mirror of
https://github.com/MillironX/XAM.jl.git
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Update CI and documentation for the general registry
- Update documentation workflow. - Update CompatHelper workflow. - Update TagBot workflow. - Update unit test workflow. - Update codecov.
This commit is contained in:
Ciarán O'Mara
Ciarán O'Mara
parent
81dbf41798
commit
eaf5c73eb5
10 changed files with 62 additions and 102 deletions
33
.github/workflows/CompatHelper.yml
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33
.github/workflows/CompatHelper.yml
vendored
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@ -2,37 +2,16 @@ name: CompatHelper
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on:
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schedule:
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- cron: '00 * * * *'
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- cron: '0 0 * * *'
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jobs:
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CompatHelper:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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julia-version: [1.3.0]
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julia-arch: [x86]
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os: [ubuntu-latest]
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runs-on: ubuntu-latest
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steps:
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- uses: julia-actions/setup-julia@latest
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with:
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version: ${{ matrix.julia-version }}
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- name: Add CompatHelper
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run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
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- name: CompatHelper.main
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run: julia --color=yes -e 'using Pkg; Pkg.add("CompatHelper")'
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- name: Run CompatHelper
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: julia -e '
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using CompatHelper, Pkg;
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my_registries = [
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Pkg.RegistrySpec(
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name = "BioJuliaRegistry",
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uuid = "ccbd2cc2-2954-11e9-1ccf-f3e7900901ca",
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url = "https://github.com/BioJulia/BioJuliaRegistry.git"
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),
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Pkg.RegistrySpec(
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name = "General",
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uuid = "23338594-aafe-5451-b93e-139f81909106",
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url = "https://github.com/JuliaRegistries/General.git"
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)
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];
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CompatHelper.main(; registries = my_registries, master_branch = "master");'
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COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
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run: julia --color=yes -e 'using CompatHelper; CompatHelper.main(master_branch = "master")'
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40
.github/workflows/Documentation.yml
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40
.github/workflows/Documentation.yml
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@ -1,34 +1,26 @@
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name: Documentation
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name: Build Documentation
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on:
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push:
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branches:
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- 'master'
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- 'develop'
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- 'release/.*'
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tags: '*'
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pull_request:
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push:
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branches:
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- master
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- develop
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- release/*
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tags: '*'
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pull_request:
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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julia-version: [1.3.0]
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julia-arch: [x86]
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os: [ubuntu-latest]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1.0.0
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- uses: julia-actions/setup-julia@latest
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- uses: actions/checkout@v2
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- uses: julia-actions/setup-julia@v1
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with:
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version: ${{ matrix.julia-version }}
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- name: Install dependencies
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run: |
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julia ci_prep.jl;
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julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
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- name: Build and deploy
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version: '1'
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- name: Install Dependencies
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run: julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
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- name: Build and Deploy
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env:
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# https://github.com/JuliaDocs/Documenter.jl/issues/1177
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# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
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DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
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run: julia --project=docs/ --color=yes docs/make.jl
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run: julia --color=yes --project=docs/ docs/make.jl
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3
.github/workflows/TagBot.yml
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3
.github/workflows/TagBot.yml
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@ -1,7 +1,7 @@
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name: TagBot
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on:
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schedule:
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- cron: '0 * * * *'
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- cron: '0 0 * * *'
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jobs:
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TagBot:
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runs-on: ubuntu-latest
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@ -10,4 +10,3 @@ jobs:
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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ssh: ${{ secrets.TAGBOT_KEY }}
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registry: BioJulia/BioJuliaRegistry
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42
.github/workflows/UnitTests.yml
vendored
42
.github/workflows/UnitTests.yml
vendored
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@ -1,22 +1,44 @@
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name: Unit tests
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name: Unit Tests
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on: [push, pull_request]
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on:
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- push
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- pull_request
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jobs:
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test:
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runs-on: ${{ matrix.os }}
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continue-on-error: ${{ matrix.experimental }}
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strategy:
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fail-fast: false
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matrix:
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julia-version: ['1.1', '1.2', '1.3']
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julia-arch: [x64]
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julia-version:
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- '1.0' # LTS
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- '1'
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julia-arch: [x64, x86]
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os: [ubuntu-latest, windows-latest, macOS-latest]
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experimental: [false]
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include:
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- julia-version: nightly
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julia-arch: x64
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os: ubuntu-latest
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experimental: true
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steps:
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- uses: actions/checkout@v1.0.0
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- uses: julia-actions/setup-julia@v1
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- name: Checkout Repository
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uses: actions/checkout@v2
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- name: Setup Julia
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uses: julia-actions/setup-julia@v1
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with:
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version: ${{ matrix.julia-version }}
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arch: ${{ matrix.julia-arch }}
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- name: Install dependencies
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run: julia ci_prep.jl
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- uses: julia-actions/julia-runtest@master
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- name: Run Tests
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uses: julia-actions/julia-runtest@latest
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- name: Create CodeCov
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uses: julia-actions/julia-processcoverage@v1
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- name: Upload CodeCov
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uses: codecov/codecov-action@v1
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with:
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file: ./lcov.info
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flags: unittests
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name: codecov-umbrella
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fail_ci_if_error: false
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token: ${{ secrets.CODECOV_TOKEN }}
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@ -23,7 +23,7 @@ BioSequences = "2"
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GenomicFeatures = "2"
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Indexes = "0.1"
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TranscodingStreams = "0.6, 0.7, 0.8, 0.9"
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julia = "1.1"
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julia = "1"
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[extras]
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FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"
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13
README.md
13
README.md
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@ -11,18 +11,11 @@
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blog post").
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## Description
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XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
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The XAM package provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
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## Installation
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The latest version of XAM is made available to install through BioJulia's package registry.
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By default, Julia's package manager only includes the "General" package registry.
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To add the BioJulia registry from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/), press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
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```julia
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registry add https://github.com/BioJulia/BioJuliaRegistry.git
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```
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Once the registry is added to your configuration, you can install XAM while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following:
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You can install the XAM package from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
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Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
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```julia
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add XAM
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```
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@ -1,3 +0,0 @@
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using Pkg.Registry
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Registry.add(Registry.RegistrySpec(url = "https://github.com/BioJulia/BioJuliaRegistry.git"))
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Registry.add(Registry.RegistrySpec(url = "https://github.com/JuliaRegistries/General.git"))
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@ -1,2 +0,0 @@
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[deps]
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Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"
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@ -1,11 +0,0 @@
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get(ENV, "TRAVIS_OS_NAME", "") == "linux" || exit()
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get(ENV, "TRAVIS_JULIA_VERSION", "") == "1.3" || exit()
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using Pkg
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Pkg.instantiate()
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using Coverage
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cd(joinpath(@__DIR__, "..")) do
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Codecov.submit(Codecov.process_folder())
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end
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@ -10,20 +10,11 @@
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> This project follows the [semver](http://semver.org) pro forma and uses the [git-flow branching model](https://nvie.com/posts/a-successful-git-branching-model/).
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## Description
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XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
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The XAM package provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
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## Installation
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The latest version of XAM is made available to install through BioJulia's package registry.
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By default, Julia's package manager only includes the "General" package registry.
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To add the BioJulia registry from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/), press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
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```julia
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registry add https://github.com/BioJulia/BioJuliaRegistry.git
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```
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Once the registry is added to your configuration, you can install XAM while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following:
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You can install the XAM package from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
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Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
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```julia
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add XAM
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```
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