Bug#910357: ITP: segemehl -- short read mapping with gaps
Package: wnpp Severity: wishlist Owner: Andreas Tille * Package name: segemehl Version : 0.3 Upstream Author : Bioinformatik Leipzig * URL : http://www.bioinf.uni-leipzig.de/Software/segemehl/ * License : GPL-3+ Programming Lang: C Description : short read mapping with gaps Segemehl is a software to map short sequencer reads to reference genomes. Segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl accepts fasta and fastq queries (gzip’ed and bgzip'ed). In addition to the alignment of reads from standard DNA- and RNA-seq protocols, it also allows the mapping of bisulfite converted reads (Lister and Cokus) and implements a split read mapping strategy. The output of segemehl is a SAM or BAM formatted alignment file. In the case of split-read mapping, additional BED files are written to the disc. These BED files may be summarized with the postprocessing tool haarz. In the case of the alignment of bisulfite converted reads, raw methylation rates may also be called with haarz. . In brief, for each suffix of a read, segemehl aims to find the best-scoring seed. Seeds might contain insertions, deletions, and mismatches (differences). The number of differences allowed within a single seed is user-controlled and is crucial for the runtime of the program. Subsequently, seeds that undercut the user-defined E-value are passed on to an exact semi-global alignment procedure. Finally, reads with a minimum accuracy of percent are reported to the user. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/segemehl
Bug#910358: ITP: grcov -- grcov collects and aggregates code coverage information for multiple source files.
Package: wnpp Severity: wishlist Owner: Sylvestre Ledru * Package name: grcov Upstream Author : Marco Castelluccio * URL : https://github.com/mozilla/grcov * License : MPL-2.0 Programming Lang: Rust Description : grcov collects and aggregates code coverage information for multiple source files.
Bug#910361: ITP: haskell-wcwidth -- Haskell bindings for system's native wcwidth
Package: wnpp Severity: wishlist Owner: Ilias Tsitsimpis * Package name: haskell-wcwidth Version : 0.0.2 Upstream Author : Jason Dusek * URL : https://hackage.haskell.org/package/wcwidth * License : BSD-3-clause Programming Lang: Haskell Description : Haskell bindings for system's native wcwidth . This package provides the wcwidth function which can be used to learn, for most of Unicode, how wide the individual Char code points will come out on the terminal. This is a dependency for newer versions of haskell-tasty (>= 1.1.0.2). -- Ilias
Re: Limiting the power of packages
On 10/4/18 12:23 PM, Jonathan Dowland wrote: > On Thu, Oct 04, 2018 at 12:09:05PM +0200, Thomas Goirand wrote: >> And prevent stuff like with the bumblebee uninstall disaster because of >> an added space, for example: >> >> rm -rf /usr /share/foo/bar.conf > > Yes, or the similar bug in steam-for-linux steam.sh. Although neither > made it into the Debian archive, so adding the features being discussed > won't protect users who run external install scripts like these two > examples. The same kind of mistake could happen in a postrm script. And we really want to prevent that. One thing which I really would love to have as a declarative thing: owned_config_file=foo.conf,username:group would create username and group if absent from the system, copy foo.conf from /usr/share/package-name/foo.conf to /etc/foo/foo.conf, with correct 640 rights owned by root:group, and remove foo.conf on purge. I don't mind where this is declared (in debian/rules, or elsewhere), but this shouldn't go in a maintainer script, as it affects multiple ones (ie: postinst, postrm, etc.). >From my experience, the more declarative things there is, the less errors one makes. I've been caught numerous time forgetting to remove foo.conf on purge... (shame on me). Lucky there's puiparts to catch them, though it should just not happen! Cheers, Thomas Goirand (zigo)
Re: Limiting the power of packages
Lars Wirzenius wrote: * default: install files in /usr only * kernel: install files in /boot, trigger initramfs * core: can install files anywhere, trigger anything * maintained-by-liw: full power to do anything This might be implemented in various ways. For example, dpkg could create a temporary directory, and bind mount the directories the profile indicates are needed, into a temporary shadow of the full system. Maintainer scripts would be run in the shadow environment. Thus, if they try to do something that isn't allowed by the packages profile, they can't. This can be done with SELinux as well, the maintainer scripts can be labeled and dpkg will run them in the desired context.
Re: Limiting the power of packages
Laurent Bigonville writes: > Lars Wirzenius wrote: > >> * default: install files in /usr only >> * kernel: install files in /boot, trigger initramfs >> * core: can install files anywhere, trigger anything >> * maintained-by-liw: full power to do anything >> >> This might be implemented in various ways. For example, dpkg could >> create a temporary directory, and bind mount the directories the >> profile indicates are needed, into a temporary shadow of the full >> system. Maintainer scripts would be run in the shadow environment. >> Thus, if they try to do something that isn't allowed by the packages >> profile, they can't. > This can be done with SELinux as well, the maintainer scripts can be > labeled and dpkg will run them in the desired context. I like the general project, but feel obliged to point out that having maintainer scripts fail is not nice for users, so we'd need to think about how to handle security/liw-classification failures. d
