Move changes from previous commit to new branch

MDU-PHL · Sep 16, 2024 · 32b81af · 32b81af
1 parent 3d0eea7
commit 32b81af
Show file tree

Hide file tree

Showing 5 changed files with 6 additions and 4 deletions.
diff --git a/.gitignore b/.gitignore
@@ -4,4 +4,5 @@ build/
 .pytest_cache/
 .coverage
 .vscode
-.idea
+.idea
+/dist
diff --git a/README.md b/README.md
@@ -105,7 +105,7 @@ Usage: emmtyper [OPTIONS] [FASTA]...
 Options:
   --version                       Show the version and exit.
   -w, --workflow [blast|pcr]      Choose workflow  [default: blast]
-  -d, --blast_db TEXT             Path to EMM BLAST DB  [default:
+  -db, --blast_db TEXT            Path to EMM BLAST DB  [default:
                                   /path/to/emmtyper/db/emm.fna]
   -k, --keep                      Keep BLAST and isPcr output files.
                                   [default: False]

diff --git a/emmtyper/__init__.py b/emmtyper/__init__.py
@@ -2,7 +2,7 @@
 emmtyper: an in silico EMM typer for Streptococcus pyogenes
 """
 __name__ = "emmtyper"
-__version__ = "0.2.1"
+__version__ = "0.2.2"
 __author__ = "Andre Tan"
 __email__ = "andre.sutanto.91@gmail.com"
 __url__ = "https://github.com/MDUPHL/emmtyper"

diff --git a/emmtyper/bin/run_emmtyper.py b/emmtyper/bin/run_emmtyper.py
@@ -34,7 +34,7 @@
     show_default=True,
 )
 @click.option(
-    "-d",
+    "-db",
     "--blast_db",
     default=os.environ.get("EMM_DB", DEFAULT_DB),
     help="Path to EMM BLAST DB",

diff --git a/environment.yml b/environment.yml
@@ -14,4 +14,5 @@ dependencies:
     - numpy>=1.23.0
     - python-dateutil>=2.8.1
     - scipy>=1.6.0
+    - -e . # editable install of emmtyper
 prefix: /usr/local/anaconda3/envs/emmtyper