Hi Evguenia,
I'm writing you on behalf of the Debian Med team that has the objective
to package all free software that is relevant in biology and medicine in
Debian. We are working closely together with BioLinux. Since we want
to upgrade to latest QIIME we want to package also SortMeRNA (as you can
read below).
When doing the packaging I stumbled upon two problems:
1. There is no source for the manual SortMeRNA-User-Manual-2.0.pdf
In Debian PDF files without the according source (*.tex or whatever)
are considered as binary without source and thus users have no
chance to change the file. Could you deliver the according source
for this file in some way?
2. For Debian we have packaged python-skbio version 0.4.0. I
realised that SortMeRNA relies on an old version (0.2.3) since
if I try to run the test I get:
$ python tests/test_sortmerna.py
Traceback (most recent call last):
File "tests/test_sortmerna.py", line 16, in <module>
from skbio.parse.sequences import parse_fasta
ImportError: No module named parse.sequences
The module interface was changed inbetween python-skbio version
0.2.3 and 0.4.0. I would recommend to adapt the code to the latest
skbio.
BTW, since Debian tries to deliver manpages to each binary in /usr/bin
I have written two manpages you might like to deliver also in your
download version. Feel free to fetch them from
https://anonscm.debian.org/viewvc/debian-med/trunk/packages/sortmerna/trunk/debian/man/
Kind regards and thanks for providing SortMeRNA as free software
Andreas.
On Tue, Aug 04, 2015 at 09:51:33PM +0200, Andreas Tille wrote:
> Package: wnpp
> Severity: wishlist
> Owner: Andreas Tille <tille@debian.org>
>
> * Package name : sortmerna
> Version : 2.0
> Upstream Author : Mengyao Zhao <zhangmp@bc.edu>
> * URL : http://bioinfo.lifl.fr/RNA/sortmerna/
> * License : MIT
> Programming Lang: C++
> Description : tool for filtering, mapping and OTU-picking NGS reads
> SortMeRNA is a biological sequence analysis tool for filtering, mapping and
> OTU-picking NGS reads. The core algorithm is based on approximate seeds and
> allows for fast and sensitive analyses of nucleotide sequences. The main
> application of SortMeRNA is filtering rRNA from metatranscriptomic data.
> Additional applications include OTU-picking and taxonomy assignation available
> through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1).
> SortMeRNA takes as input a file of reads (fasta or fastq format) and one or
> multiple rRNA database file(s), and sorts apart rRNA and rejected reads into
> two files specified by the user. Optionally, it can provide high quality local
> alignments of rRNA reads against the rRNA database. SortMeRNA works with
> Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and
> BLAST-like alignments.
>
>
> Remark: This package was prepared by Tim Booth of BioLinux as a predependency
> of the new version of qiime. It is maintained at
> svn://anonscm.debian.org/debian-med/trunk/packages/sortmerna/trunk/
>
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>
--
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