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.
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