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. 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] >> >
