Repository: sdsc-ordes/modos-api
Pull request #121: feat(deploy): setup refget service
Author: login: almutlue
Labels: name: enhancement
description: New feature or request
Created: 2025-03-10T12:56:34Z | Merged: 2025-03-20T13:14:02Z

### Aim: 
Deploy [refget](https://samtools.github.io/hts-specs/refget.html) service to give hash-identifier based access to reference sequences as part of modos deployment

### Changes:

#### Deployment:
- add a new public bucket (genome-references) to minio deployment
- deploy [refget-cloud](https://github.com/ga4gh/refget-cloud) with the genome-references bucket as source

#### Python api
- generate sequence hashes via [gtars](https://github.com/databio/gtars)
- build minimal metadata object as described in refget specs
- upload reference sequences, their metadata objects and alternative ids to s3 bucket with required `Content-Type` and `website-rdirect-location` header (see [refget-cloud s3 docs](https://github.com/ga4gh/refget-cloud/blob/master/docs/guides/DataSourceAwsS3.md); this replaces refget-compliant sequence upload via [refget-loader](https://github.com/ga4gh/refget-loader/blob/master/ga4gh/refget/loader/destinations/aws/s3/upload.py) in ga4gh pipeline)

### Testing
To test the refget deployment a reference genome can be uploaded as fasta file via:
```python
from modos.genomics.refget import RefgetStorage
from modos.storage import connect_s3
import modos.remote as remo


s3_opts = {"anon": True}
em=remo.EndpointManager(modos="http://localhost")

fasta_file="data/reference1.fa"
fs = connect_s3(em.s3, s3_opts)

rg = RefgetStorage(fs, bucket="genome-references")
rg.upload_fasta(fasta_file)
```

### Limitations
- currently the metadata object only fulfills minimal metadata requirements. This might needs to be expanded or become more flexible, when we want to be refget v.2.0.0 compliant (see next point).  
- [refget-cloud](https://github.com/ga4gh/refget-cloud) is based on refget v.1.0.0. Here, we already use `md5-checksums` as primary id and `ga4gh identifier` instead of `TRUNC512` as the default SHA-512 based hash identifier. This means this implementations is not fully compliant with neither v1.0.0 nor v2.0.0. 
Overall changes seem relatively small (mostly the use of namespaced identifiers; see [refget-appendix](https://samtools.github.io/hts-specs/refget.html#appendix-2---changes)). I would propose to make a PR to make refget-cloud v.2.0.0 compliant to solve this issue.
- [out-of-scope, priority] integration with `modos-api` and `modos-schema:ReferenceGenome` is not part of this PR. Comments on its design can be made on https://github.com/sdsc-ordes/modos-api/issues/120 
- [out-of-scope, low priority] in contrast to refget-loader we only support refget-server compliant sequence upload, but no automatic download from ENA as imlemented via [ena-processor](https://github.com/andrewyatz/ena-refget-processor). We could provide something similar in a later PR, if this really is a useful?


Diff:
diff --git a/deploy/.example.env b/deploy/.example.env
index 287a3e3c..41cb9ca1 100644
--- a/deploy/.example.env
+++ b/deploy/.example.env
@@ -4,7 +4,8 @@ MINIO_ROOT_PASSWORD="minio123"
 MINIO_SERVER_ACCESS_KEY="user"
 MINIO_SERVER_SECRET_KEY="pass"
 S3_BUCKET=modos-demo
-MINIO_DEFAULT_BUCKET="${S3_BUCKET}:public"
+REFERENCE_BUCKET=reference-genomes
+MINIO_DEFAULT_BUCKET="${S3_BUCKET}:public,${REFERENCE_BUCKET}:public"
 # defines s3 url format (host/bucket vs bucket.host)
 S3_ADDRESSING_STYLE="auto" # one of auto, path, virtual
 
@@ -16,3 +17,4 @@ HTSGET_DATA_DIR="/data"
 # S3_PUBLIC_URL="${URL_PREFIX}/s3"
 # FUZON_PUBLIC_URL="${URL_PREFIX}/fuzon"
 # HTSGET_PUBLIC_URL="${URL_PREFIX}/htsget"
+# REFGET_PUBLIC_URL="${URL_PREFIX}/refget"
diff --git a/deploy/README.md b/deploy/README.md
index 3c388581..4888f503 100644
--- a/deploy/README.md
+++ b/deploy/README.md
@@ -13,9 +13,10 @@ The modos-server is meant to provide remote access to the MODOs. Currently, it c
 - [x] return their metadata
 - [x] expose a MODO directly as a client-accessible S3 bucket / folder
 - [x] stream CRAM slices using htsget
+- [x] give hash-based access to reference sequences using refget
 - [ ] manage authentication and access control
 
-The MODOs are stored in an s3 (minio) bucket, and an htsget server is deployed alongside the modos-server to handle slicing and streaming of CRAM files. A REST API is exposed to the client to interact with the remote MODOs.
+The MODOs are stored in an s3 (minio) bucket, and an htsget server is deployed alongside the modos-server to handle slicing and streaming of CRAM files. A REST API is exposed to the client to interact with the remote MODOs. Reference sequences are stored in another s3 bucket. Access is managed by a refget server.
 
 All services are accessible at a single access point through an nginx reverse proxy on port 80.
 
@@ -26,14 +27,18 @@ subgraph " "
   Vnginxdefaultconftemplate{{./nginx/default.conf.template}} -. "/etc/nginx/templates/default.conf.template" .-x nginx
   Vminiodata([minio-data]) x-. /bitnami/minio/data .-x minio
   Vminiodata x-. /data/s3 .-x htsget
+  Vminioreferences([minio-references]) x-. /bitnami/minio/references .-x minio
+  Vminioreferences x-. /references/s3 .-x refget
+  
   P1((9001)) -.-> minio
   nginx -.- modonetwork[/modos-network/]
   minio -.- modonetwork
   htsget -.- modonetwork
+  refget -.- modonetwork
   modoserver[modos-server] -.- modonetwork
 
   classDef volumes fill:#fdfae4,stroke:#867a22
-  class Vnginxdefaultconftemplate,Vminiodata,Vminiodata volumes
+  class Vnginxdefaultconftemplate,Vminiodata,Vminiodata,Vminioreferences, volumes
   classDef ports fill:#f8f8f8,stroke:#ccc
   class P0,P1 ports
   classDef nets fill:#fbfff7,stroke:#8bc34a
@@ -63,6 +68,7 @@ make deploy
 Once the server is started, a client can connect to the following endpoints:
 
 - `http://localhost:80/htsget`: directly access the htsget server
+- `http://localhost:80/refget`: directly access the refget server
 - `http://localhost:80/s3`: directly access the s3 server
 - `http://localhost:80/list`: list modos on the server
 - `http://localhost:80/meta`: return all metadata on the server
@@ -81,9 +87,9 @@ docker compose up --build
 
 In the `.env` file, each service has a `<service>_PUBLIC_URL` and a `<service>_LOCAL_URL` variable. The public URL is the address used by external clients, whereas LOCAL_URL is the address used by other services. For services deployed as part of the compose setup, the local address is `http://<service-name>:<service-port>` and the public address is the endpoint exposed by the nginx reverse proxy, typically `http://<server-host>/<service-name>`. If a service is deployed outside the compose, e.g. an external s3 bucket, the public and local address will both be pointing to the external address.
 
-### Streaming with minio
+### Streaming and requesting reference sequences with minio
 
-There are two options to use htsget streaming with the minio embedded in the compose setup:
+There are two options to let the htsget and refget servers talk to the minio embedded in the compose setup:
 
 1. Set `S3_PUBLIC_URL=http://<LOCAL-IP>:9000` where `<LOCAL-IP>` is your local IP address (find it using hostname -I). **This is done automatically when starting the server with `make deploy`**.
 
@@ -94,4 +100,4 @@ There are two options to use htsget streaming with the minio embedded in the com
 These steps are not needed when using an external S3 server, in which case `S3_PUBLIC_URL` can just be set to the external S3 endpoint.
 
 > [!NOTE]
-> These steps are needed because the S3 host must be available under the same name to both the client and htsget. This is because the canonical URI (incl. hostname) is used to [derive s3 signature keys](https://docs.aws.amazon.com/IAM/latest/UserGuide/create-signed-request.html).
+> These steps are needed because the S3 host must be available under the same name to both the client and htsget/refget. This is because the canonical URI (incl. hostname) is used to [derive s3 signature keys](https://docs.aws.amazon.com/IAM/latest/UserGuide/create-signed-request.html).
diff --git a/deploy/docker-compose.yml b/deploy/docker-compose.yml
index 1d4594ae..d7260358 100644
--- a/deploy/docker-compose.yml
+++ b/deploy/docker-compose.yml
@@ -15,10 +15,12 @@ services:
     volumes:
       - ./nginx/default.conf.template:/etc/nginx/templates/default.conf.template:ro
     environment:
+      - REFGET_PUBLIC_URL=${REFGET_PUBLIC_URL:-http://localhost/refget}
       - FUZON_PUBLIC_URL=${FUZON_PUBLIC_URL:-http://localhost/fuzon}
       - HTSGET_PUBLIC_URL=${HTSGET_PUBLIC_URL:-http://localhost/htsget}
-      - S3_PUBLIC_URL=${S3_PUBLIC_URL:-http://localhost/s3/}
+      - S3_PUBLIC_URL=${S3_PUBLIC_URL:-http://localhost/s3}
       - FUZON_LOCAL_URL=${FUZON_LOCAL_URL:-http://fuzon:8080}
+      - REFGET_LOCAL_URL=${REFGET_LOCAL_URL:-http://refget:8080}
       - HTSGET_LOCAL_URL=${HTSGET_LOCAL_URL:-http://htsget:8080}
       - MODOS_LOCAL_URL=${MODOS_LOCAL_URL:-http://modos-server:8000}
       - S3_LOCAL_URL=${S3_LOCAL_URL:-http://minio:9000}
@@ -41,7 +43,7 @@ services:
       - MINIO_ROOT_PASSWORD=${MINIO_ROOT_PASSWORD:-miniosecret}
       - MINIO_SERVER_ACCESS_KEY=${MINIO_SERVER_ACCESS_KEY:-user}
       - MINIO_SERVER_SECRET_KEY=${MINIO_SERVER_SECRET_KEY:-pass}
-      - MINIO_DEFAULT_BUCKETS=${MINIO_DEFAULT_BUCKET:-modos-demo:public}
+      - MINIO_DEFAULT_BUCKETS=${MINIO_DEFAULT_BUCKET:-modos-demo:public,genome-references:public}
       - MINIO_REGION=us-east-1
       - AWS_REQUEST_CHECKSUM_CALCULATION='WHEN_REQUIRED'
 
@@ -58,7 +60,7 @@ services:
     networks:
       - modos-network
     environment:
-      - ENDPOINT=${S3_PUBLIC_URL:-http://minio:9000}
+      - ENDPOINT=${S3_PUBLIC_URL:-http://localhost/s3}
       - BUCKET=${S3_BUCKET:-modos-demo}
       - S3_ADDRESSING_STYLE=${S3_ADDRESSING_STYLE:-auto}
       - AWS_ACCESS_KEY_ID=${MINIO_ROOT_USER:-minio}
@@ -77,6 +79,20 @@ services:
       - modos-network
 
 
+  refget:
+    build: ./refget
+    depends_on:
+        - minio
+    volumes:
+      - ./refget/config.properties.template:/refget/config.properties.template:ro
+    expose:
+      - "8080"
+    networks:
+      - modos-network
+    environment:
+      - ENDPOINT=${S3_PUBLIC_URL:-http://localhost/s3}
+      - BUCKET=${REFERENCE_BUCKET:-reference-genomes}
+
   modos-server:
     build: ./modos-server
     expose:
diff --git a/deploy/nginx/default.conf.template b/deploy/nginx/default.conf.template
index 29b9ae81..62b68c95 100644
--- a/deploy/nginx/default.conf.template
+++ b/deploy/nginx/default.conf.template
@@ -15,7 +15,8 @@ server {
         "status": "success",
         "s3": "${S3_PUBLIC_URL}",
         "htsget": "${HTSGET_PUBLIC_URL}",
-        "fuzon": "${FUZON_PUBLIC_URL}"
+        "fuzon": "${FUZON_PUBLIC_URL}",
+        "refget": "${REFGET_PUBLIC_URL}"
       }' ;
   }
   # S3 bucket service
@@ -47,4 +48,11 @@ server {
     rewrite ^/fuzon/(.*) /$1 break ;
     proxy_pass ${FUZON_LOCAL_URL} ;
   }
+  # reference sequence server
+  location /refget {
+    rewrite ^/refget/(.*) /$1 break ;
+    proxy_pass ${REFGET_LOCAL_URL} ;
+    # Ensure Nginx does not override Content-Type
+    default_type off ;
+  }
 }
diff --git a/deploy/refget/Dockerfile b/deploy/refget/Dockerfile
new file mode 100644
index 00000000..c24351fe
--- /dev/null
+++ b/deploy/refget/Dockerfile
@@ -0,0 +1,23 @@
+FROM python:3.12-slim-bookworm
+
+EXPOSE 8080
+
+# gettext-base is required for envsubst (config templating)
+RUN apt update && apt install -y gettext-base libc6-dev git && apt-get clean
+
+# install uv
+COPY --from=ghcr.io/astral-sh/uv:0.6.3 /uv /uvx /bin/
+
+# install refget-cloud from github
+RUN uv pip install --system "git+https://github.com/ga4gh/refget-cloud/@c39a65acba9818414789f004cced487562012bf0"
+
+ADD . /app
+WORKDIR /app
+
+COPY --chmod=755 docker-entrypoint.sh /
+
+ENTRYPOINT ["/docker-entrypoint.sh"]
+
+CMD ["refget-server", "--properties-file", "/refget/config.properties"]
+
+### TODO: Enable open-api swagger deployment
diff --git a/deploy/refget/config.properties.template b/deploy/refget/config.properties.template
new file mode 100644
index 00000000..1804fb77
--- /dev/null
+++ b/deploy/refget/config.properties.template
@@ -0,0 +1,4 @@
+source.base_url=${ENDPOINT}/${BUCKET}
+source.sequence_path=/sequence/{seqid}
+source.metadata_path=/metadata/json/{seqid}.json
+server.port=8080
diff --git a/deploy/refget/docker-entrypoint.sh b/deploy/refget/docker-entrypoint.sh
new file mode 100644
index 00000000..dec52ca3
--- /dev/null
+++ b/deploy/refget/docker-entrypoint.sh
@@ -0,0 +1,24 @@
+#!/bin/sh
+set -e
+
+# only use entrypoint if running refget-server
+if [ "$1" = "refget-server" ] ; then
+
+  # Templating
+  if [ -e "/refget/config.properties" ]; then
+    echo "Using existing config.properties"
+
+  elif [ -e "/refget/config.properties.template" ]; then
+    echo "Generating config.properties from config.properties.template"
+    envsubst < /refget/config.properties.template > /refget/config.properties
+    cat /refget/config.properties
+    echo "$@"
+
+  else
+    echo "No config.properties or config.properties.template found. Exiting."
+    exit 1
+
+  fi
+fi
+
+exec "$@"
diff --git a/modos/genomics/refget.py b/modos/genomics/refget.py
new file mode 100644
index 00000000..8149ceab
--- /dev/null
+++ b/modos/genomics/refget.py
@@ -0,0 +1,119 @@
+"""refget loader implementation
+
+In the refget specifications each sequence object is associated by a metadata object.
+Metadata provide a json encoded list of all known identifiers and aliases (see [1]_).
+
+Sequence and metadata objects must have content-type header to fulfill the refget specification.
+
+In S3 redirection can be used to enable sequence access via different ids.
+This can be achieved by an empty object with the alternative id as filename and a Website-Redirect-Location header mapping to the sequence location (see [2]_).
+
+
+References
+----------
+
+.. [1] http://samtools.github.io/hts-specs/refget.html
+.. [2] https://github.com/ga4gh/refget-cloud/blob/master/docs/guides/DataSourceAwsS3.md
+
+"""
+import json
+from typing import Dict, Optional
+
+from gtars.digests import digest_fasta, sha512t24u_digest, md5_digest
+from pydantic import ConfigDict
+from pydantic.dataclasses import dataclass
+import pysam
+import s3fs
+
+
+@dataclass(config=ConfigDict(arbitrary_types_allowed=True))
+class RefgetStorage:
+    fs: s3fs.S3FileSystem
+    bucket: str
+
+    # TODO: Restrict checksums to TypedDict?
+    def upload_seq(
+        self,
+        seq: str,
+        primary: str = "md5",
+        checksums: Optional[Dict[str, str]] = None,
+    ):
+        checksums = checksums or calculate_checksums(seq)
+        meta = {**checksums, "length": seq.__len__()}
+
+        # upload primary checksum
+        primary_path = f"sequence/{checksums.get(primary)}"
+        primary_meta_path = f"metadata/json/{checksums.get(primary)}.json"
+        upload_to_s3(
+            fs=self.fs,
+            bucket=self.bucket,
+            key=primary_path,
+            data=seq,
+            headers={"Content-Type": "text/vnd.ga4gh.refget.v1.0.0+plain"},
+        )
+        upload_to_s3(
+            fs=self.fs,
+            bucket=self.bucket,
+            key=primary_meta_path,
+            data=json.dumps(meta),
+            headers={
+                "Content-Type": "application/vnd.ga4gh.refget.v1.0.0+json"
+            },
+        )
+
+        # upload secondary checksums
+        for alias, id in checksums.items():
+            if alias == primary:
+                continue
+            else:
+                secondary_path = f"sequence/{id}"
+                secondary_meta_path = f"metadata/json/{id}.json"
+                upload_to_s3(
+                    fs=self.fs,
+                    bucket=self.bucket,
+                    key=secondary_path,
+                    headers={"Website-Redirect-Location": f"/{primary_path}"},
+                )
+                upload_to_s3(
+                    fs=self.fs,
+                    bucket=self.bucket,
+                    key=secondary_meta_path,
+                    headers={
+                        "Website-Redirect-Location": f"/{primary_meta_path}"
+                    },
+                )
+
+    # NOTE: gtars ^0.2.3 should be able to handle pathlib.Path as input, but pysam expects a str
+    def upload_fasta(self, fasta_file: str):
+        digest = digest_fasta(fasta_file)
+        fasta = pysam.FastaFile(fasta_file)
+        for ref in digest:
+            seq = fasta.fetch(ref.id)
+            checksums = {"md5": ref.md5, "ga4gh": f"SQ.{ref.sha512t24u}"}
+            self.upload_seq(seq, checksums=checksums)
+
+
+def calculate_checksums(seq: str) -> Dict:
+    checksums: Dict = {}
+    checksums["md5"] = md5_digest(seq)
+    checksums["ga4gh"] = "SQ.{}".format(sha512t24u_digest(seq))
+    return checksums
+
+
+def upload_to_s3(
+    fs: s3fs.S3FileSystem,
+    bucket: str,
+    key: str,
+    data: str = "",
+    headers: Optional[Dict[str, str]] = None,
+):
+    s3_path = f"{bucket}/{key}"
+
+    # Setting headers for S3 object
+    s3_metadata = headers if headers else {}
+    file_data = data.encode("utf-8")
+
+    with fs.open(s3_path, "wb", metadata=s3_metadata) as f:
+        f.write(file_data)
+
+    print(f"File uploaded successfully to {s3_path}")
diff --git a/modos/remote.py b/modos/remote.py
index 5e622548..b8332833 100644
--- a/modos/remote.py
+++ b/modos/remote.py
@@ -62,6 +62,10 @@ def fuzon(self) -> Optional[HttpUrl]:
     def htsget(self) -> Optional[HttpUrl]:
         return self.list().get("htsget")
 
+    @property
+    def refget(self) -> Optional[HttpUrl]:
+        return self.list().get("refget")
+
 
 @validate_call
 def list_remote_items(url: HttpUrl) -> list[HttpUrl]:
diff --git a/poetry.lock b/poetry.lock
index fb4bc203..0c8b1864 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -20,128 +20,127 @@ tests = ["hypothesis", "pytest"]
 
 [[package]]
 name = "aiobotocore"
-version = "2.17.0"
+version = "2.21.0"
 description = "Async client for aws services using botocore and aiohttp"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "aiobotocore-2.17.0-py3-none-any.whl", hash = "sha256:aedccd5368a64401233ef9f27983d3d3cb6a507a6ca981f5ec1df014c00e260e"},
-    {file = "aiobotocore-2.17.0.tar.gz", hash = "sha256:a3041333c565bff9d63b4468bee4944f2d81cff63a45b10e5cc652f3837f9cc2"},
+    {file = "aiobotocore-2.21.0-py3-none-any.whl", hash = "sha256:05b4e29690a07913297686d819dc8dac341a5361f14fedf444bdd77ae1e36554"},
+    {file = "aiobotocore-2.21.0.tar.gz", hash = "sha256:03d64a41e313ebce76fd7c3e4c854e560032ac5cf71f4d5072616ca6fb9701b5"},
 ]
 
 [package.dependencies]
 aiohttp = ">=3.9.2,<4.0.0"
 aioitertools = ">=0.5.1,<1.0.0"
-botocore = ">=1.35.74,<1.35.94"
+botocore = ">=1.37.0,<1.37.2"
 jmespath = ">=0.7.1,<2.0.0"
 multidict = ">=6.0.0,<7.0.0"
 python-dateutil = ">=2.1,<3.0.0"
-urllib3 = {version = ">=1.25.4,<2.2.0 || >2.2.0,<3", markers = "python_version >= \"3.10\""}
 wrapt = ">=1.10.10,<2.0.0"
 
 [package.extras]
-awscli = ["awscli (>=1.36.15,<1.36.35)"]
-boto3 = ["boto3 (>=1.35.74,<1.35.94)"]
+awscli = ["awscli (>=1.38.0,<1.38.2)"]
+boto3 = ["boto3 (>=1.37.0,<1.37.2)"]
 
 [[package]]
 name = "aiohappyeyeballs"
-version = "2.4.6"
+version = "2.4.8"
 description = "Happy Eyeballs for asyncio"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "aiohappyeyeballs-2.4.6-py3-none-any.whl", hash = "sha256:147ec992cf873d74f5062644332c539fcd42956dc69453fe5204195e560517e1"},
-    {file = "aiohappyeyeballs-2.4.6.tar.gz", hash = "sha256:9b05052f9042985d32ecbe4b59a77ae19c006a78f1344d7fdad69d28ded3d0b0"},
+    {file = "aiohappyeyeballs-2.4.8-py3-none-any.whl", hash = "sha256:6cac4f5dd6e34a9644e69cf9021ef679e4394f54e58a183056d12009e42ea9e3"},
+    {file = "aiohappyeyeballs-2.4.8.tar.gz", hash = "sha256:19728772cb12263077982d2f55453babd8bec6a052a926cd5c0c42796da8bf62"},
 ]
 
 [[package]]
 name = "aiohttp"
-version = "3.11.12"
+version = "3.11.13"
 description = "Async http client/server framework (asyncio)"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "aiohttp-3.11.12-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:aa8a8caca81c0a3e765f19c6953416c58e2f4cc1b84829af01dd1c771bb2f91f"},
-    {file = "aiohttp-3.11.12-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:84ede78acde96ca57f6cf8ccb8a13fbaf569f6011b9a52f870c662d4dc8cd854"},
-    {file = "aiohttp-3.11.12-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:584096938a001378484aa4ee54e05dc79c7b9dd933e271c744a97b3b6f644957"},
-    {file = "aiohttp-3.11.12-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:392432a2dde22b86f70dd4a0e9671a349446c93965f261dbaecfaf28813e5c42"},
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 ]
 
 [package.dependencies]
@@ -386,13 +385,13 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "botocore"
-version = "1.35.93"
+version = "1.37.1"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -401,17 +400,17 @@ python-dateutil = ">=2.1,<3.0.0"
 urllib3 = {version = ">=1.25.4,<2.2.0 || >2.2.0,<3", markers = "python_version >= \"3.10\""}
 
 [package.extras]
-crt = ["awscrt (==0.22.0)"]
+crt = ["awscrt (==0.23.8)"]
 
 [[package]]
 name = "cachetools"
-version = "5.5.1"
+version = "5.5.2"
 description = "Extensible memoizing collections and decorators"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
@@ -738,13 +737,13 @@ toml = ["tomli"]
 
 [[package]]
 name = "curies"
-version = "0.10.4"
+version = "0.10.6"
 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)"
 optional = false
 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -1036,6 +1035,50 @@ test-downstream = ["aiobotocore (>=2.5.4,<3.0.0)", "dask-expr", "dask[dataframe,
 test-full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "cloudpickle", "dask", "distributed", "dropbox", "dropboxdrivefs", "fastparquet", "fusepy", "gcsfs", "jinja2", "kerchunk", "libarchive-c", "lz4", "notebook", "numpy", "ocifs", "pandas", "panel", "paramiko", "pyarrow", "pyarrow (>=1)", "pyftpdlib", "pygit2", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "python-snappy", "requests", "smbprotocol", "tqdm", "urllib3", "zarr", "zstandard"]
 tqdm = ["tqdm"]
 
+[[package]]
+name = "gtars"
+version = "0.2.2"
+description = ""
+optional = false
+python-versions = ">=3.8"
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 [[package]]
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 [[package]]
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+version = "8.3.5"
 description = "pytest: simple powerful testing with Python"
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 [package.dependencies]
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 ]
 
 [[package]]
@@ -3457,4 +3516,4 @@ pyfuzon = ["pyfuzon"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "af1ced8a4df557f3bb0eaff0b6e7e7b51ab0849730cec37670c535064af16557"
+content-hash = "b84df92d4b67eb9c9135497d17f5da70d3ab50799da64ee0ac94f0899ccd8e4f"
diff --git a/pyproject.toml b/pyproject.toml
index 0991e665..f2e2530b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,6 +9,7 @@ packages = [{ include = "modos" }]
 
 [tool.poetry.dependencies]
 calamus = "^0.4.2"
+gtars = "^0.2.2"
 modos_schema = "^0.3"
 pysam = "^0.22.0"
 python = "^3.11"
@@ -18,7 +19,6 @@ s3fs = "^2024.3.1"
 typer = "^0.9.0"
 zarr = "^2.16.1"
 pydantic = "^2.8.2"
-botocore = "<1.36.0"
 
 pyfuzon = { version = "^0.2", optional = true}
 prompt-toolkit = "^3.0.48"


Reviews:
user: login: cmdoret
body: A few minor nitpicks, but this looks like a great start!

One question: all the refget stuff is computed on client side in this implementation, and all server interactions are with s3.

(When) do we need to query the refget server from modos client?

Also tests fail on my side (gonna debug in a bit)
state: COMMENTED
author_association: MEMBER
submitted_at: 2025-03-13T09:24:20Z
user: login: cmdoret
body: :zap: :dna: :zap: 
state: APPROVED
author_association: MEMBER
submitted_at: 2025-03-18T18:24:00Z

Review comments:
diff_hunk: @@ -4,7 +4,8 @@ MINIO_ROOT_PASSWORD="minio123"
 MINIO_SERVER_ACCESS_KEY="user"
 MINIO_SERVER_SECRET_KEY="pass"
 S3_BUCKET=modos-demo
-MINIO_DEFAULT_BUCKET="${S3_BUCKET}:public"
+REFERENCE_BUCKET=genome-references
path: deploy/.example.env
user: login: cmdoret
body: ```suggestion
REFERENCE_BUCKET=reference-genomes
```
**suggestion(non-blocking):** sounds like a more intuitive name to me
created_at: 2025-03-13T08:13:37Z
author_association: MEMBER
diff_hunk: @@ -81,9 +87,9 @@ docker compose up --build
 
 In the `.env` file, each service has a `<service>_PUBLIC_URL` and a `<service>_LOCAL_URL` variable. The public URL is the address used by external clients, whereas LOCAL_URL is the address used by other services. For services deployed as part of the compose setup, the local address is `http://<service-name>:<service-port>` and the public address is the endpoint exposed by the nginx reverse proxy, typically `http://<server-host>/<service-name>`. If a service is deployed outside the compose, e.g. an external s3 bucket, the public and local address will both be pointing to the external address.
 
-### Streaming with minio
+### Streaming and requesting reference sequences with minio
 
-There are two options to use htsget streaming with the minio embedded in the compose setup:
+There are two options to use htsget streaming or request a reference sequence with the minio embedded in the compose setup:
path: deploy/README.md
user: login: cmdoret
body: ```suggestion
There are two options to let the htsget and refget servers talk to the minio embedded in the compose setup:
```
**suggestion(non-blocking):** rephrase for deployment (not stream consumer).
created_at: 2025-03-13T08:53:07Z
author_association: MEMBER
diff_hunk: @@ -0,0 +1,23 @@
+FROM python:3.12-slim-bookworm
+
+EXPOSE 8080
+
+# gettext-base is required for envsubst (config templating)
+RUN apt update && apt install -y gettext-base libc6-dev git && apt-get clean
+
+# install uv
+COPY --from=ghcr.io/astral-sh/uv:0.6.3 /uv /uvx /bin/
+
+# install refget-cloud from github
+RUN uv pip install --system "git+https://github.com/ga4gh/refget-cloud/@c39a65acba9818414789f004cced487562012bf0"
path: deploy/refget/Dockerfile
user: login: cmdoret
body: **praise:** nice and secure :sunglasses: 
created_at: 2025-03-13T09:11:05Z
author_association: MEMBER
diff_hunk: @@ -77,6 +79,20 @@ services:
       - modos-network
 
 
+  refget:
+    build: ./refget
+    depends_on:
+        - minio
+    volumes:
+      - ./refget/config.properties.template:/refget/config.properties.template:ro
+    expose:
+      - "8080"
+    networks:
+      - modos-network
+    environment:
+      - ENDPOINT=${S3_PUBLIC_URL:-http://localhost/s3}
+      - BUCKET=${REFERENCE_BUCKET:-genome-references}
path: deploy/docker-compose.yml
user: login: cmdoret
body: ```suggestion
      - BUCKET=${REFERENCE_BUCKET:-reference-genomes}
```
**suggestion(non-blocking):** in case bucket renaming was applied above.
created_at: 2025-03-13T09:16:26Z
author_association: MEMBER

PR comments:
user: login: almutlue
created_at: 2025-03-17T10:21:53Z
body: Thanks a lot for the review and comments @cmdoret!
IIUC we might need/want a way to list all existing reference genomes and check if a reference sequence already exists (by hash comparison?) or did you refer to something else? 
author_association: CONTRIBUTOR
user: login: cmdoret
created_at: 2025-03-18T18:22:27Z
body: I was just surprised by the absence of interaction between the modos client and the refget server, but this is indeed not yet needed.

This discussion is probably for another PR, but here are the flows as I understand them:

* modos client uploads new reference (client -> s3)
  1. sequences+digests computed locally and uploaded to reference bucket (if not already present)
  2. ReferenceGenome+ReferenceSequence json uploaded to modos bucket
    +  json links to reference sequence uri via `ReferenceSequence->data_path`
* client or other software (e.g. samtools) reads cram file (client -> refget ->s3, client ->s3)
  1. cram file header contains link to our refget sequence uri
  2. samtools queries this uri
  4. refget server crafts s3 request from uri and returns it
  5. samtools queries crafted s3 request

Maybe at some point we want to provide the option to materialize or even stream a fasta file. In that case, there would indeed be direct interaction between client and refget.
author_association: MEMBER