Hi Andreas, Thank you for reporting these issues,
I will add the .tex file for the user manual 2.0 to github (SortMeRNA development <https://github.com/biocore/sortmerna>). The latest QIIME release (1.9.1 <https://github.com/biocore/qiime/releases>) requires scikit-bio >= 0.2.3, < 0.3.0 and SortMeRNA 2.0 (many of QIIME's scripts for 1.9.1 import parse_fasta). I can update the SortMeRNA tests to work with the latest release of scikit-bio on the SortMeRNA development version, however they will remain incompatible with QIIME 1.9.1 (and the development version) since several other minor changes have been made (mainly the --blast option) that will require additional changes in QIIME's tests. Greg, perhaps you can comment more on the scikit-bio release? Jenya On Wed, Aug 5, 2015 at 6:58 AM, Andreas Tille <[email protected]> wrote: > 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 <[email protected]> > > > > * Package name : sortmerna > > Version : 2.0 > > Upstream Author : Mengyao Zhao <[email protected]> > > * 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/ > > > > _______________________________________________ > > Debian-med-packaging mailing list > > [email protected] > > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > > > > -- > http://fam-tille.de > -- Jenya Kopylova, Ph.D., Postdoctoral fellow, Knight Lab Department of Pediatrics, UCSD https://sites.google.com/site/kopyloe/
