problems installing sara on vagrant

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Barry Kesner

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Apr 11, 2020, 7:21:01 AM4/11/20
to tco...@googlegroups.com, cedric.n...@crg.eu, modoc kesner
Hi,

I am trying to run sara on OSX(latest).

It looks like your files Vagrantfile and bootstrap.sh are out of date.

1. The shipped Vagrantfile for percision64 does not get downloaded so I downloaded my own. It looks like your is out of date.
2. bootstrap.sh is out of date and does not point to the binaries for t-coffee correctly. I tried updating it by hunting for it in
your directory structure and found what I think is tcoffee.org/Packages/Stable/Latest/*.bin

<old
>my modifications

< tcoffee=`ls tcoffee.org/Packages/Stable/Latest/linux/*.bin`
---
> #wget -q -r -l1 --no-parent -A "T-COFFEE_installer*_linux_x64.bin" http://tcoffee.org/Packages/Stable/Latest/linux/
> #tcoffee=`ls tcoffee.org/Packages/Stable/Latest/linux/*.bin`
> #BAK replaced with might try to replace with beta version later
> # http://tcoffee.org/Packages/Beta/Latest/
> wget -q -r -l1 --no-parent -A "T-COFFEE_installer*_linux_x64.bin" http://tcoffee.org/Packages/Stable/Latest/
> tcoffee=`ls tcoffee.org/Packages/Stable/Latest/*.bin`

However, after getting a virtual machine, t-coffee and RNAfold did not seem to exist so maybe I took
the wrong binary.

I am in the process of trying to install the dependencies on the VM.
For instance, I did a

sudo apt-get install t-coffee

to get t-coffee.

I am looking to get others also.

Maybe you can fix these problems for me and I won't have to do this.

Thanks,
Barry


I have attached my error file when I try to do
vagrant init.
errors.out
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