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kallisto: 0.46.1 -> 0.46.2 #80122

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merged 1 commit into from Feb 15, 2020
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r-ryantm commented Feb 14, 2020

Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://github.com/pachterlab/kallisto/releases.

meta.description for kallisto is: '"Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data"'.

meta.homepage for kallisto is: '"https://pachterlab.github.io/kallisto"

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Rebuild report (if merged into master) (click to expand)

3 total rebuild path(s)

1 package rebuild(s)

1 x86_64-linux rebuild(s)
1 i686-linux rebuild(s)
0 x86_64-darwin rebuild(s)
1 aarch64-linux rebuild(s)

First fifty rebuilds by attrpath
kallisto

Instructions to test this update (click to expand)

Either download from Cachix:

nix-store -r /nix/store/yxm2cfbbsf30wkps65igarph3sxzl3vd-kallisto-0.46.2 \
  --option binary-caches 'https://cache.nixos.org/ https://r-ryantm.cachix.org/' \
  --option trusted-public-keys '
  r-ryantm.cachix.org-1:gkUbLkouDAyvBdpBX0JOdIiD2/DP1ldF3Z3Y6Gqcc4c=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(r-ryantm's Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.

Or, build yourself:

nix-build -A kallisto https://github.com/r-ryantm/nixpkgs/archive/dc7efb4934345e37c4d054d60d5fa883724b563a.tar.gz

After you've downloaded or built it, look at the files and if there are any, run the binaries:

ls -la /nix/store/yxm2cfbbsf30wkps65igarph3sxzl3vd-kallisto-0.46.2
ls -la /nix/store/yxm2cfbbsf30wkps65igarph3sxzl3vd-kallisto-0.46.2/bin

cc @arcadio for testing.

Co-authored-by: Daniel Schaefer <git@danielschaefer.me>
@JohnAZoidberg JohnAZoidberg force-pushed the r-ryantm:auto-update/kallisto branch from dc7efb4 to 4c6c40d Feb 15, 2020
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JohnAZoidberg commented Feb 15, 2020

To keep HDF5 support, this new version requires -DUSE_HDF5=ON, so I added that.

For this release HDF5 is not a required dependency for running kallisto bus for single cell RNA-seq analysis. It is still required for compatibility with sleuth and other downstream tools. By default kallisto will not be built with HDF5 support

@JohnAZoidberg JohnAZoidberg merged commit 1e61323 into NixOS:master Feb 15, 2020
@r-ryantm r-ryantm deleted the r-ryantm:auto-update/kallisto branch Feb 18, 2020
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