Re: PIQUE packaging (Was: request for r-cran packages) [correction]
On 23/07/2020 07:56, Andreas Tille wrote:
Hi Tony,
On Wed, Jul 22, 2020 at 11:46:03PM +0100, Tony Travis wrote:
Analysis finished: Mon Jul 20 13:56:47 2020
Create sativas_GWAS.covar file...
smartpca -p sativas_GWAS.par > sativas_GWAS-smartpca.log
OOPS -i flag not specified at /usr/bin/smartpca line 21.
pique: error - Can't read sativas_GWAS.evec
make: *** [Makefile:29: input] Fehler 255
Hi, Andreas.
The "pique-input" script should be running /usr/lib/eigensoft/smartpca,
not /usr/bin/smartpca and my version does:
root@beluga:/opt/local/src/GWAS/PIQUE/test# make |& tee make.log
[...] > root@beluga:/opt/local/src/GWAS/PIQUE/test# fgrep smartpca *.log
make.log:/usr/lib/eigensoft/smartpca -p sativas_GWAS.par > sativas_GWAS-smartpca.log
sativas_GWAS-pique-input.log:/usr/lib/eigensoft/smartpca -p sativas_GWAS.par
Please will you try a "git pull" to make sure your copy of my PIQUE
GitHub repo is up-to-date - Thanks.
[...]
libparallel-forkmanager-perl is in the list of Depends of the pique
package uploaded to new - so this should be settled.
Yes, I understand that - I'm just letting you know that all the other
dependencies of PIQUE are already satisfied by installing the "med-bio"
and "med-bio-dev" meta-packages, which is a vast improvement over the
way we used to install it in the bad old days :-)hadhad
I'll update PIQUE on Github and remove the tar-ball dependencies from it now
that everything I need is available in "med-bio" or "med-bio-dev".
Well, "everything you need" is (hopefully) specified as Depends of the
pique package - if not that should be fixed. IMHO we need to sort out
the details of the error above. Could you please check with a recent
version of eigensoft the issue behing the
OOPS -i flag not specified at /usr/bin/smartpca line 21.
message? The version that was used in this test is 7.2.1+dfsg-1.
See above, "pique-input" should run "/usr/lib/eigensoft/smartpca".
root@beluga:/opt/local/src/GWAS/PIQUE/test# apt policy eigensoft
eigensoft:
Installed: 7.2.1+dfsg-1build1
Candidate: 7.2.1+dfsg-1build1
Version table:
*** 7.2.1+dfsg-1build1 500
500 http://gb.archive.ubuntu.com/ubuntu focal/multiverse amd64 Packages
100 /var/lib/dpkg/status
[...]
Regarding testing I'd like to refresh my mail from March of last
year which I somehow can not find inside the web archive, so
I'm copying its content here:
Regarding testing pique (and to find such missing depends): test/Makefile
also uses wget to download data. Could you provide a simple shell script
that is using only the available data to test the functionality of pique
a) in a build time test
b) as autopkgtest
It's not possible to test PIQUE without a data-set large enough to use
for GWAS, which is why I use "wget" to download one and avoid storing
large blob in the GitHub repo. The data-sets we normally use contain
millions of SNPS, but this small data-set is what we used during the
development of PIQUE and what we use when teaching how to use it.
Not sure if that helps?
Thanks again,
Tony.
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