Transrate broken and unsupported?

Question

Transrate broken and unsupported?

Shellfishgene opened this issue 5 years ago · comments

Hi,
I just tried to use this for a project before I realized there are a number of bugs (nicely listed in issue #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.

Matt MacManes · Answer 1 · Thu Sep 05 2019 21:01:15 GMT+0800 (China Standard Time)

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 · Answer 2 · Thu Sep 05 2019 21:18:46 GMT+0800 (China Standard Time)

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

Matt MacManes · Answer 3 · Thu Sep 05 2019 21:20:55 GMT+0800 (China Standard Time)

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: 603-862-4052<tel://Phone:%20603-862-4052> | Web: genomebio.org<http://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: Caution - External Email

________________________________ Thanks, unfortunately I can't use Docker on our cluster but I'll have a look. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_blahah_transrate_issues_230-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DAABIHEHUB76L4YZF4MBRXJ3QIEBLNA5CNFSM4IT5NRO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD57B6HY-23issuecomment-2D528359199&d=DwMCaQ&c=c6MrceVCY5m5A_KAUkrdoA&r=lFmSBplGfvpPNKk6W2tN6-UcUrgjlsdpj7JuHtA6g_Y&m=6SZy2mAGkXFuHS9RVBt4-M90W02Tiq4NHA-jSco969w&s=tXEBTO1u4VjW0NCBBurML_NkSkIOK60_cb4IA0OXJ58&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AABIHECOOUTFJIXNPIEVEBDQIEBLNANCNFSM4IT5NROQ&d=DwMCaQ&c=c6MrceVCY5m5A_KAUkrdoA&r=lFmSBplGfvpPNKk6W2tN6-UcUrgjlsdpj7JuHtA6g_Y&m=6SZy2mAGkXFuHS9RVBt4-M90W02Tiq4NHA-jSco969w&s=LC5FipfdKOvYjICt9wRTKyBT3dd5wozBYE6-YMuLDUE&e=>.

Shellfishgene · Answer 4 · Fri Sep 06 2019 17:15:54 GMT+0800 (China Standard Time)

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...