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#1 2013-10-07 17:53:41

aberkoke
Member
From: Murcia - España
Registered: 2010-01-13
Posts: 25

[REQUEST] Qiime on ArchLinux

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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#2 2013-10-07 20:32:18

Lone_Wolf
Member
From: Netherlands, Europe
Registered: 2005-10-04
Posts: 4,390

Re: [REQUEST] Qiime on ArchLinux

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).


Booting with apg Openrc, NOT systemd.
Automounting : not needed, i prefer pmount
Aur helpers : makepkg + my own local repo === rarely need them

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#3 2013-10-07 21:30:29

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 5,119

Re: [REQUEST] Qiime on ArchLinux

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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#4 2013-10-07 22:33:44

aberkoke
Member
From: Murcia - España
Registered: 2010-01-13
Posts: 25

Re: [REQUEST] Qiime on ArchLinux

Lone_Wolf wrote:

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).

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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#5 2013-10-07 22:40:52

aberkoke
Member
From: Murcia - España
Registered: 2010-01-13
Posts: 25

Re: [REQUEST] Qiime on ArchLinux

Scimmia wrote:

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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#6 2013-10-07 22:46:51

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 5,119

Re: [REQUEST] Qiime on ArchLinux

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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