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add dbcan_build
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linnabrown committed Jan 10, 2024
1 parent 0273941 commit 5d3ce6f
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Showing 4 changed files with 23 additions and 4 deletions.
6 changes: 4 additions & 2 deletions conda-recipe/meta.yaml
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@@ -1,5 +1,5 @@
{% set name = "dbcan" %}
{% set version = "4.1.0" %}
{% set version = "4.1.1" %}

package:
name: "{{ name|lower }}"
Expand All @@ -9,7 +9,7 @@ source:
# the sha256 sum is generated by doing
# wget -0- [URL] | shasum -a 256
url: https://github.com/linnabrown/run_dbcan/releases/download/{{ version }}/dbcan-{{ version }}.tar.gz
sha256: cb0907eb10eb916bcf676c58f54e67a67dd4ed559152e5547bb44d071f063b8f
sha256: e2167ec0848f23797f0ee1063ee540fa43c5b889ed7992b208dcfb2e0d84ef2e

build:
number: 0
Expand Down Expand Up @@ -42,6 +42,8 @@ requirements:
- numpy >1.19
- biopython
- pandas
- tqdm
- shutil
- session-info

test:
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2 changes: 1 addition & 1 deletion dbcan/cli/run_dbcan.py
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Expand Up @@ -1015,7 +1015,7 @@ def rundbCAN_parser():
default="all",
help="Choose gram+(p) or gram-(n) for proteome/prokaryote nucleotide, which are params of SingalP, only if user use singalP",
)
parser.add_argument("-v", "--version", default="4.1.0", type=str)
parser.add_argument("-v", "--version", default="4.1.1", type=str)
# dbCAN-sub
dbCAN_sub_group = parser.add_argument_group("dbCAN-sub parameters")
dbCAN_sub_group.add_argument("--dbcan_thread", "-dt", default=12, type=int)
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16 changes: 16 additions & 0 deletions docs/installation.rst
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Expand Up @@ -37,6 +37,22 @@ To install the `dbcan`_ package, use the ``conda install`` command:
conda install dbcan -c conda-forge -c bioconda
Build database
--------------

You can build database via this command,

.. code-block:: shell
dbcan_build --cpus 8 --db-dir db --clean
`--cpu` indicates count of cpu you can use. Try as many as possible for fast building.
`--db-dir` indicates database folder path. Default is `db` on your current database
`--clean` indicates clean the folder indicated by `--db-dir`.
You can remove this parameter if you don't want to clean, but we recommend you add this to keep
away from index contamination.


Installing with PyPI
--------------------

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3 changes: 2 additions & 1 deletion pyproject.toml
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Expand Up @@ -4,7 +4,7 @@ requires = ["hatchling"]

[project]
name = "dbcan"
version = "4.1.0"
version = "4.1.1"
description = "Standalone version of dbCAN annotation tool for automated CAZyme annotation"
readme = "README.md"
requires-python = ">=3.6"
Expand All @@ -26,6 +26,7 @@ dependencies = [
"pandas",
"biopython",
"tqdm",
"shutil",
# for debug logging (referenced from the issue template)
"session-info"
]
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