hall

On Sep 5, 2019, at 09:18, Shellfishgene notifications@github.com<mailto:notifications@github.com> wrote:

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Thanks, unfortunately I can't use Docker on our cluster but I'll have a look.

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Shellfishgene commented 5 years ago

For now I used the version found in https://github.com/macmanes-lab/Oyster_River_Protocol/tree/master/software and that seems to run fine, thanks! I'll have to build the ORP docker image with ubuntu 16 and convert to singularity to run it, I'll try that later...