Re: Pique #986194 Bug closing

On 13/12/2023 00:16, Tony Travis wrote:
> On 12/12/2023 19:29, Komolehin Israel wrote:
>> Hi Team,
>>
>> I worked on Pique package by providing autopkgtest and providing a 
>> patch to fix the smartpca command that blocks the upstream test from 
>> running successfully. CI was successful.
>>
>> This closes #986194 bug.
>>
>> I look forward to review and upload.
> 
> Hi, Israel.
> 
> I'm the upstream author of PIQUE: I was not aware of a problem with 
> "smartpca". Have you checked the version on GitHub?
> 
>> https://github.com/tony-travis/PIQUE
> 
> AFAIK, this version works correctly under Ubuntu 22.04 LTS but I've not 
> tested it under Debian.

Hi, Israel.

This is the version of EIGENSOFT that I have under Ubuntu-MATE 22.04:

> root@wildcat:/usr/local/src/bioinformatics/PIQUE/master/test# apt policy eigensoft
> eigensoft:
>   Installed: 7.2.1+dfsg-3build1
>   Candidate: 7.2.1+dfsg-3build1
>   Version table:
>  *** 7.2.1+dfsg-3build1 500
>         500 http://gb.archive.ubuntu.com/ubuntu jammy/universe amd64 Packages
>         100 /var/lib/dpkg/status

PIQUE uses "smartpca" like this in the upstream test:

> /usr/bin/smartpca -i sativas_GWAS.ped -a ../sativas413_recode12.map -b sativas_GWAS.ped -o sativas_GWAS -p sativas_GWAS -e sativas_GWAS.eval -k 5 -l sativas_GWAS-smartpca.log
> /usr/lib/eigensoft/smartpca -p sativas_GWAS.par >sativas_GWAS-smartpca.log
> ploteig -i sativas_GWAS.evec -c 1:2  -p ???  -x  -y  -o sativas_GWAS.xtxt
> evec2pca-ped.perl 5 sativas_GWAS.evec sativas_GWAS.ped sativas_GWAS

I've just run the upstream tests without error under Ubuntu-MATE 22.04

As you probably know, /usr/bin/smartpca is a Perl script that creates a 
parameter file for /usr/lib/eigensoft/smartpca from its arguments.

Bye,

   Tony.