Your message dated Thu, 28 May 2020 15:43:22 +0200 with message-id <[email protected]> and subject line Please do not hide clearly bioinformatics related stuff in language teams (Was: Bug#961730: ITP: presto -- REpertoire Sequencing TOolkit) has caused the Debian Bug report #961730, regarding ITP: presto -- REpertoire Sequencing TOolkit to be marked as done.
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--- Begin Message ---Package: wnpp Severity: wishlist Subject: ITP: presto -- REpertoire Sequencing TOolkit Package: wnpp Owner: Andreas Tille <[email protected]> Severity: wishlist * Package name : presto Version : 0.6.0 Upstream Author : Kleinstein Lab, Yale University * URL : https://presto.readthedocs.io/ * License : AGPL-3 Programming Lang: Python Description : REpertoire Sequencing TOolkit pRESTO is a toolkit for processing raw reads from high-throughput sequencing of B cell and T cell repertoires. . Dramatic improvements in high-throughput sequencing technologies now enable large-scale characterization of lymphocyte repertoires, defined as the collection of trans-membrane antigen-receptor proteins located on the surface of B cells and T cells. The REpertoire Sequencing TOolkit (pRESTO) is composed of a suite of utilities to handle all stages of sequence processing prior to germline segment assignment. pRESTO is designed to handle either single reads or paired-end reads. It includes features for quality control, primer masking, annotation of reads with sequence embedded barcodes, generation of unique molecular identifier (UMI) consensus sequences, assembly of paired-end reads and identification of duplicate sequences. Numerous options for sequence sorting, sampling and conversion operations are also included. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/presto
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--- Begin Message ---Hi Steffen, well, its probably my fault to not have checked tasks for the string presto but this name was pretty new to me and I admit I would not have assumed that something which I consider rather a user application toolset is prefixed by python3 in the package name. I'd love that we in the Debian Med team would agree that it makes no sense to move the software we are packaging into "random" language teams without really good reasons. Currently we have bio-ruby inside the Ruby team since they have asked for maintaining it (which makes sense since we have no Ruby competence here). We have golang-github-biogo-hts-dev in pkg-go team for similar reasons. There are also quite some Perl modules maintained by pkg-perl team and I admit I'm not really happy about having some Perl modules here and some there. However, the Uploaders of these packages have at least discussed this here. For presto I definitely see no reason and I'd love to move the package to Debian Med (surely after I have removed my duplicated work - but I realised that I have at least not written the manpages vainly. ;-) ) I noticed that python3-presto is actually used in changeo as a module while I was foxussing on the user application. Once we are touching the package do we want to split the binary into presto and python3-presto ? I'd volunteer to move the package (which we should do IMHO in any case) and if you agree also doing the split of the binary package. Kind regards Andreas. On Thu, May 28, 2020 at 03:22:36PM +0200, Andreas Tille wrote: > Package: wnpp > Severity: wishlist > > Subject: ITP: presto -- REpertoire Sequencing TOolkit > Package: wnpp > Owner: Andreas Tille <[email protected]> > Severity: wishlist > > * Package name : presto > Version : 0.6.0 > Upstream Author : Kleinstein Lab, Yale University > * URL : https://presto.readthedocs.io/ > * License : AGPL-3 > Programming Lang: Python > Description : REpertoire Sequencing TOolkit > pRESTO is a toolkit for processing raw reads from high-throughput > sequencing of B cell and T cell repertoires. > . > Dramatic improvements in high-throughput sequencing technologies now > enable large-scale characterization of lymphocyte repertoires, defined > as the collection of trans-membrane antigen-receptor proteins located on > the surface of B cells and T cells. The REpertoire Sequencing TOolkit > (pRESTO) is composed of a suite of utilities to handle all stages of > sequence processing prior to germline segment assignment. pRESTO is > designed to handle either single reads or paired-end reads. It includes > features for quality control, primer masking, annotation of reads with > sequence embedded barcodes, generation of unique molecular identifier > (UMI) consensus sequences, assembly of paired-end reads and > identification of duplicate sequences. Numerous options for sequence > sorting, sampling and conversion operations are also included. > > Remark: This package is maintained by Debian Med Packaging Team at > https://salsa.debian.org/med-team/presto > > _______________________________________________ > Debian-med-packaging mailing list > [email protected] > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de
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