Merge branch 'release_v18.0.0' into develop

Author: mathiasbio

docs/install.rst

@@ -25,7 +25,7 @@ Step 1. Installing BALSAMIC
 
 ::
 
-    conda create -n S_balsamic -y -c conda-forge -c bioconda python=3.11 pip "cython<3" pygraphviz wkhtmltopdf snakemake-executor-plugin-slurm pysam=0.23.3 cyvcf2=0.31.1 htslib samtools
+    conda create --name S_balsamic -c conda-forge python=3.11 pip "cython<3" pygraphviz wkhtmltopdf snakemake-executor-plugin-slurm
 
 
 
@@ -41,7 +41,7 @@ Step 1. Installing BALSAMIC
 
 ::
 
-  pip install --no-cache-dir --no-deps -U git+https://github.com/Clinical-Genomics/BALSAMIC
+  pip install --no-build-isolation --no-cache-dir -U git+https://github.com/Clinical-Genomics/BALSAMIC
 
 
 Or if you have repository cloned and want it in editable mode:

setup.py

@@ -84,7 +84,6 @@
     "pyOpenSSL==23.2.0",
     "pyparsing==3.0.9",
     "pypdf==3.17.1",
-    "pysam==0.23.0",
     "pytest==7.4.0",
     "python-dateutil==2.8.2",
     "pytz==2023.3",
@@ -110,7 +109,7 @@
     "typing_extensions==4.7.1",
     "tzdata==2023.3",
     "urllib3==1.26.16",
-    "vcfpy==0.13.8",
+    "vcfpy==0.13.4",
     "wrapt==1.15.0",
     "yapf==0.40.1",
     "yarl==1.9.2",