add dbcan_build

linnabrown · Jan 10, 2024 · 5d3ce6f · 5d3ce6f
1 parent 0273941
commit 5d3ce6f
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Showing 4 changed files with 23 additions and 4 deletions.
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "dbcan" %}
-{% set version = "4.1.0" %}
+{% set version = "4.1.1" %}
 
 package:
   name: "{{ name|lower }}"
@@ -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
@@ -42,6 +42,8 @@ requirements:
     - numpy >1.19
     - biopython
     - pandas
+    - tqdm
+    - shutil
     - session-info
 
 test:

diff --git a/dbcan/cli/run_dbcan.py b/dbcan/cli/run_dbcan.py
@@ -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)

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -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
 --------------------
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -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"
@@ -26,6 +26,7 @@ dependencies = [
     "pandas",
     "biopython",
     "tqdm",
+    "shutil",
     # for debug logging (referenced from the issue template)
     "session-info"
 ]