These are chat archives for nextflow-io/nextflow

Jan 2018
Michael L Heuer
Jan 03 2018 04:16
Note Nextflow is no longer available via homebrew. Homebrew-science was forcibly shut down by the Homebrew organization (well, that is how I interpret what went down) and all "non-notable" formulae removed. Homebrew/homebrew-science#6365
$ brew update
==> Deleted Formulae
homebrew/science/adam ✔                                             homebrew/science/mathomatic
homebrew/science/blat ✔                                             homebrew/science/matplotlib
homebrew/science/bowtie ✔                                           homebrew/science/maude
homebrew/science/clustal-omega ✔                                    homebrew/science/mcl
homebrew/science/cytoscape ✔                                        homebrew/science/med-file
homebrew/science/freebayes ✔                                        homebrew/science/megahit
homebrew/science/lastz ✔                                            homebrew/science/megam
homebrew/science/nextflow ✔                                         homebrew/science/meme
homebrew/science/snpeff ✔                                           homebrew/science/meraculous
homebrew/science/vcflib ✔
Paolo Di Tommaso
Jan 03 2018 08:32
@heuermh oh, I was told to migrate NF to the core but I didn't know that homebrew science was going to be shutdown.
Frankly I not sure if it's really need to maintain a homebrew recipe anymore. NF is straightforward to install and a package manager is not really needed .
Paolo Di Tommaso
Jan 03 2018 08:38
@timdiels you may want to fill a feature request for that
Michael L Heuer
Jan 03 2018 16:08
@pditommaso Same here, we made the "notable" list but didn't make some arbitrary number of downloads cutoff, so the pull request to core was closed without merging.
Agreed that NF is easy to install, I rely on homebrew to let me know when things need updating for development and docker images when I need to pin to a specific version for reproduciblity. Frustrating the way things went down.
Paolo Di Tommaso
Jan 03 2018 16:11
yes, it's a bit bizarre to see how they have shutdown homebrew science
however if you need to stick with a specific version you can simply use the NXF_VER=<version number> variable
each NF version is stored in the maven archive and you can switch to any version at any point in time