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bcgsc / transabyss

de novo assembly of RNA-seq data using ABySS
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make fail for abyss1.5.2/1.5.1 #7

Closed cd-ccmb closed 6 years ago

cd-ccmb commented 7 years ago

I need to work with transabyss for RNAseq analysis, I am unable to install abyss1.5.2 as the make fails for one or other module (Layout, Overlap,Konnector,etc) depending on what boost I use. I have tried the latest boost (1.64.0) as well several other (1.55.0,1.52.0,1.40.0) to configure and make abyss but I have failed. I even tried installing transabyss 1.5.3 with abyss 1.5.1 but failed to do so too. Could you please help me with this. I am working on Fedora 4.8

  1. how to install abyss1,5,2 successfully for using transabyss? Which boost library to use? 2.Can I use the latest abyss2.0 for transabyss 1.5.5?

Thanks

sjackman commented 7 years ago

@benvvalk Any thoughts?

benvvalk commented 7 years ago

@kmnip did some brief testing of TransABySS with ABySS 2.0 and unfortunately he said he ran into some issues beyond just adding graph=dot to the abyss-pe command. He said one of the dependent ABySS tools was crashing (abyss-junction, I think), and there were perhaps some other issues as well.

I agree it would be good to address these things and make a new Trans-ABySS release that works with the latest ABySS. I've got a lot to do at the moment w.r.t. to ABySS itself, though. It would be nice if we could get someone else on the team to be the official Trans-ABySS steward.

cd-ccmb commented 7 years ago

Yes I tried running transabyss with abyss 2.0 as well and the abyss-junction module fails to run. Can we expect a newer release of transabyss with abyss2.0 soon? Additionally the boost library issue needs to be addressed well for abyss 1.5.2.

Thanks

kmnip commented 7 years ago

Yes, that was part of the reason why a new version of Trans-ABySS hasn't been released. That being said, we still use ABySS 1.5.3 routinely with Trans-ABySS for our projects. Not sure why ABySS didn't compile on your system?

cd-ccmb commented 7 years ago

Ok the installation guideline for transabyss 1.5.5 says to use abyss 1.5.2, will try compiling abyss1.5.3 and using it. Thanks

kmnip commented 6 years ago

You may use ABySS 2.0 with Trans-ABySS now. Please see our latest release. I am closing this issue. Let us know if you encounter any more problems with running Trans-ABySS.

Thanks, Ka Ming

benvvalk commented 6 years ago

You rock, @kmnip!

sjackman commented 6 years ago

Thanks, Ka Ming!