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Would be wonderful if someone can do a PKGBUILD for Qiime, a pipeline for data analysis of NGS (Next Generation Sequencing).
Qiime is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data)
It works officialy on Ubuntu, but, due to I work with ArchLinux i would like to see a PKGBUILD. I don't know how make a PKGBUILD from scratch.
Thanks
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Next time please include links to the software and the code.
website : qiime.org
code : https://github.com/qiime/qiime
I took a quick peek at the git repos, and it looks like there are 2 options :
- use qiime-deploy with qiime-deply-conf and tweak the options for archlinux
- compile from scratch
there don't seem to be instructions to do that, so qiime-deploy would seem the way to go.
Given the code is on github, and i only see a master branch, the packages would be *-git packages .
Check the wiki pages for PKGBUILD and VCS PKGBUILD Guidelines (git is a Version Control System).
Disliking systemd intensely, but not satisfied with alternatives so focusing on taming systemd.
(A works at time B) && (time C > time B ) ≠ (A works at time C)
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try this:
pkgname=qiime
pkgver=1.7.0
pkgrel=1
pkgdesc="Quantitative Insights Into Microbial Ecology"
arch=('any')
url="http://www.qiime.org"
license=('unknown')
depends=('python2-pycogent' 'python2-matplotlib' 'java-environment')
source=("https://github.com/$pkgname/$pkgname/archive/$pkgver.tar.gz")
sha256sums=('38e42fc1ea2cd78342e5c06408f9d7904c86d6221e6ac1cde6cd6b3539f0b205')
prepare() {
find "$srcdir/$pkgname-$pkgver/" -name *.py -exec sed -i 's/env python$/&2/' {} \;
}
package() {
cd "$srcdir/$pkgname-$pkgver"
python2 setup.py install --root="$pkgdir"
}
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Next time please include links to the software and the code.
website : qiime.org
code : https://github.com/qiime/qiimeI took a quick peek at the git repos, and it looks like there are 2 options :
- use qiime-deploy with qiime-deply-conf and tweak the options for archlinux
- compile from scratch
there don't seem to be instructions to do that, so qiime-deploy would seem the way to go.Given the code is on github, and i only see a master branch, the packages would be *-git packages .
Check the wiki pages for PKGBUILD and VCS PKGBUILD Guidelines (git is a Version Control System).
Thank you very much for your reply. I'll remember that for next time. I forgot to put the link. I'm sorry.
Here is the instructions for compile from scratch http://qiime.org/install/install.html
I will work in learn and do a good package.
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try this:
pkgname=qiime pkgver=1.7.0 pkgrel=1 pkgdesc="Quantitative Insights Into Microbial Ecology" arch=('any') url="http://www.qiime.org" license=('unknown') depends=('python2-pycogent' 'python2-matplotlib' 'java-environment') source=("https://github.com/$pkgname/$pkgname/archive/$pkgver.tar.gz") sha256sums=('38e42fc1ea2cd78342e5c06408f9d7904c86d6221e6ac1cde6cd6b3539f0b205') prepare() { find "$srcdir/$pkgname-$pkgver/" -name *.py -exec sed -i 's/env python$/&2/' {} \; } package() { cd "$srcdir/$pkgname-$pkgver" python2 setup.py install --root="$pkgdir" }
Thank you very much. Your package doesn't compile, but it's a good start. I'll try to work on it!
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Builds fine here. I'm sure I'm missing some deps, though, what error are you getting? I was just going by the source repo, I didn't find that page about installing natively, so I probably missed a few things there, too. I just noticed that some of the scripts have a space at the end of the shebang line and aren't getting modified, that will cause a problem, too.
Last edited by Scimmia (2013-10-07 22:47:58)
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