Ubuntu Manpage: htslib-s3-plugin - htslib AWS S3 plugin

NAME

       htslib-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, addressing_style and expiry_time (unofficial, see SHORT-LIVED CREDENTIALS
below). 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.

SHORT-LIVED CREDENTIALS

       Some cloud identity and access management (IAM) systems  can  make  short-lived  credentials  that  allow
       access to resources.  These credentials will expire after a time and need to be renewed to give continued
       access.  To enable this, the S3 plugin allows an expiry_time entry to  be  set  in  the  .aws/credentials
       file.   The  value  for  this  entry  should  be the time when the token expires, following the format in
       RFC3339 section 5.6, which takes the form:

          2012-04-29T05:20:48Z

       That is, year - month - day, the letter "T", hour : minute : second.  The time can  be  followed  by  the
       letter "Z", indicating the UTC timezone, or an offset from UTC which is a "+" or "-" sign followed by two
       digits for the hours offset, ":", and two digits for the minutes.

       The S3 plugin will attempt to re-read the credentials file up to 1 minute before the given  expiry  time,
       which  means  the  file  needs to be updated with new credentials before then.  As the exact way of doing
       this can vary between services and IAM providers, the S3 plugin expects this to be done  by  an  external
       user-supplied  process.   This  may  be  achieved  by  running  a  program  that replaces the file as new
       credentials become available.  The following  script  shows  how  it  might  be  done  for  AWS  instance
       credentials:

         #!/bin/sh
         instance='http://169.254.169.254'
         tok_url="$instance/latest/api/token"
         ttl_hdr='X-aws-ec2-metadata-token-ttl-seconds: 10'
         creds_url="$instance/latest/meta-data/iam/security-credentials"
         key1='aws_access_key_id = \(.AccessKeyId)\n'
         key2='aws_secret_access_key = \(.SecretAccessKey)\n'
         key3='aws_session_token = \(.Token)\n'
         key4='expiry_time = \(.Expiration)\n'
         while true; do
             token=`curl -X PUT -H "$ttl_hdr" "$tok_url"`
             tok_hdr="X-aws-ec2-metadata-token: $token"
             role=`curl -H "$tok_hdr" "$creds_url/"`
             expires='now'
             ( curl -H "$tok_hdr" "$creds_url/$role" \
               | jq -r "\"${key1}${key2}${key3}${key4}\"" > credentials.new ) \
               && mv -f credentials.new credentials \
               && expires=`grep expiry_time credentials | cut -d ' ' -f 3-`
             if test $? -ne 0 ; then break ; fi
             expiry=`date -d "$expires - 3 minutes" '+%s'`
             now=`date '+%s'`
             test "$expiry" -gt "$now" && sleep $((($expiry - $now) / 2))
             sleep 30
         done

       Note  that  the  expiry_time  key  is currently only supported for the .aws/credentials file (or the file
       referred to in the AWS_SHARED_CREDENTIALS_FILE environment variable).

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.

NAME

DESCRIPTION

SHORT-LIVED CREDENTIALS

NOTES

SEE ALSO