Can you make a PR for your patch (for Medaka 1.5.0), I don't believe we should have dropped that? That is likely to affect other people...
On Wed, 18 May 2022 at 13:49, Loris Bennett <[email protected]> wrote: > Hi Alan, > > "Alan O'Cais" <[email protected]> writes: > > > Hmm, the patch for that ( > https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/m/medaka/medaka-1.4.3_use-SAMtools-dep.patch) > seems to have been dropped in 1.5.0. > > > > Bringing that patch back may fix your problem. > > Thanks for the pointer. I was able to port the patch and that did > indeed fix my problem. > > However, my next problem is that medaka 1.6.0 needs TensorFlow 2.7.0. > Unfortunately there are no ECs beyond 2.6.0, even though the current > version is 2.9.0 (ML on HPC is not going out of fashion, is it?). > > I see Sam has put in a PR #14990 for 2.7.0, but for foss/2021b, so I > guess I'll have to look into bumping my EC up to that toolchain. > > Cheers, > > Loris > > > Alan > > > > On Tue, 17 May 2022 at 15:41, Alan O'Cais <[email protected]> wrote: > > > > Seems like Medaka is doing naughty stuff: > > https://github.com/nanoporetech/medaka/blob/master/Makefile#L76 > > > > You probably need to patch the Makefile so an EB-provided version of > those downloaded deps are used. > > > > On Tue, 17 May 2022 at 15:27, Loris Bennett <[email protected]> > wrote: > > > > Hi, > > > > I have successfully installed > > > > medaka-1.5.0-foss-2021a.eb > > > > I then created an EC with the following changes for medaka 1.6.0: > > > > $ diff > /trinity/shared/easybuild/software/EasyBuild/4.5.4/easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb > medaka-1.6.0-foss-2021a.eb > > 13c13 > > < version = '1.5.0' > > --- > > > version = '1.6.0' > > 26c26 > > < ('TensorFlow', '2.5.3'), > > --- > > > ('TensorFlow', '2.6.0'), > > 35c35 > > < ('ont-fast5-api', '4.0.0'), > > --- > > > ('ont-fast5-api', '4.0.2'), > > 47c47 > > < 'checksums': > ['8a0b8d5997fe45b8d5a1317b2b6bfe117cb6b551928faef62e4e958cf14b5ea4'], > > --- > > > 'checksums': > ['a8389f90cba77095061c4ff22c7cce8d73908e2451fa1d07b94c2f8ce4152628'], > > > > The new TensorFlow and ont-fast5-api packages seem to be built and > > installed correctly, but building medaka itself fails with the following > > error: > > > > ld.gold: error: libhts.a(hts.o): requires unsupported dynamic reloc > 11; recompile with -fPIC > > > > Does anyone have an idea what might be causing this? > > > > Cheers, > > > > Loris > > > > -- > > Dr. Loris Bennett (Herr/Mr) > > ZEDAT, Freie Universität Berlin Email > [email protected] > > > -- > Dr. Loris Bennett (Herr/Mr) > ZEDAT, Freie Universität Berlin Email [email protected] >
