Hi Andreas, I've uploaded the user manual 2.0 in tex format (see here <https://github.com/biocore/sortmerna>). Also, thank you for the man pages! I'll take a more thorough look later today. This month I plan to do a lot of updates to the overall code, so it's a good time to incorporate these.
Let me know if you have other questions regarding the installation with QIIME. Jenya On Wed, Aug 5, 2015 at 7:23 AM, Jenya Kopylov <[email protected]> wrote: > 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/ >
