install and run RELAX-scan

mlosilla commented 3 years ago

Hi,

I can't figure out how to install and run RELAX-scan. I have downloaded and installed hyphy-analyses as explained in this ReadMe: https://github.com/veg/hyphy-analyses. All 21 tests executed by "make test" complete successfully.

But the only RELAX.bf file I get seems to be the standard RELAX test. When I run it as:

./HYPHYMP ./res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf --alignment path_to_alignment/alignment.fasta

I get the error: Error:RELAX requires at least one designated set of branches in the tree. in call to assert(CUJAIACd.option_count>=2, error_msg); RELAX requires at least one designated set of branches in the tree. in call to assert(CUJAIACd.option_count>=2, error_msg);

Furthermore:

1) with the exception of FEL.bf, all the .bf files in hyphy-develop/res/TemplateBatchFiles/SelectionAnalyses/ have the same md5 hash as those in hyphy/share/hyphy/TemplateBatchFiles/SelectionAnalyses (this is where I installed hyphy (https://github.com/veg/hyphy), via conda install hyphy)

2) I can't find the .bf files for the tests listed in https://github.com/veg/hyphy-analyses : BUSTED-MH, BUSTED-SR, etc.

Clearly, I am doing something wrong. Could someone please provide me some guidance? I am installing on a computer cluster running CentOS7, and I don't have sudo privileges

Thanks

spond commented 3 years ago

Dear @mlosilla,

The RELAX-scan analysis is an add-on. It is not a part of the standard HyPhy distribution. To use, assuming you have hyphy installed

$git clone https://github.com/veg/hyphy-analyses
$cd hyphy-analyses/RELAX-scan
$/path/to/hyphy ./RELAX.bf --alignment ...

Best, Sergei

mlosilla commented 3 years ago

Hi Sergei,

I did as you suggested but the run failed after 1-2 seconds. I attach the error log.

Thanks errors.log

mlosilla commented 3 years ago

The error is similar to the first one reported here: https://github.com/veg/hyphy-analyses/issues/12

spond commented 3 years ago

Dear @mlosilla,

I was able to reproduce the error. Will require a fix to RELAX-scan. Stay tuned.

Best, Sergei

PS Fix issued. Do

$cd hyphy-analyses/RELAX-scan
$git pull
$/path/to/hyphy ./RELAX.bf --alignment ...

mlosilla commented 3 years ago

Thank you Sergei, that was super fast!

It seems to be running now, thank you very much!

I was wondering, does RELAX-scan support the option to include a synonymous rate variation (--srv Yes)?

Thanks Mau

veg / hyphy-analyses

install and run RELAX-scan #16