Re: All predependencies for qiime 1.9? [Was: Bug#793585: ITP: ea-utils -- command-line tools for processing biological sequencing data]
Hi Andreas,
I've confirmed ea-utils builds fine on Trusty and switched to your
improved package, thanks.
So, QIIME...
I've just packaged and tested an initial QIIME 1.9.1 on my local
machine. This is a bugfix release on 1.9.0, as the version suggests,
but I'm getting test failures relating to RDP-Classifier so I need to
work out what has happened there and fix the issue.
QIIME now relies on a thing called "burrito-fillings" and associated
"burrito". As far as I can see these are supposed to replace the
troublesome Python-Cogent but they don't - you need both for QIIME
1.9.x! (Yes, there is obvious copy-paste code between the two).
My current RDP test failure is to do with something in the latest
burrito-fillings library.
Furthermore, burrito needs the python-future library from here:
https://github.com/PythonCharmers/python-future
I've pushed the packaging for that to SVN (I still don't understand how
the heck GIT is supposed to work on Alioth) but it's not a biomedical
library at all, just a generic compatibility layer, so maybe should not
be under Deb Med. What do you think?
I'll let you know when I'm done with my debugging and push the Burrito
stuff too.
Cheers,
TIM
On Sat, 2015-07-25 at 12:44 +0200, Andreas Tille wrote:
> Hi Tim,
>
> I took over ea-utils from BioLinux PPA as you can see. Please test and
> confirm that it works for you. Do you think all dependencies for qiime
> 1.9 are now ready since rdp-classifier was accepted now.
>
> Kind regards
>
> Andreas.
>
> ----- Forwarded message from Andreas Tille <tille@debian.org> -----
>
> Date: Sat, 25 Jul 2015 12:23:22 +0200
> From: Andreas Tille <tille@debian.org>
> To: Debian Bug Tracking System <submit@bugs.debian.org>
> Subject: Bug#793585: ITP: ea-utils -- command-line tools for processing biological sequencing data
> X-Debian-PR-Message: report 793585
> X-Debian-PR-Package: wnpp
> X-Debian-PR-Keywords:
>
> Package: wnpp
> Severity: wishlist
> Owner: Andreas Tille <tille@debian.org>
>
> * Package name : ea-utils
> Version : 1.1.2
> Upstream Author : Erik Aronesty <erik@q32.com>
> * URL : https://code.google.com/p/ea-utils/
> * License : MIT
> Programming Lang: C
> Description : command-line tools for processing biological sequencing data
> i Ea-utils provides a set of command-line tools for processing biological
> sequencing data, barcode demultiplexing, adapter trimming, etc.
> .
> Primarily written to support an Illumina based pipeline - but should work with
> any FASTQs.
> .
> Main Tools are:
> .
> * fastq-mcf
> Scans a sequence file for adapters, and, based on a log-scaled threshold,
> determines a set of clipping parameters and performs clipping. Also does
> skewing detection and quality filtering.
> * fastq-multx
> Demultiplexes a fastq. Capable of auto-determining barcode id's based on a
> master set fields. Keeps multiple reads in-sync during demultiplexing. Can
> verify that the reads are in-sync as well, and fail if they're not.
> * fastq-join
> Similar to audy's stitch program, but in C, more efficient and supports some
> automatic benchmarking and tuning. It uses the same "squared distance for
> anchored alignment" as other tools.
> * varcall
> Takes a pileup and calculates variants in a more easily parameterized manner
> than some other tools.
>
>
> This package was prepared by Tim Booth for BioLinux to update the qiime
> package. It is taken over into the Debian Med team and will be maintained
> at
>
> git://anonscm.debian.org/debian-med/ea-utils.git
>
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
>
> ----- End forwarded message -----
>
> --
> http://fam-tille.de
>
>
--
Tim Booth <tbooth@ceh.ac.uk>
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://environmentalomics.org/bio-linux
+44 1491 69 2297
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