Steffen Möller pushed to branch master at Debian Med / bcbio
Commits: 7cee64ad by Steffen Möller at 2019-08-03T14:34:01Z Update, mention crash space - - - - - 1 changed file: - debian/TODO Changes: ===================================== debian/TODO ===================================== @@ -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 ------------------------ @@ -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 @@ -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 @@ -155,15 +168,18 @@ package mosdepth of which the first already is in the new queue package oncofuse - https://salsa.debian.org/med-team/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 View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/7cee64ad75f23d4a1bd6c680098791c6708ea262 -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/7cee64ad75f23d4a1bd6c680098791c6708ea262 You're receiving this email because of your account on salsa.debian.org.
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