Hi all, pigx-rnaseq runs a set of RNAseq tools within snakemake and then prepares reports with pandoc that look neat since the tables are all jquery-javascripted dynamic. Just, when pandoc expected the .js/.css files in a location that is not matching reality, then the whole process comes to an end. When removed all the embedded *js files from our R packages, our job with symlinks had imperfections. Particularly so, when a script uses the symlinks with source and dest exchanged, this has weird effects that are not repared by just updating a package. One needs to manually remove the link. That hurt. And with a symlink hidden in a post-inst script, this does not pop up in "dpkg -c" or so, as would anything that goes through dh_link. I need to make up my mind about this, but somehow I feel this is something that lintian and friends should in part address.
My merge request on https://salsa.debian.org/js-team/datatables-extensions/-/merge_requests I sense is the last technical hurdle before an upload to main. And we then indeed have a checkpointed parallel workflow for RNAseq with snakemake. Next on my list now is pigx-scrnaseq. Then, hm, I think I will look into the Nanopore a bit more. The LamPORE https://www.biotechniques.com/diagnostics-preclinical/oxford-nanopore-makes-deal-with-the-uk-government-to-provide-450000-covid-19-tests/ looks interesting. Best, Steffen On 24.08.20 16:40, Steffen Möller wrote: > Hi Andreas, > > On 24.08.20 15:16, Steffen Möller wrote: >> On 24.08.20 11:08, Andreas Tille wrote: >>> Hi Steffen, >>> >>> On Mon, Aug 24, 2020 at 04:17:37AM +0200, Steffen Möller wrote: >>>> @Andreas, >>>> >>>> good news: I made quite some inroads on why pigx-rnaseq does not work. >>>> But that is for another email. >>>> >>>> My current hurdle is that vfs_fonts.js is missed by pandoc: >>>> >>>> pandoc: >>>> /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/vfs_fonts.js: >>>> openBinaryFile: does not exist (No such file or directory) >>>> >>>> This file should have been located next to pdfmake in >>>> >>>> /usr/share/javascript/jquery-datatables-extensions/pdfmake/build >>>> >>>> but >>>> >>>> Files-Excluded: */buttons.flash* >>>> */*.swf >>>> */vfs_fonts.js >>>> >>>> does not want that. There are suggestions on >>>> https://stackoverflow.com/questions/48835055/pdfmake-cant-find-the-font-files-on-vfs >>>> to create one's own variant, but this should then happen within that >>>> JavaScript package, right? >>> May be you file a bug report to datatables-extensions upstream to provide >>> a free font version? >> Here is the original >> https://raw.githubusercontent.com/naoa/pdfmake/master/build/vfs_fonts.js >> >> and this GenShinGothic has a "non-commercial use only" license, indeed. >> >> https://en.m.fontke.com/font/23789742/detail/ >> >> I just submitted https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=968944. >> >> On a sidenote, Rebecca reopened >> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=927787 since >> DataTables apparently has a new repository on github where each >> subdirectory is presented as its very own package, like >> https://github.com/DataTables/Select or (more prominently) >> https://github.com/DataTables/Buttons . >> >> I also checked >> https://github.com/DataTables/pdfmake/blob/master/build/vfs_fonts.js >> which now just ships with a an embedded "LICENSE.txt" and no font which >> I presume to be fine to redistribute. I'll see if this also works with >> the current version and am not unlikely to close my own bug that way. >> >> As Rebecca stated, this new DataTables repository also affects >> snakemake. I consider it remote to our cause for now. Would not mind a >> "JavaScript" Tab in our Spreadsheet. > I added a patch that adds the future free version of vfs_fonts.js. > Please kindly review and merge. > > Best, > > Steffen > > >