Re: Project idea: port GKL to non-x86
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 <michael.crusoe@gmail.com> 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 <jaruga@redhat.com> 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 <jaruga@redhat.com> 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 <michael.crusoe@gmail.com> 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
>> > jaruga@redhat.com / IRC: jaruga
>>
>>
>>
>> --
>> Jun | He - His - Him
>> jaruga@redhat.com / IRC: jaruga
>>
>
>
> --
> Michael R. Crusoe
--
Jun | He - His - Him
jaruga@redhat.com / IRC: jaruga
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