From 25b71aa32e0cacca8c8b1ce1bdcab9c89de92e79 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 22 Jul 2026 17:01:30 +0200 Subject: [PATCH 1/2] Add data_manager_repeatmasker Downloads a Dfam repeat library in the partitioned FamDB (v3) format and registers it in the new repeatmasker_famdb data table, so RepeatMasker (>= 4.2.4) can screen sequences against a real library instead of the empty placeholder shipped in the RepeatMasker Conda package. The root partition is always fetched; curated/uncurated consensus and HMM components are selectable. Each file is md5-verified against its Dfam sidecar and decompressed into a single -libdir directory. Partition counts are discovered by probing rather than hard-coded per release. --- .../data_manager_repeatmasker/.shed.yml | 14 ++ .../data_manager_repeatmasker/README.md | 35 ++++ .../data_manager/repeatmasker_download.py | 190 ++++++++++++++++++ .../data_manager/repeatmasker_download.xml | 77 +++++++ .../data_manager_conf.xml | 19 ++ .../test-data/repeatmasker_famdb.loc | 1 + .../tool-data/repeatmasker_famdb.loc.sample | 14 ++ .../tool_data_table_conf.xml.sample | 8 + .../tool_data_table_conf.xml.test | 8 + 9 files changed, 366 insertions(+) create mode 100644 data_managers/data_manager_repeatmasker/.shed.yml create mode 100644 data_managers/data_manager_repeatmasker/README.md create mode 100644 data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.py create mode 100644 data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.xml create mode 100644 data_managers/data_manager_repeatmasker/data_manager_conf.xml create mode 100644 data_managers/data_manager_repeatmasker/test-data/repeatmasker_famdb.loc create mode 100644 data_managers/data_manager_repeatmasker/tool-data/repeatmasker_famdb.loc.sample create mode 100644 data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.sample create mode 100644 data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.test diff --git a/data_managers/data_manager_repeatmasker/.shed.yml b/data_managers/data_manager_repeatmasker/.shed.yml new file mode 100644 index 00000000000..e01fa85511d --- /dev/null +++ b/data_managers/data_manager_repeatmasker/.shed.yml @@ -0,0 +1,14 @@ +categories: +- Data Managers +description: Download Dfam FamDB libraries for RepeatMasker +homepage_url: https://www.dfam.org/ +long_description: | + Downloads a Dfam repeat library in the partitioned FamDB (v3) format and + registers it in the repeatmasker_famdb data table, so RepeatMasker (>= 4.2.4) + can screen sequences against a real library instead of the empty placeholder + shipped in the RepeatMasker Conda package. The root partition is always + downloaded; curated/uncurated consensus and HMM components are selectable. +owner: iuc +name: data_manager_repeatmasker +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_repeatmasker +type: unrestricted diff --git a/data_managers/data_manager_repeatmasker/README.md b/data_managers/data_manager_repeatmasker/README.md new file mode 100644 index 00000000000..0ea1033dfd8 --- /dev/null +++ b/data_managers/data_manager_repeatmasker/README.md @@ -0,0 +1,35 @@ +# RepeatMasker Dfam library data manager + +This data manager downloads a [Dfam](https://www.dfam.org/) repeat library in +the partitioned FamDB (v3) format and registers it in the `repeatmasker_famdb` +tool data table for use by the RepeatMasker Galaxy tool (RepeatMasker >= 4.2.4). + +## Why this is needed + +The RepeatMasker Conda package no longer ships a populated repeat library: the +`Dfam.h5` bundled in the package is a placeholder, and running RepeatMasker +against it fails with `Species "..." is not known to RepeatMasker` because the +library contains no families. The library must be downloaded separately; this +data manager automates that and makes the result available through a data table. + +## What it downloads + +Dfam distributes its library as a required **root** partition plus optional +**component** partitions, split by curation status (curated/uncurated) and model +type (consensus sequences for the rmblast engine, profile HMMs for nhmmer): + +| Component | Engine | Notes | +|-----------|--------|-------| +| Curated consensus | rmblast | Recommended default | +| Uncurated consensus | rmblast | Very large | +| Curated HMM | nhmmer | | +| Uncurated HMM | nhmmer | Very large (100+ partitions) | + +The root partition is always downloaded. Each file is verified against its Dfam +md5 checksum, decompressed, and placed in a single directory that RepeatMasker +consumes via `-libdir`. + +## Data table + +`repeatmasker_famdb` with columns `value, name, version, path`, where `path` +points at the directory holding the FamDB `.h5` partition files. diff --git a/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.py b/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.py new file mode 100644 index 00000000000..b6770716644 --- /dev/null +++ b/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.py @@ -0,0 +1,190 @@ +#!/usr/bin/env python +"""Download a Dfam FamDB library for RepeatMasker and register it in a data table. + +Dfam distributes its libraries in the partitioned FamDB (v3) format: a single +required *root* partition plus one file per *component* partition. The +components are split by curation status (curated/uncurated) and model type +(consensus sequences, used by the rmblast search engine, or profile HMMs, used +by nhmmer). This data manager downloads the root partition (always) together +with whichever components the admin selects, laying the ``*.h5`` files out in a +single directory that RepeatMasker (>= 4.2.4) can consume via ``-libdir``. + +See https://www.dfam.org/releases/current/families/FamDB/README.txt +""" + +import argparse +import gzip +import hashlib +import json +import os +import shutil +import sys +from datetime import date +from urllib.error import HTTPError +from urllib.request import Request, urlopen + +# Map a Dfam release to its release directory and FamDB file-name prefix. +# Adding a new release is a one-line change here (the file layout is stable). +RELEASES = { + "4.0": {"dir": "Dfam_4.0", "prefix": "dfam40"}, + "3.9": {"dir": "Dfam_3.9", "prefix": "dfam39"}, + "3.8": {"dir": "Dfam_3.8", "prefix": "dfam38"}, +} + +BASE_URL = "https://www.dfam.org/releases/{dir}/families/FamDB/" + +# component key -> FamDB file-name infix +COMPONENTS = { + "curated_consensus": "curated.consensus", + "uncurated_consensus": "uncurated.consensus", + "curated_hmm": "curated.hmm", + "uncurated_hmm": "uncurated.hmm", +} + +# A tiny (~0.3 MB) real partition used to exercise the full download / gunzip / +# checksum / registration path quickly during automated testing. +TEST_COMPONENT = "uncurated_consensus" +CHUNK = 2 ** 16 + + +def url_exists(url): + """Return True if a HEAD-like GET on url succeeds with status < 400.""" + try: + return urlopen(Request(url)).getcode() < 400 + except HTTPError: + return False + + +def fetch_md5(url): + """Return the expected md5 hex digest from Dfam's ``.md5`` sidecar.""" + with urlopen(Request(url + ".md5")) as response: + # sidecar format: " " + return response.read().decode().split()[0] + + +def download_and_extract(url, target_directory): + """Download a gzipped ``.h5.gz`` partition, verify its md5, gunzip it. + + The uncompressed ``.h5`` file is written into ``target_directory`` and the + compressed download is removed. Raises on a checksum mismatch so a + truncated or corrupted download never registers as a usable library. + """ + gz_name = url.rsplit("/", 1)[1] + gz_path = os.path.join(target_directory, gz_name) + h5_path = os.path.join(target_directory, gz_name[: -len(".gz")]) + + expected_md5 = fetch_md5(url) + md5 = hashlib.md5() + with urlopen(Request(url)) as src, open(gz_path, "wb") as dst: + while True: + chunk = src.read(CHUNK) + if not chunk: + break + md5.update(chunk) + dst.write(chunk) + if md5.hexdigest() != expected_md5: + sys.exit( + "Checksum mismatch for {}: expected {}, got {}".format( + gz_name, expected_md5, md5.hexdigest() + ) + ) + + with gzip.open(gz_path, "rb") as f_in, open(h5_path, "wb") as f_out: + shutil.copyfileobj(f_in, f_out, CHUNK) + os.remove(gz_path) + return os.path.basename(h5_path) + + +def iter_partition_urls(base_url, prefix, infix): + """Yield partition URLs for a component, probing 0,1,2,... until one is absent. + + Dfam numbers component partitions contiguously from 0, so the first missing + index marks the end. This adapts automatically to how many partitions a + component has in a given release instead of hard-coding per-release counts. + """ + part = 0 + while True: + url = "{}{}.{}.{}.h5.gz".format(base_url, prefix, infix, part) + if not url_exists(url): + break + yield url + part += 1 + + +def download(release, components, test, out_file): + if release not in RELEASES: + sys.exit( + "Unknown Dfam release '{}'. Known releases: {}".format( + release, ", ".join(sorted(RELEASES)) + ) + ) + rel = RELEASES[release] + base_url = BASE_URL.format(dir=rel["dir"]) + prefix = rel["prefix"] + + with open(out_file) as fh: + params = json.load(fh) + target_directory = params["output_data"][0]["extra_files_path"] + os.makedirs(target_directory) + + if test: + # Exercise the real code path cheaply: fetch only the smallest partition + # of a single component, and skip the large root/curated downloads. + components = [TEST_COMPONENT] + infix = COMPONENTS[TEST_COMPONENT] + installed = [ + download_and_extract( + "{}{}.{}.0.h5.gz".format(base_url, prefix, infix), target_directory + ) + ] + else: + # The root partition is always required. + installed = [ + download_and_extract( + "{}{}.0.h5.gz".format(base_url, prefix), target_directory + ) + ] + for component in components: + infix = COMPONENTS[component] + for url in iter_partition_urls(base_url, prefix, infix): + installed.append(download_and_extract(url, target_directory)) + + today = date.today().strftime("%Y-%m-%d") + selected = "+".join(components) if components else "root" + entry = { + "value": "dfam_{}_{}_{}".format(release, selected, today).replace(".", "_"), + "name": "Dfam {} ({}) [{}]".format(release, ", ".join(components) or "root only", today), + "version": release, + "path": target_directory, + } + data_manager_json = {"data_tables": {"repeatmasker_famdb": [entry]}} + + sys.stderr.write( + "Installed {} FamDB partition file(s) into {}\n".format( + len(installed), target_directory + ) + ) + with open(out_file, "w") as fh: + json.dump(data_manager_json, fh, sort_keys=True) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--release", required=True, help="Dfam release, e.g. 4.0") + parser.add_argument( + "--components", + default="", + help="comma-separated component keys to install in addition to the root partition", + ) + parser.add_argument("--out_file", required=True, help="JSON output file") + parser.add_argument( + "--test", action="store_true", help="download only a tiny partition for testing" + ) + args = parser.parse_args() + + components = [c for c in args.components.split(",") if c] + unknown = [c for c in components if c not in COMPONENTS] + if unknown: + sys.exit("Unknown component(s): {}".format(", ".join(unknown))) + + download(args.release, components, args.test, args.out_file) diff --git a/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.xml b/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.xml new file mode 100644 index 00000000000..2770e0c45eb --- /dev/null +++ b/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.xml @@ -0,0 +1,77 @@ + + download a Dfam FamDB library for RepeatMasker + + 4.0 + 0 + 22.01 + + + python + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1186/s13100-020-00230-y + + diff --git a/data_managers/data_manager_repeatmasker/data_manager_conf.xml b/data_managers/data_manager_repeatmasker/data_manager_conf.xml new file mode 100644 index 00000000000..5988064cc71 --- /dev/null +++ b/data_managers/data_manager_repeatmasker/data_manager_conf.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + repeatmasker_famdb/${value} + + ${GALAXY_DATA_MANAGER_DATA_PATH}/repeatmasker_famdb/${value} + abspath + + + + + diff --git a/data_managers/data_manager_repeatmasker/test-data/repeatmasker_famdb.loc b/data_managers/data_manager_repeatmasker/test-data/repeatmasker_famdb.loc new file mode 100644 index 00000000000..dc309ef95a3 --- /dev/null +++ b/data_managers/data_manager_repeatmasker/test-data/repeatmasker_famdb.loc @@ -0,0 +1 @@ +## Populated by the data manager during testing. diff --git a/data_managers/data_manager_repeatmasker/tool-data/repeatmasker_famdb.loc.sample b/data_managers/data_manager_repeatmasker/tool-data/repeatmasker_famdb.loc.sample new file mode 100644 index 00000000000..c6556e78775 --- /dev/null +++ b/data_managers/data_manager_repeatmasker/tool-data/repeatmasker_famdb.loc.sample @@ -0,0 +1,14 @@ +## Dfam FamDB libraries for RepeatMasker, installed by data_manager_repeatmasker +## +## This file lists directories holding a Dfam library in the partitioned FamDB +## (v3) format (a root partition plus selected component partitions). Each such +## directory can be passed to RepeatMasker (>= 4.2.4) via -libdir. +## +## The tab-separated columns are: +## +## +## +## For example: +## +## dfam_4_0_curated_consensus_2026-07-22 Dfam 4.0 (curated_consensus) [2026-07-22] 4.0 /depot/repeatmasker_famdb/dfam_4_0_curated_consensus_2026-07-22 +## diff --git a/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.sample b/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.sample new file mode 100644 index 00000000000..a972ea3c1f0 --- /dev/null +++ b/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.sample @@ -0,0 +1,8 @@ + + + + + value, name, version, path + +
+ diff --git a/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.test b/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.test new file mode 100644 index 00000000000..b5123909f55 --- /dev/null +++ b/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.test @@ -0,0 +1,8 @@ + + + + + value, name, version, path + +
+ From 05ec01ff0c7cab998e9d7f95d75db6c28049a76f Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sat, 1 Aug 2026 21:03:53 +0200 Subject: [PATCH 2/2] data_manager_repeatmasker: address review comments - Record the admin's selection in the data table: new `components` and `engines` columns, so a consuming tool can filter libraries by the search engine their partitions actually support (consensus -> rmblast, HMM -> nhmmer). Both are comma-separated for use with a multiple_splitter filter. - Move the README content into the tool help, where admins installing the data manager will see it, and drop README.md. - Require at least one component: the root partition alone contains almost no families, and an empty multi-select rendered as the string "None", which failed with a confusing "Unknown component(s): None". --- .../data_manager_repeatmasker/README.md | 35 --------------- .../data_manager/repeatmasker_download.py | 45 ++++++++++++++----- .../data_manager/repeatmasker_download.xml | 39 ++++++++++++---- .../data_manager_conf.xml | 2 + .../tool-data/repeatmasker_famdb.loc.sample | 10 ++++- .../tool_data_table_conf.xml.sample | 2 +- .../tool_data_table_conf.xml.test | 2 +- 7 files changed, 76 insertions(+), 59 deletions(-) delete mode 100644 data_managers/data_manager_repeatmasker/README.md diff --git a/data_managers/data_manager_repeatmasker/README.md b/data_managers/data_manager_repeatmasker/README.md deleted file mode 100644 index 0ea1033dfd8..00000000000 --- a/data_managers/data_manager_repeatmasker/README.md +++ /dev/null @@ -1,35 +0,0 @@ -# RepeatMasker Dfam library data manager - -This data manager downloads a [Dfam](https://www.dfam.org/) repeat library in -the partitioned FamDB (v3) format and registers it in the `repeatmasker_famdb` -tool data table for use by the RepeatMasker Galaxy tool (RepeatMasker >= 4.2.4). - -## Why this is needed - -The RepeatMasker Conda package no longer ships a populated repeat library: the -`Dfam.h5` bundled in the package is a placeholder, and running RepeatMasker -against it fails with `Species "..." is not known to RepeatMasker` because the -library contains no families. The library must be downloaded separately; this -data manager automates that and makes the result available through a data table. - -## What it downloads - -Dfam distributes its library as a required **root** partition plus optional -**component** partitions, split by curation status (curated/uncurated) and model -type (consensus sequences for the rmblast engine, profile HMMs for nhmmer): - -| Component | Engine | Notes | -|-----------|--------|-------| -| Curated consensus | rmblast | Recommended default | -| Uncurated consensus | rmblast | Very large | -| Curated HMM | nhmmer | | -| Uncurated HMM | nhmmer | Very large (100+ partitions) | - -The root partition is always downloaded. Each file is verified against its Dfam -md5 checksum, decompressed, and placed in a single directory that RepeatMasker -consumes via `-libdir`. - -## Data table - -`repeatmasker_famdb` with columns `value, name, version, path`, where `path` -points at the directory holding the FamDB `.h5` partition files. diff --git a/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.py b/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.py index b6770716644..2d353f88032 100644 --- a/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.py +++ b/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.py @@ -7,7 +7,9 @@ (consensus sequences, used by the rmblast search engine, or profile HMMs, used by nhmmer). This data manager downloads the root partition (always) together with whichever components the admin selects, laying the ``*.h5`` files out in a -single directory that RepeatMasker (>= 4.2.4) can consume via ``-libdir``. +single directory that RepeatMasker (>= 4.2.4) can consume via ``-libdir``. The +selected components, and the search engines they support, are recorded in the +data table so consuming tools can filter on them. See https://www.dfam.org/releases/current/families/FamDB/README.txt """ @@ -33,14 +35,19 @@ BASE_URL = "https://www.dfam.org/releases/{dir}/families/FamDB/" -# component key -> FamDB file-name infix +# component key -> FamDB file-name infix and the search engine that can use it. +# Consensus sequences are searched with rmblast, profile HMMs with nhmmer, so the +# selected components determine which engines the installed library supports. COMPONENTS = { - "curated_consensus": "curated.consensus", - "uncurated_consensus": "uncurated.consensus", - "curated_hmm": "curated.hmm", - "uncurated_hmm": "uncurated.hmm", + "curated_consensus": {"infix": "curated.consensus", "engine": "rmblast"}, + "uncurated_consensus": {"infix": "uncurated.consensus", "engine": "rmblast"}, + "curated_hmm": {"infix": "curated.hmm", "engine": "nhmmer"}, + "uncurated_hmm": {"infix": "uncurated.hmm", "engine": "nhmmer"}, } +# Search engines, in the order they are reported in the data table. +ENGINES = ("rmblast", "nhmmer") + # A tiny (~0.3 MB) real partition used to exercise the full download / gunzip / # checksum / registration path quickly during automated testing. TEST_COMPONENT = "uncurated_consensus" @@ -131,7 +138,7 @@ def download(release, components, test, out_file): # Exercise the real code path cheaply: fetch only the smallest partition # of a single component, and skip the large root/curated downloads. components = [TEST_COMPONENT] - infix = COMPONENTS[TEST_COMPONENT] + infix = COMPONENTS[TEST_COMPONENT]["infix"] installed = [ download_and_extract( "{}{}.{}.0.h5.gz".format(base_url, prefix, infix), target_directory @@ -145,16 +152,25 @@ def download(release, components, test, out_file): ) ] for component in components: - infix = COMPONENTS[component] + infix = COMPONENTS[component]["infix"] for url in iter_partition_urls(base_url, prefix, infix): installed.append(download_and_extract(url, target_directory)) today = date.today().strftime("%Y-%m-%d") - selected = "+".join(components) if components else "root" + selected = "+".join(components) + # Record what was installed so consuming tools can filter on it, e.g. offer a + # library only for a search engine its components actually support. + engines = [ + engine + for engine in ENGINES + if any(COMPONENTS[c]["engine"] == engine for c in components) + ] entry = { "value": "dfam_{}_{}_{}".format(release, selected, today).replace(".", "_"), - "name": "Dfam {} ({}) [{}]".format(release, ", ".join(components) or "root only", today), + "name": "Dfam {} ({}) [{}]".format(release, ", ".join(components), today), "version": release, + "components": ",".join(components), + "engines": ",".join(engines), "path": target_directory, } data_manager_json = {"data_tables": {"repeatmasker_famdb": [entry]}} @@ -182,7 +198,14 @@ def download(release, components, test, out_file): ) args = parser.parse_args() - components = [c for c in args.components.split(",") if c] + # Cheetah renders an empty multi-select as the string "None". + components = [c for c in args.components.split(",") if c and c != "None"] + if not components: + sys.exit( + "No components selected. Select at least one of: {}".format( + ", ".join(sorted(COMPONENTS)) + ) + ) unknown = [c for c in components if c not in COMPONENTS] if unknown: sys.exit("Unknown component(s): {}".format(", ".join(unknown))) diff --git a/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.xml b/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.xml index 2770e0c45eb..7a5350f86c4 100644 --- a/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.xml +++ b/data_managers/data_manager_repeatmasker/data_manager/repeatmasker_download.xml @@ -21,9 +21,9 @@ python '$__tool_directory__/repeatmasker_download.py' - + help="At least one component is required: the root partition on its own contains almost no families. The curated consensus component is recommended for the default rmblast search engine. HMM components are only needed for the nhmmer engine. Uncurated components are very large."> @@ -44,30 +44,51 @@ python '$__tool_directory__/repeatmasker_download.py' + + = 4.2.4). + +**Why this is needed** + +The RepeatMasker Conda package no longer ships a populated repeat library: the +``Dfam.h5`` bundled in the package is a placeholder, and running RepeatMasker +against it fails with ``Species "..." is not known to RepeatMasker`` because the +library contains no families. The library has to be downloaded separately; this +data manager automates that and makes the result available through a data table. **Components** Dfam is distributed as a required *root* partition (taxonomy and index) plus -optional *component* partitions: +optional *component* partitions, split by curation status (curated/uncurated) +and model type (consensus sequences for the rmblast search engine, profile HMMs +for nhmmer): - **Curated consensus** — curated families as consensus sequences; used by the default rmblast search engine. Recommended for most installations. - **Uncurated consensus** — uncurated families as consensus sequences. Much larger; only needed for broad, sensitive searches. - **Curated / Uncurated HMMs** — profile HMMs, used only by the nhmmer search - engine. + engine. The uncurated HMM component has 100+ partitions. + +The root partition is always downloaded, and at least one component must be +selected. Each file is verified against its Dfam md5 checksum, decompressed, and +placed in a single directory that RepeatMasker consumes via ``-libdir``. + +**Data table** -The root partition is always downloaded; select the components you need. Each -file's md5 checksum is verified after download. +``repeatmasker_famdb``, with the columns +``value, name, version, components, engines, path``, where ``path`` points at +the directory holding the FamDB ``.h5`` partition files. ``components`` records +which components were selected and ``engines`` the search engines they can be +used with (``rmblast`` and/or ``nhmmer``); both are comma-separated so a +consuming tool can filter on them with a ``multiple_splitter`` filter. .. _Dfam: https://www.dfam.org/ ]]> diff --git a/data_managers/data_manager_repeatmasker/data_manager_conf.xml b/data_managers/data_manager_repeatmasker/data_manager_conf.xml index 5988064cc71..c3c2d1e1bbb 100644 --- a/data_managers/data_manager_repeatmasker/data_manager_conf.xml +++ b/data_managers/data_manager_repeatmasker/data_manager_conf.xml @@ -6,6 +6,8 @@ + + repeatmasker_famdb/${value} diff --git a/data_managers/data_manager_repeatmasker/tool-data/repeatmasker_famdb.loc.sample b/data_managers/data_manager_repeatmasker/tool-data/repeatmasker_famdb.loc.sample index c6556e78775..3050930f3e6 100644 --- a/data_managers/data_manager_repeatmasker/tool-data/repeatmasker_famdb.loc.sample +++ b/data_managers/data_manager_repeatmasker/tool-data/repeatmasker_famdb.loc.sample @@ -6,9 +6,15 @@ ## ## The tab-separated columns are: ## -## +## +## +## lists the component partitions installed alongside the root +## partition, and the search engines those components can be used with +## (consensus sequences -> rmblast, profile HMMs -> nhmmer). Both are +## comma-separated, so a consuming tool can filter on them with a +## multiple_splitter filter. ## ## For example: ## -## dfam_4_0_curated_consensus_2026-07-22 Dfam 4.0 (curated_consensus) [2026-07-22] 4.0 /depot/repeatmasker_famdb/dfam_4_0_curated_consensus_2026-07-22 +## dfam_4_0_curated_consensus_2026-07-22 Dfam 4.0 (curated_consensus) [2026-07-22] 4.0 curated_consensus rmblast /depot/repeatmasker_famdb/dfam_4_0_curated_consensus_2026-07-22 ## diff --git a/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.sample b/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.sample index a972ea3c1f0..87355cc5e48 100644 --- a/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.sample +++ b/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.sample @@ -2,7 +2,7 @@ - value, name, version, path + value, name, version, components, engines, path
diff --git a/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.test b/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.test index b5123909f55..79374b04533 100644 --- a/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.test +++ b/data_managers/data_manager_repeatmasker/tool_data_table_conf.xml.test @@ -2,7 +2,7 @@ - value, name, version, path + value, name, version, components, engines, path