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

Provided by: libhts3t64_1.19+ds-1.1build3_amd64

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