Loading debian/TODO +9 −4 Original line number Diff line number Diff line Loading @@ -2,11 +2,15 @@ TODO for bcbio with Debian ========================== The following is a list of packages that are used by at least one of the workflows it aggregates. A complete coverage by Debian of all these tools workflows bcbio aggregates. A complete coverage by Debian of all these tools seems increasingly unlikely - their packaging would take longer than the tools scientific lifespan, i.e. there is a new generation of problem solving tools' scientific lifespan, i.e. there is a new generation of problem solving emerging and/or the workflow as a whole will have mutated in the meantime. We yet have to find an answer to this challenge. For quite some this is to just go and use Conda. We should also consider mixing Conda with Debian, though. But let us first see where we are with bcbio: Packages already accepted ------------------------ Loading Loading @@ -64,6 +68,7 @@ package seqcluster Some nitty-gritty was going on there wrt Python3 transition and an upcoming new release. Needs another review and likely some communication with upstream. Steffen addresses this. Packages presumed easy to package Loading @@ -87,8 +92,8 @@ Package MutliQC - in salsa Packages of importance for basic NGS workflow well beyond bcbio --------------------------------------------------------------- Packages of importance for basic NGS workflows with motivation beyond bcbio --------------------------------------------------------------------------- package mosdepth https://salsa.debian.org/med-team/mosdepth Loading Loading
debian/TODO +9 −4 Original line number Diff line number Diff line Loading @@ -2,11 +2,15 @@ TODO for bcbio with Debian ========================== The following is a list of packages that are used by at least one of the workflows it aggregates. A complete coverage by Debian of all these tools workflows bcbio aggregates. A complete coverage by Debian of all these tools seems increasingly unlikely - their packaging would take longer than the tools scientific lifespan, i.e. there is a new generation of problem solving tools' scientific lifespan, i.e. there is a new generation of problem solving emerging and/or the workflow as a whole will have mutated in the meantime. We yet have to find an answer to this challenge. For quite some this is to just go and use Conda. We should also consider mixing Conda with Debian, though. But let us first see where we are with bcbio: Packages already accepted ------------------------ Loading Loading @@ -64,6 +68,7 @@ package seqcluster Some nitty-gritty was going on there wrt Python3 transition and an upcoming new release. Needs another review and likely some communication with upstream. Steffen addresses this. Packages presumed easy to package Loading @@ -87,8 +92,8 @@ Package MutliQC - in salsa Packages of importance for basic NGS workflow well beyond bcbio --------------------------------------------------------------- Packages of importance for basic NGS workflows with motivation beyond bcbio --------------------------------------------------------------------------- package mosdepth https://salsa.debian.org/med-team/mosdepth Loading