SeqAn for Debian ================ Quoting upstream namely Manuel Holtgrewe in a private mail to Andreas Tille and Filippo Rusconi at Wed, 27 Nov 2013 09:38:30 +0100: The SeqAn apps are a pretty diverse collection. Some are just simple tools for Bioinformaticians, some are results from our research. The tools should be useful for useful but from the research result, only some are. I would suggest placing the following binaries in /usr/bin since they are tools useful for and used by users/scientists: alf gustaf insegt masai_indexer masai_mapper masai_output_pe masai_output_se mason micro_razers pair_align rabema_build_gold_standard rabema_evaluate rabema_prepare_sam razers razers3 sak seqan_tcoffee snp_store splazers stellar tree_recon [list was sorted and wildcard expanded (masai_*, rabema_*) by Andreas Tille] The other binaries could live happily in /usr/bin/seqan. If there is a collision, one could prefix seqan_ to the binary name. According to this advise all binary applications are moved to /usr/lib/seqan/bin and the ones mentioned above symlinked to /usr/bin. Manpages were created using help2man for the symlinked binaried. If you set your PATH like PATH=${PATH}:/usr/lib/seqan/bin you can call all seqan tools straight from command line with exception of /usr/lib/seqan/bin/join since there is a /usr/bin/join inside the coreutils package which will be found first so you need to explicitly specify the full path. If there are good reasons to provide any additional binary under /usr/bin please file a bug report using `reportbug seqan` and let us know about your preference. -- Andreas Tille Wed, 27 Nov 2013 10:26:17 +0100 Note: some apps are not built for some architectures due to memory limitations: Apps not built for mips & mipsel: - razers - razers3 - yara Apps not built for armhf: - yara Apps not built for sh4: - yara - razers3 Apps not built for armel: - yara Apps not built for kfreebsd-i386: - yara Apps not built for hurd-i386: - yara Apps not built for ia64: - searchjoin (assembler errors) Sending patches to improve the build experience on any of these architectures would be welcome by the Debian-Med team and upstream. -- Michael R. Crusoe Fri, 03 Nov 2017 09:29:40 -0700