In dialog 'Cygwin Setup - Choose Installation Directory' you should select root directory in wich CygWin has been installed & press Next, and again, and again & again. Your will see dialog 'Cygwin Setup - Select Package', in the 'View' combobox you should select 'Full', and in the 'Search' edit you should enter 'gcc'. The Mac instructions as a guide. Download cygwin.zip and extract the contents onto your portable drive or hard-disk. You are advised to extract to the root directory of a drive (e.g. Navigate to your drive and/or folder where the files were extracted, and you will see three files. Cygwin This folder contains all the necessary files. Download Installation Files. We will download installation files from Cygwin site. This is the long-standing method where you download a precompiled version of NCL from a list of binaries that are available for various MacOS and Linux systems. Cygwin binaries are no longer available. Downloading the NCL source code and building it yourself. This is the most difficult method.
Current releases
SAMtools and BCFtools are distributed as individual packages.The code uses HTSlib internally, but these source packages contain their owncopies of htslib so they can be built independently.
HTSlib is also distributed as a separate package which can be installedif you are writing your own programs against the HTSlib API.HTSlib also provides the bgzip, htsfile, and tabix utilities,so you may also want to build and install HTSlib to get these utilities,or see the additional instructions in
INSTALL
to install them from asamtools or bcftools source package.This is the long-standing method where you download a precompiled version of NCL from a list of binaries that are available for various MacOS and Linux systems. Cygwin binaries are no longer available. Downloading the NCL source code and building it yourself. This is the most difficult method.
Download current source releases: samtools-1.11 bcftools-1.11 htslib-1.11
See also release notes forsamtools,bcftools,and htslib.
New releases are announced on the samtools mailing lists and by @htslibon Twitter.Previous releases are available from thesamtools GitHub organisation(see samtools,bcftools,or htslib releases)or from thesamtools Sourceforge project.
Building and installing
Building each desired package from source is very simple:
See
INSTALL
in each of the source directories for further details.The executable programs will be installed to a
bin
subdirectory underyour specified prefix, so you may wish to add this directory to your $PATH:Historical SAMtools/BCFtools 0.1.x releases
Prior to the introduction of HTSlib, SAMtools and BCFtools were distributedin a single samtools-0.1.x package.These old versions remain available from the Sourceforge samtools project.
Alpine
On Alpine Linux (3.6+), you can install Yarn with apk.
Currently, there are no Alpine packages available for RC or nightly builds of Yarn. Please use the tarball:
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Installation Script
One of the easiest ways to install Yarn on macOS and generic Unix environmentsis via our shell script. You can install Yarn by running the following code inyour terminal:
The installation process includes verifying a GPG signature.View the source on GitHub
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You can also specify a version by running the following code in your terminal:
See the releases for possible versions.
Manual Install via tarball
You can install Yarn by downloading a tarball andextracting it anywhere.
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Before extracting Yarn, it is recommended that you verify the tarball using GPG:
Path Setup
If Yarn is not found in your PATH, follow these steps to add it and allow it to be run from anywhere.
Note: your profile may be in your
.profile
, .bash_profile
, .bashrc
, .zshrc
, etc.- Add this to your profile:
export PATH='$PATH:/opt/yarn-[version]/bin'
(the path may vary depending on where you extracted Yarn to) - In the terminal, log in and log out for the changes to take effect
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To have access to Yarn’s executables globally, you will need to set up the
PATH
environment variable in your terminal. To do this, add export PATH='$PATH:`yarn global bin`'
to your profile, or if you use Fish shell, simply run the command set -U fish_user_paths (yarn global bin) $fish_user_paths