NAME

       s3 plugin - htslib AWS S3 plugin

DESCRIPTION

       The  S3  plugin  allows  htslib  file functions to communicate with servers that use the AWS S3 protocol.
       Files are identified by their bucket and object key in a URL format e.g.

       s3://mybucket/path/to/file

       With path/to/file being the object key.

       Necessary security information can be provided in as part of the URL, in environment  variables  or  from
       configuration files.

       The full URL format is:

       s3[+SCHEME]://[ID[:SECRET[:TOKEN]]@]BUCKET/PATH

       The elements are:

       SCHEME The protocol used.  Defaults to https.

       ID     The user AWS access key.

       SECRET The secret key for use with the access key.

       TOKEN  Token used for temporary security credentials.

       BUCKET AWS S3 bucket.

       PATH   Path to the object under the bucket.

       The environment variables below will be used if the user ID is not set.

       AWS_ACCESS_KEY_ID
              The user AWS access key.

       AWS_SECRET_ACCESS_KEY
              The secret key for use with the access key.

       AWS_DEFAULT_REGION
              The region to use. Defaults to us-east-1.

       AWS_SESSION_TOKEN
              Token used for temporary security credentials.

       AWS_DEFAULT_PROFILE
              The profile to use in credentials, config or s3cfg files.  Defaults to default.

       AWS_PROFILE
              Same as above.

       AWS_SHARED_CREDENTIALS_FILE
              Location of the credentials file.  Defaults to ~/.aws/credentials.

       HTS_S3_S3CFG
              Location of the s3cfg file.  Defaults to ~/.s3cfg.

       HTS_S3_HOST
              Sets the host.  Defaults to s3.amazonaws.com.

       HTS_S3_V2
              If set use signature v2 rather the default v4.  This will limit the plugin to reading only.

       HTS_S3_PART_SIZE
              Sets  the  upload  part size in Mb, the minimum being 5Mb.  By default the part size starts at 5Mb
              and expands at regular intervals to accommodate bigger files (up to 2.5 Tbytes  with  the  current
              rate).  Using this setting disables the automatic part size expansion.

       HTS_S3_ADDRESS_STYLE
              Sets the URL style.  Options are auto (default), virtual or path.

       In  the  absence  of  an  ID from the previous two methods the credential/config files will be used.  The
       default file locations are either ~/.aws/credentials or ~/.s3cfg (in that order).

       Entries  used   in   aws   style   credentials   file   are   aws_access_key_id,   aws_secret_access_key,
       aws_session_token, region and addressing_style.  Only the first two are usually needed.

       Entries   used  in  s3cmd  style  config  files  are  access_key,  secret_key,  access_token,  host_base,
       bucket_location and host_bucket. Again only the first two are usually needed. The host_bucket  option  is
       only used to set a path-style URL, see below.

NOTES

       In   most   cases   this  plugin  transforms  the  given  URL  into  a  virtual  host-style  format  e.g.
       https://bucket.host/path/to/file.  A path-style format is used where the URL is not DNS compliant or  the
       bucket name contains a dot e.g.  https://host/bu.cket/path/to/file.

       Path-style  can  be  forced  by setting one either HTS_S3_ADDRESS_STYLE, addressing_style or host_bucket.
       The first two can be set to path while host_bucket must not include the %(bucket).s string.

SEE ALSO

       htsfile(1) samtools(1)

       htslib website: <http://www.htslib.org/>

htslib-1.13                                        7 July 2021                               htslib-s3-plugin(7)