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software.hpc: Tracking PR #1

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Commits on Jun 23, 2023

  1. [farm] reorg packages.yaml

    spack-user@peloton committed Jun 23, 2023
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  2. [peloton] initital configurations.

    spack-user@peloton committed Jun 23, 2023
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  3. [peloton] core environment.

    spack-user@peloton committed Jun 23, 2023
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  4. [peloton] compilers from core environment.

    spack-user@peloton committed Jun 23, 2023
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Commits on Jun 28, 2023

  1. WIP main

    spack-user@peloton committed Jun 28, 2023
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Commits on Jun 30, 2023

  1. Split hpccf repo into version-pinned repos'

    spack-user@peloton committed Jun 30, 2023
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  2. Add v0.20 which removes many backported packages

    spack-user@peloton committed Jun 30, 2023
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Commits on Jul 11, 2023

  1. Peloton v0.20 production config.

    @camillescottatwork
    camillescottatwork committed Jul 11, 2023
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  2. Peloton modulefiles post upgrade

    @camillescottatwork
    camillescottatwork committed Jul 11, 2023
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  3. [peloton] v0.20 packages post peloton upgrade

    @camillescottatwork
    camillescottatwork committed Jul 11, 2023
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  4. Template for external gcc

    @camillescottatwork
    camillescottatwork committed Jul 11, 2023
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  5. [peloton] main env, post upgrade.

    @camillescottatwork
    camillescottatwork committed Jul 11, 2023
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Commits on Jul 21, 2023

  1. [peloton] update modulefiles

    spack-user@peloton committed Jul 21, 2023
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  2. Update gcc 7.5.0 compiler paths

    spack-user@peloton committed Jul 21, 2023
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  3. Get working bwa-mem2 package.

    spack-user@peloton committed Jul 21, 2023
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  4. add dashing package

    spack-user@peloton committed Jul 21, 2023
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  5. bwa-mem2 patches.

    spack-user@peloton committed Jul 21, 2023
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  6. idl package

    spack-user@peloton committed Jul 21, 2023
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  7. coverm package

    spack-user@peloton committed Jul 21, 2023
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  8. [peloton] many package updates in main environment.

    spack-user@peloton committed Jul 21, 2023
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  9. [peloton] reconcretized main lockfile

    spack-user@peloton committed Jul 21, 2023
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  10. [peloton] remove unused core envuironment

    spack-user@peloton committed Jul 21, 2023
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  11. remove duplicates.txt

    @camillescottatwork
    camillescottatwork committed Jul 21, 2023
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Commits on Aug 14, 2023

  1. [peloton] add numactl to main environment.

    @camillescottatwork
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  2. Simple environment for EPYC CPU benchmarking.

    @camillescottatwork
    camillescottatwork committed Aug 14, 2023
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  3. [peloton] add aocc to spack compiler configuration

    @camillescottatwork
    camillescottatwork committed Aug 14, 2023
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  4. Edits to stream package.

    @camillescottatwork
    camillescottatwork committed Aug 14, 2023
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Commits on Aug 28, 2023

  1. [peloton] new modulefile

    @camillescottatwork
    camillescottatwork committed Aug 28, 2023
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Commits on Aug 29, 2023

  1. [peloton] update for slurm patch

    @camillescottatwork
    camillescottatwork committed Aug 29, 2023
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Commits on Sep 15, 2023

  1. Bump the Slurm stack to use PMIx 4.2.6 + newer ucx and hwloc.

    @OmenWild
    OmenWild committed Sep 15, 2023
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  2. Bump the Slurm stack to use PMIx 4.2.6 + newer ucx and hwloc.

    @OmenWild
    OmenWild committed Sep 15, 2023
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  3. Comment out julia, does not build with Spack yet.

    @OmenWild
    OmenWild committed Sep 15, 2023
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  4. Normalize backports and hpccf environments

    spack-user@peloton committed Sep 15, 2023
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  5. [peloton] bump minimap2 version.

    spack-user@peloton committed Sep 15, 2023
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  6. [peloton] reconcretize main

    spack-user@peloton committed Sep 15, 2023
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  7. [peloton] regenerate modulefiles

    spack-user@peloton committed Sep 15, 2023
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  8. [peloton] concretize benchmarking environment.

    spack-user@peloton committed Sep 15, 2023
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Commits on Sep 19, 2023

  1. Merge farm/franklin main

    @camillescott
    camillescott committed Sep 19, 2023
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  2. Move ont-guppy and py-deeptools into forked

    @camillescott
    camillescott committed Sep 19, 2023
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  3. [franklin][peloton] add new 'forked' repo

    @camillescott
    camillescott committed Sep 19, 2023
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  4. Fix package links

    @camillescott
    camillescott committed Sep 19, 2023
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Commits on Sep 20, 2023

  1. [franklin] start v0.20 config

    @camillescott
    camillescott committed Sep 20, 2023
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Commits on Oct 3, 2023

  1. [Peloton] [INC1724503] Update coverm to use the newest minimap2 ^mini… 

    …[email protected]
    @OmenWild
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  2. Snapshot.

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  3. [Peloton] [INC1724503] Update coverm to use the newest minimap2 ^mini… 

    …[email protected]
    @OmenWild
    OmenWild committed Oct 3, 2023
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Commits on Oct 6, 2023

  1. Snapshot.

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  2. [Peloton] Upgrade the external Slurm to 23.02.5

    @OmenWild
    OmenWild committed Oct 6, 2023
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Commits on Oct 12, 2023

  1. [franklin] Initial base configs: common, core, software

    @camillescottatwork
    camillescottatwork committed Oct 12, 2023
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  2. [franklin] Mostly finalized core environment.

    @camillescottatwork
    camillescottatwork committed Oct 12, 2023
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  3. [franklin] concretized core environment

    @camillescottatwork
    camillescottatwork committed Oct 12, 2023
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  4. Fork openssl to export proper environment variables to allow more bui… 

    …lds with Ubuntu external
    @camillescottatwork
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  5. Fork slurm to bump to for emergency CVE release 2023-10-12 (v23.02.6)

    @camillescottatwork
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  6. [franklin] Add merge script for common and software packages.yaml; Ad… 

    …d software compilers.yaml
    @camillescottatwork
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  7. [franklin] first pass software spack.yaml

    @camillescottatwork
    camillescottatwork committed Oct 12, 2023
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  8. [franklin] add cuda 8

    @camillescottatwork
    camillescottatwork committed Oct 12, 2023
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Commits on Oct 14, 2023

  1. [franklin] external llvm; update slurm and envmod prefixes

    @camillescottatwork
    camillescottatwork committed Oct 14, 2023
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  2. [franklin] convert templates from lua to tcl; sanitize extra relion f… 

    …ields between cpu and gpu
    @camillescottatwork
    camillescottatwork committed Oct 14, 2023
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  3. Fork unzip to fix build for oneapi

    @camillescottatwork
    camillescottatwork committed Oct 14, 2023
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Commits on Oct 16, 2023

  1. [franklin] update relion templates and modulefile vars

    @camillescottatwork
    camillescottatwork committed Oct 16, 2023
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  2. Remove some unnecessary packages.

    @camillescottatwork
    camillescottatwork committed Oct 16, 2023
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  3. Add missing dbus dependency back in to Slurm package.py

    @camillescottatwork
    camillescottatwork committed Oct 16, 2023
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  4. [franklin] core: roll back to environment modules 5.2.0 due to tcl li… 

    …bs path regression; add more CUDAs
    @camillescottatwork
    camillescottatwork committed Oct 16, 2023
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  5. [franklin] properly fill out mirrors.yaml

    @camillescottatwork
    camillescottatwork committed Oct 16, 2023
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  6. [franklin] autoload:direct

    @camillescottatwork
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  7. [franklin] force xmlto to use %gcc due to a OneAPI build bug.

    @camillescottatwork
    camillescottatwork committed Oct 16, 2023
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  8. [franklin] regenerated software packages.yaml

    @camillescottatwork
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  9. [franklin] reconcretize core.

    @camillescottatwork
    camillescottatwork committed Oct 16, 2023
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  10. [franklin] reconcretize software

    @camillescottatwork
    camillescottatwork committed Oct 16, 2023
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  11. [franklin] generate tcl modulefiles.

    @camillescottatwork
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Commits on Oct 17, 2023

  1. Snapshot.

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  2. [Peloton] Upgrade Slurm to the newest (23.02.6).

    @OmenWild
    OmenWild committed Oct 17, 2023
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Commits on Oct 26, 2023

  1. Add a full featured squashfs for apptainer.

    @OmenWild
    OmenWild committed Oct 26, 2023
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  2. Add an explicit version to apptainer. 

    Add an explicit load of an apptainer requirement as the
depends_on(type="run") is not autogenerating those modules.
    @OmenWild
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  3. TODO: move to the -forked repo. 

    Take the uppstream packages and fix them to install the newest
versions, and to install correctly.
    @OmenWild
    OmenWild committed Oct 26, 2023
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  4. Snapshot.

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Commits on Nov 2, 2023

  1. [franklin] update modulefiles

    @camillescottatwork
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  2. Update alphafold and dependencies

    @camillescottatwork
    camillescottatwork committed Nov 2, 2023
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  3. Update relion templates

    @camillescottatwork
    camillescottatwork committed Nov 2, 2023
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  4. Add wrappers for deepemhancer, topaz

    @camillescottatwork
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  5. [franklin] main env: alphafold and variables, relion 5, relion variab… 

    …les update for new templates
    @camillescottatwork
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  6. Add relion 5-beta

    @camillescottatwork
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  7. [franklin] main env: reconcretize

    @camillescottatwork
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Commits on Nov 9, 2023

  1. Add gctf variant to relion

    @camillescottatwork
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  2. [franklin] reconcretize software

    @camillescottatwork
    camillescottatwork committed Nov 9, 2023
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  3. Merge branch 'franklin-reorg' into versioned-reorganization

    @camillescott
    camillescott committed Nov 9, 2023
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Commits on Nov 27, 2023

  1. [Peloton] [INC1783336] Add Matlab R2023a as a Spack external.

    @OmenWild
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  2. Snapshot.

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Commits on Dec 14, 2023

  1. [Peloton] Upgrade slurm to the newest bugfix release (23-02-7).

    @OmenWild
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  2. Snapshot.

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Commits on Mar 1, 2024

  1. openmm

    @camillescott
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  2. Merge branch 'versioned-reorganization' of github.com:ucdavis/spack-u… 

    …cdavis into versioned-reorganization
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Commits on Mar 7, 2024

  1. Move all packages that exist in both hpccf and builtin to forked

    @camillescottatwork
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  2. Bring in upstream changes to libxml2, preserving our +ftp variant

    @camillescottatwork
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  3. Upstream changes to bpp-phyl-omics

    @camillescottatwork
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  4. [package] openssl: merge upstream changes, preserve out dependent bui… 

    …ld environment
    @camillescottatwork
    camillescottatwork committed Mar 7, 2024
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  5. [package] bpp-phyl, bpp-popgen: upstream changes

    @camillescottatwork
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  6. [package] bpp-core,seq-omics,seq,suite: upstream merge

    @camillescottatwork
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  7. [package] r-raster: remove backported package

    @camillescottatwork
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  8. [package] py-gdc-client: upstream merge

    @camillescottatwork
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  9. [package] r-units: remove essentially backported package

    @camillescottatwork
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  10. [package] blat: merge upstream

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  11. [package] htslib: merge major upstream changes; preserve our out-of-s… 

    …ource build
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  12. [package] circos: upstream changes

    @camillescottatwork
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  13. [package] salmon: remove out outdated fork for upstream version

    @camillescottatwork
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  14. [package] r-ensembldb: remove out outdated backport

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  15. [package] lmod: deprecate our fork for now (we don't use it anymore)

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  16. [package] for now, deprecate our maker

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  17. [package] py-cyvcf2: upstream changes

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  18. [package] mark: deprecate in favor of upstream

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  19. [package] gffcompare: merge upstream changes

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  20. [package] motioncor2: upstream now patches binaries for cuda the same… 

    … way we do, deprecate
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  21. [package] libxpm: remove outdated backport

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  22. [package] sailfish: bring in upstream changes (use tbb provider)

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  23. [package] unblur: deprecate fork, 1.0.2 now in upstream

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  24. [package] r-v8: deprecate fork for much newer upstream

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  25. [package] unzip: deprecate what appears to be a backport

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  26. [package] r-genomicfeatures: deprecate outdated backport

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  27. [package] r-genomeinfodb: upstream is newer, deprecate our fork

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  28. [package] dbus: upstream now supports the --with-system-socket flag, … 

    …which replaces the purpose of our local_state_dir implementation
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  29. [package] libseccomp: upstream merge

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  30. [package] r-ggtree: upstream is newer, deprecate

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  31. [package] gatk: upstream has much newer versions, deprecate

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  32. [package] plink-ng: merge upstream zlib=>zlib-api changes

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  33. [package] apptainer: bring in license from upstream

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  34. [package] gffread: update to new-style maintainers directive

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  35. [package] julia: deprecate our (non-working) julia in favor of much-u… 

    …pdated upstream
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  36. [package] py-dm-haiku: bring upstream license directive

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  37. [package] r-bsgenome: remove outdated backport

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  38. [package] r-terra: remove outdated backport

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  39. [package] py-deeptools: deprecate our version in favor of upstream wh… 

    …ich is newer
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  40. [package] r-insight: remove outdated backport

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  41. [package] openmm: remove unneeded link to backports/openmm

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  42. [package] node-js: add v18.18.2 (farm liftover, 4abf72c)

    @camillescottatwork
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  43. [package] cmake: fork and bring in v3.28.1 (farm liftover)

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  44. [package] homer: fork and liftover changes from farm

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  45. [package] npm: farm liftover; add v9.8.1 and installer arg fixes

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  46. [package] plink: lift over farm's fork with newer version, patch

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  47. [package] qualimap: bring over farm version with patch for java > 8

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  48. [package] censor-norb: new package, bring over from farm branch

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  49. [package] distangsd: bring in farm -libdeflate update; update for new… 

    …spack
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  50. [package] ngsrelate: bring in new package from farm, clean up

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  51. [package] py-basevar: bring in new package from farm, clean up

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  52. [package] py-logbook: bring in new package from farm, clean up

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  53. [package] rstudio: bring over farm 2023.12.1-402 updates

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  54. [modulefile] base.tcl: lift over deprecation functionality from farm

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  55. [modulefile] rstudio-server,turbovnc: bring over farm template changes

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Commits on Mar 8, 2024

  1. [package] delete backports repo; remove unneeded and dead backports l… 

    …inks
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  2. [package] glimpse2: remove link to v0.19 packages and move package

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  3. [package] h5z-zfp: remove forked package in favor of fixed upstream

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  4. [package] remove v0.19 repo

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  5. [package] flatten hpccf repo

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  6. [package] remove forked slurm; upstream properly does dbus and has ne… 

    …wer versions
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  7. [package] openmm: need link to builtin for patched dependency bug

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  8. [package] environment-modules: fork environment modules and support o… 

    …ut-of-prefix etcdir
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  9. [config] software.hpc: first pass core conf

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  10. [config] software.hpc: first pass core env

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Commits on Mar 23, 2024

  1. [lock] software.hpc: concretized core environment

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  2. [config] software.hpc: finalized core environment config.

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  3. [config] software.hpc: enable arch_folder for modules

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  4. [config] software.hpc: add spack-installed compilers to core config

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  5. [meta] add .cvmfs to git ignore:

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  6. [config] software.hpc: update main environment externals for core

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  7. [config] software.hpc: regenerate main packages config

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Commits on Apr 10, 2024

  1. [package] openblas: fork openblas and set a specific target for gener… 

    …ic v2 and v3 to avoid incorrect Zen guess on v3 QEMU
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  2. [package] linux-pam: fork and add libintl dependency

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Commits on Apr 30, 2024

  1. [config] software.hpc: core environment externals, additional core pa… 

    …ckages, remove LD_LIBRARY_PATH from modules
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Commits on May 13, 2024

  1. [config] software.hpc: convert compilers defined in packages.yaml

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  2. [config] software.hpc: remove prequisites: direct from common modules… 

    … config
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  3. [env: main] software.hpc: main defs

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  4. [config, env: core] software.hpc: fully peel off definitions from core

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Commits on Oct 4, 2024

  1. Add the older versions of virtualgl and turbovnc so they get added to 

    the view so the module works.
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Commits on Oct 17, 2024

  1. Update core externals

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  2. Don't export modules from core environment

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  3. [package] fork libjpeg-turbo

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  4. [package] fork phyluce

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  5. [package] fork virtualgl

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  6. [package] add new turbovnc version:

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  7. [lock] concretize core

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  8. [env:main] Fix iq-tree version, remove phyluce, add code-server

    @camillescottatwork
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  9. [lock] concretize main

    @camillescottatwork
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  10. [env:main] camw: added [email protected]

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  11. [lock] reconcretize main

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Commits on Oct 21, 2024

  1. [package] node-js: backport

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  2. [package] npm: 10.9.0

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  3. [package] re2c: backport re2c

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    camillescottatwork committed Oct 21, 2024
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  4. [package] rstudio: 2024.09.0-375

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  5. [env:main] [email protected]

    @camillescottatwork
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  6. [lock] reconcretize main

    @camillescottatwork
    camillescottatwork committed Oct 21, 2024
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