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/>