Loading debian/TODO +21 −5 Original line number Diff line number Diff line Loading @@ -7,9 +7,18 @@ seems increasingly unlikely - their packaging would take longer than the 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: We yet have to find an answer to this challenge. A series of repositories of packages that are still waiting in the new queue for their acceptance in the distribution is available as deb http://med.functional.domains/r unstable main contrib non-free deb http://med.functional.domains/med unstable main contrib non-free deb http://med.functional.domains/python unstable main contrib non-free deb http://med.functional.domains/science unstable main contrib non-free Anyway, 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 @@ -98,6 +107,10 @@ package python-seqcluster (in crash space) apparently optional for bcbio: r-bioc-isomiRs - (needs r-bioc-DEGreport) all pre-depends except edgeR are in new apparently optional for bcbio: install_github('rstudio/rmarkdown') -- this may be the same we have from CRAN - not checked python3-dateutils (in new queue) (in crash space) https://salsa.debian.org/python-team/modules/python-dateutils Needed by python-seqcluster - actually I am not 100% sure about where in the latest version of seqcluster that is package viennarna (in crash space) https://github.com/ViennaRNA/ViennaRNA https://salsa.debian.org/med-team/vienna-rna/blob/master/debian/changelog Loading @@ -110,7 +123,7 @@ package viennarna (in crash space) Python and Perl packages are not functional, yet, not needed for seqcluster Waiting for acceptance of cthreadpool. Package MutliQC - (in crash space) Package MutliQC (in crash space) https://salsa.debian.org/med-team/multiqc Not redistributable until we have removed the highcharts library from that source tree https://github.com/ewels/MultiQC/issues/800 Loading Loading @@ -156,14 +169,17 @@ package mosdepth package oncofuse https://salsa.debian.org/med-team/oncofuse Stuck over typical Java issue package optitype https://salsa.debian.org/med-team/optitype (rudimentary) Stuck over too many dependencies package vcfanno https://salsa.debian.org/med-team/vcfanno Not fun because of many GO packages that are still missing, "biogo" being one of them. Stuck over too many dependencies Loading Loading
debian/TODO +21 −5 Original line number Diff line number Diff line Loading @@ -7,9 +7,18 @@ seems increasingly unlikely - their packaging would take longer than the 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: We yet have to find an answer to this challenge. A series of repositories of packages that are still waiting in the new queue for their acceptance in the distribution is available as deb http://med.functional.domains/r unstable main contrib non-free deb http://med.functional.domains/med unstable main contrib non-free deb http://med.functional.domains/python unstable main contrib non-free deb http://med.functional.domains/science unstable main contrib non-free Anyway, 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 @@ -98,6 +107,10 @@ package python-seqcluster (in crash space) apparently optional for bcbio: r-bioc-isomiRs - (needs r-bioc-DEGreport) all pre-depends except edgeR are in new apparently optional for bcbio: install_github('rstudio/rmarkdown') -- this may be the same we have from CRAN - not checked python3-dateutils (in new queue) (in crash space) https://salsa.debian.org/python-team/modules/python-dateutils Needed by python-seqcluster - actually I am not 100% sure about where in the latest version of seqcluster that is package viennarna (in crash space) https://github.com/ViennaRNA/ViennaRNA https://salsa.debian.org/med-team/vienna-rna/blob/master/debian/changelog Loading @@ -110,7 +123,7 @@ package viennarna (in crash space) Python and Perl packages are not functional, yet, not needed for seqcluster Waiting for acceptance of cthreadpool. Package MutliQC - (in crash space) Package MutliQC (in crash space) https://salsa.debian.org/med-team/multiqc Not redistributable until we have removed the highcharts library from that source tree https://github.com/ewels/MultiQC/issues/800 Loading Loading @@ -156,14 +169,17 @@ package mosdepth package oncofuse https://salsa.debian.org/med-team/oncofuse Stuck over typical Java issue package optitype https://salsa.debian.org/med-team/optitype (rudimentary) Stuck over too many dependencies package vcfanno https://salsa.debian.org/med-team/vcfanno Not fun because of many GO packages that are still missing, "biogo" being one of them. Stuck over too many dependencies Loading
