Hi,
> I am installing the rnaseq Pigx pipeline from > https://github.com/BIMSBbioinfo/pigx/tree/master/pipelines/rnaseq Oh, nice! > I miss something with the Guix installation. > > `guix environment -l guix.scm` fails because of these unbounded variables: > - fastqc > - salmon > - ghc-pandoc-1 > - ghc-pandoc-citeproc-with-pandoc-1 These variables are defined in Guix since quite some time, so you are probably using a rather old version of Guix. (The first two are defined in (gnu packages bioinformatics), the latter two in (gnu packages haskell).) Note that you can also install the “pigx-rnaseq” or “pigx” packages with the latest version of Guix; you don’t need to build the pipeline yourself. > Then, I have tried `guix pull`, which leads to: > > building path(s) `/gnu/store/7mw3mxnb5py6g2q6qaqf5mbaqxwr0jz3-perl-5.26.1' > FATAL: kernel too old > > I am not sure what does it mean ? > > (`uname -r` is 3.0.80-0.7-default) It means that your kernel is too old to work with the current version of the GNU C library (glibc). We applied some patches to the C library to ensure that it will work with the particular kernel that comes with RHEL 6 (i.e. a heavily modified kernel that self-reports its version as 2.6.32). The patched glibc package is not yet available in the master branch; it is currently only available in the “core-updates” branch, which is due to be merged in the next few days. 3.0 is just a tad too old for the C library. What system is this? Is this SLES from mid 2013? Are you able to upgrade to at least Linux 3.10 or install the RHEL 6 kernel, which is known to work? I’m afraid there’s no easy way to convince the C library that your kernel is compatible, because it’s very likely that it isn’t if it wasn’t heavily patched. -- Ricardo
