v1.8.2

.github/workflows/ci.yaml

@@ -13,8 +13,8 @@ jobs:
 
     strategy:
       matrix:
-        os: [macos-13, ubuntu-latest] #macos-latest/macos-14 is M1 - some deps fail it due to not having M1 build (MMSeqs2)
-        python-version: ["3.9", "3.12"]
+        os: [macos-latest, ubuntu-latest] #macos-latest/macos-14 is M1 - some deps fail it due to not having M1 build (MMSeqs2)
+        python-version: ["3.12"]
 
     steps:
       - uses: "actions/checkout@v3"

.github/workflows/release.yaml

@@ -14,13 +14,13 @@ jobs:
       - uses: actions/checkout@v3
       - uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: 3.9
+          python-version: 3.12
           activate-environment: plassembler
           environment-file: build/environment.yaml
           auto-activate-base: false
           channels: conda-forge,bioconda,defaults
           channel-priority: strict
-          auto-update-conda: true
+          auto-update-conda: true 
 
       - name: Install plassembler
         shell: bash -l {0}

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "plassembler"
-version = "1.8.1" # change VERSION too
+version = "1.8.2" # change VERSION too
 description = "Quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates"
 authors = ["George Bouras <george.bouras@adelaide.edu.au>"]
 license = "MIT"

src/plassembler/utils/VERSION

@@ -1 +1 @@
-1.8.1
+1.8.2

src/plassembler/utils/db.py

@@ -14,6 +14,7 @@
 from loguru import logger
 
 from plassembler.utils.cleanup import remove_directory
+from plassembler.utils.util import get_version
 
 
 def check_db_installation(db_dir: Path, force: bool, install_flag: bool):
@@ -75,8 +76,16 @@ def get_database_zenodo(db_dir: Path):
     db_url = "https://zenodo.org/record/10158040/files/201123_plassembler_v1.5.0_databases.tar.gz"
     requiredmd5 = "3a24bacc05bb857dc044fc6662b58db7"
 
+    version = get_version().strip()
+
+    headers = {
+        "User-Agent": f"plassembler/{version} (contact: george.bouras@adelaide.edu.au)"
+    }
+
     try:
-        with tar_path.open("wb") as fh_out, requests.get(db_url, stream=True) as resp:
+        with tar_path.open("wb") as fh_out, requests.get(
+            db_url, stream=True, headers=headers
+        ) as resp:
             total_length = resp.headers.get("content-length")
             if total_length is not None:  # content length header is set
                 total_length = int(total_length)

src/plassembler/utils/run_canu.py

@@ -33,7 +33,7 @@ def run_canu_correct(
             tool="canu -correct",
             input="",
             output="",
-            params=f" -p canu -d {canu_output_dir} genomeSize={total_flye_plasmid_length}m maxInputCoverage={coverage} stopOnLowCoverage=1 maxThreads={threads} -{canu_nano_or_pacbio} correctedErrorRate={corrected_error_rate} {longreads}",
+            params=f" -p canu -d {canu_output_dir} genomeSize={total_flye_plasmid_length}m maxInputCoverage={coverage} stopOnLowCoverage=1 maxThreads={threads} useGrid=false -{canu_nano_or_pacbio} correctedErrorRate={corrected_error_rate} {longreads}",
             logdir=logdir,
             outfile="",
         )
@@ -69,7 +69,7 @@ def run_canu(
             tool="canu",
             input="",
             output="",
-            params=f" -p canu -d {canu_output_dir} genomeSize={total_flye_plasmid_length}m maxInputCoverage={coverage} stopOnLowCoverage=1 maxThreads={threads} -{canu_nano_or_pacbio} correctedErrorRate={corrected_error_rate} {longreads}",
+            params=f" -p canu -d {canu_output_dir} genomeSize={total_flye_plasmid_length}m maxInputCoverage={coverage} stopOnLowCoverage=1 maxThreads={threads} useGrid=false -{canu_nano_or_pacbio} correctedErrorRate={corrected_error_rate} {longreads}",
             logdir=logdir,
             outfile="",
         )