As I heard that igv, artemis depending on picard-tools depending on gkl (Intel specific code), I opened a ticket for picard-tools.
This ticket might be a good start to make picard run on multiple CPUs. https://github.com/broadinstitute/picard/issues/1467 On Sat, Feb 8, 2020 at 4:39 PM Michael Crusoe <[email protected]> wrote: > > Oh, I was mistaken about the GATK link. > > picard-tools depends on gkl, and igv and artemis depend on picard-tools > > On Sat, Feb 8, 2020 at 4:22 PM Jun Aruga <[email protected]> wrote: >> >> This part is related to building on ARM. >> >> > @GraceZou, You will have to build from source for ARM. The repo is >> > gatk-bwamem-jni. There are instructions in the README on the repo landing >> > page. Set the environmental variable to then point to the built library. >> >> On Sat, Feb 8, 2020 at 4:19 PM Jun Aruga <[email protected]> wrote: >> > >> > For GATK depending on GKL, I found an interesting page about building >> > GATK on ARM. >> > >> > https://gatkforums.broadinstitute.org/gatk/discussion/9971/gatk4-beta1-problem-some-questions-about-bwa-faga-pipeline-in-gatk4-beta1 >> > > We use GATK4-beta1 in ARM,and have several questions about it: >> > >> > Jun >> > >> > On Sat, Feb 8, 2020 at 2:53 PM Michael Crusoe <[email protected]> >> > wrote: >> > > >> > > https://github.com/Intel-HLS/GKL >> > > A Java wrapper around an Intel optimized implementations of PairHMM, >> > > Smith-Waterman, and DEFLATE. >> > > >> > > Uses SIMD intrinsics and assembly. >> > > >> > > At https://salsa.debian.org/misterc-guest/gkl/tree/experimental/simde is >> > > a fork using the SIMD Everywhere library, but I lack the expertise to >> > > produce source versions of the many assembler only routines. >> > > >> > > Any suggestions / contributions? >> > > >> > > -- >> > > Michael R. Crusoe >> > >> > >> > >> > -- >> > Jun | He - His - Him >> > [email protected] / IRC: jaruga >> >> >> >> -- >> Jun | He - His - Him >> [email protected] / IRC: jaruga >> > > > -- > Michael R. Crusoe -- Jun | He - His - Him [email protected] / IRC: jaruga
