refactor: Fix all containers dependencies to specific versions (#1096)

BALSAMIC/commands/config/case.py

@@ -280,7 +280,8 @@ def case_config(
         vcf=VCF_DICT,
         bioinfo_tools=BIOINFO_TOOL_ENV,
         bioinfo_tools_version=get_bioinfo_tools_version(
-            BIOINFO_TOOL_ENV, CONTAINERS_CONDA_ENV_PATH
+            bioinfo_tools=BIOINFO_TOOL_ENV,
+            container_conda_env_path=CONTAINERS_CONDA_ENV_PATH,
         ),
         panel={
             "capture_kit": panel_bed,

BALSAMIC/commands/config/pon.py

@@ -137,7 +137,8 @@ def pon_config(
         singularity=os.path.join(balsamic_cache, balsamic_version, "containers"),
         bioinfo_tools=BIOINFO_TOOL_ENV,
         bioinfo_tools_version=get_bioinfo_tools_version(
-            BIOINFO_TOOL_ENV, CONTAINERS_CONDA_ENV_PATH
+            bioinfo_tools=BIOINFO_TOOL_ENV,
+            container_conda_env_path=CONTAINERS_CONDA_ENV_PATH,
         ),
         panel={"capture_kit": panel_bed} if panel_bed else None,
     ).dict(by_alias=True, exclude_none=True)

BALSAMIC/containers/align_qc/align_qc.sh

@@ -1 +1 @@
-conda env update -n base --file ${1}.yaml --prune
+conda env update -n base --file "${1}".yaml

BALSAMIC/containers/align_qc/align_qc.yaml

@@ -1,16 +1,192 @@
 channels:
+  - conda-forge
+  - bioconda
   - defaults
 
 dependencies:
-  - bioconda::bedtools=2.30.0
-  - bioconda::bwa=0.7.17
-  - bioconda::fastqc=0.11.9
-  - bioconda::samtools=1.15.1
-  - bioconda::tabix=0.2.6
-  - bioconda::picard=2.27.1
-  - bioconda::multiqc=1.12
-  - bioconda::fastp=0.23.2
-  - conda-forge::csvkit=1.0.7
-  - conda-forge::libiconv=1.16
-  - conda-forge::fontconfig=2.14.0
-  - conda-forge::r-base=4.1.3
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - _r-mutex=1.0.0
+  - agate=1.7.1
+  - agate-dbf=0.2.2
+  - agate-excel=0.2.5
+  - agate-sql=0.5.8
+  - babel=2.11.0
+  - bedtools=2.30.0
+  - binutils_impl_linux-64=2.39
+  - binutils_linux-64=2.39
+  - brotli=1.0.9
+  - brotli-bin=1.0.9
+  - brotlipy=0.7.0
+  - bwa=0.7.17
+  - bwidget=1.9.11
+  - bzip2=1.0.8
+  - c-ares=1.18.1
+  - ca-certificates=2023.01.10
+  - cairo=1.16.0
+  - certifi=2022.12.7
+  - cffi=1.15.1
+  - chardet=4.0.0
+  - click=8.0.4
+  - coloredlogs=15.0.1
+  - colormath=3.0.0
+  - commonmark=0.9.1
+  - conda=4.10.3
+  - conda-package-handling=1.7.3
+  - contourpy=1.0.5
+  - cryptography=3.4.7
+  - csvkit=1.0.7
+  - curl=7.82.0
+  - cycler=0.11.0
+  - dataclasses=0.8
+  - dbfread=2.0.7
+  - dbus=1.13.18
+  - et_xmlfile=1.1.0
+  - expat=2.4.9
+  - fastp=0.23.2
+  - fastqc=0.11.9
+  - flit-core=3.6.0
+  - font-ttf-dejavu-sans-mono=2.37
+  - fontconfig=2.14.0
+  - fonttools=4.25.0
+  - freetype=2.11.0
+  - fribidi=1.0.10
+  - future=0.18.2
+  - gcc_impl_linux-64=10.4.0
+  - gcc_linux-64=10.4.0
+  - gdbm=1.18
+  - gettext=0.21.0
+  - gfortran_impl_linux-64=10.4.0
+  - gfortran_linux-64=10.4.0
+  - giflib=5.2.1
+  - glib=2.70.2
+  - glib-tools=2.70.2
+  - graphite2=1.3.14
+  - greenlet=2.0.1
+  - gsl=2.7.1
+  - gxx_impl_linux-64=10.4.0
+  - gxx_linux-64=10.4.0
+  - harfbuzz=4.3.0
+  - htslib=1.15.1
+  - humanfriendly=10.0
+  - icu=70.1
+  - idna=2.10
+  - importlib-metadata=4.11.3
+  - isa-l=2.30.0
+  - isodate=0.6.0
+  - jbig=2.1
+  - jinja2=3.1.2
+  - jpeg=9e
+  - kernel-headers_linux-64=2.6.32
+  - kiwisolver=1.4.4
+  - krb5=1.19.4
+  - lcms2=2.12
+  - ld_impl_linux-64=2.39
+  - leather=0.3.4
+  - lerc=3.0
+  - libblas=3.9.0
+  - libbrotlicommon=1.0.9
+  - libbrotlidec=1.0.9
+  - libbrotlienc=1.0.9
+  - libcblas=3.9.0
+  - libcurl=7.82.0
+  - libdeflate=1.10
+  - libedit=3.1.20221030
+  - libev=4.33
+  - libffi=3.4.2
+  - libgcc-devel_linux-64=10.4.0
+  - libgcc-ng=11.2.0
+  - libgfortran-ng=11.2.0
+  - libgfortran5=11.2.0
+  - libglib=2.70.2
+  - libgomp=11.2.0
+  - libiconv=1.16
+  - liblapack=3.9.0
+  - libnghttp2=1.46.0
+  - libopenblas=0.3.21
+  - libpng=1.6.37
+  - libsanitizer=10.4.0
+  - libssh2=1.10.0
+  - libstdcxx-devel_linux-64=10.4.0
+  - libstdcxx-ng=11.2.0
+  - libtiff=4.3.0
+  - libuuid=2.32.1
+  - libwebp=1.2.4
+  - libwebp-base=1.2.4
+  - libxcb=1.15
+  - libxml2=2.9.14
+  - libzlib=1.2.11
+  - lz4-c=1.9.4
+  - lzstring=1.0.4
+  - make=4.2.1
+  - markdown=3.4.1
+  - markupsafe=2.1.1
+  - matplotlib-base=3.6.2
+  - multiqc=1.12
+  - munkres=1.1.4
+  - ncurses=6.4
+  - networkx=2.8.4
+  - numpy=1.22.3
+  - olefile=0.46
+  - openjdk=11.0.13
+  - openpyxl=3.0.10
+  - openssl=1.1.1t
+  - packaging=22.0
+  - pango=1.50.7
+  - parsedatetime=2.4
+  - pcre=8.45
+  - pcre2=10.37
+  - perl=5.34.0
+  - picard=2.27.1
+  - pillow=9.0.1
+  - pip=21.1.3
+  - pixman=0.40.0
+  - pycosat=0.6.3
+  - pycparser=2.20
+  - pygments=2.11.2
+  - pyopenssl=20.0.1
+  - pyparsing=3.0.9
+  - pysocks=1.7.1
+  - python=3.9.7
+  - python-dateutil=2.8.2
+  - python-slugify=5.0.2
+  - python_abi=3.9
+  - pytimeparse=1.1.8
+  - pytz=2022.7
+  - pyyaml=6.0
+  - r-base=4.1.3
+  - readline=8.1
+  - requests=2.25.1
+  - rich=12.5.1
+  - ruamel_yaml=0.15.100
+  - samtools=1.15.1
+  - sed=4.8
+  - setuptools=52.0.0
+  - simplejson=3.17.6
+  - six=1.16.0
+  - spectra=0.0.11
+  - sqlalchemy=1.4.39
+  - sqlite=3.36.0
+  - sysroot_linux-64=2.12
+  - tabix=0.2.6
+  - text-unidecode=1.3
+  - tk=8.6.12
+  - tktable=2.10
+  - tqdm=4.61.2
+  - typing_extensions=4.4.0
+  - tzdata=2021a
+  - unidecode=1.2.0
+  - urllib3=1.26.6
+  - wheel=0.36.2
+  - xlrd=2.0.1
+  - xorg-kbproto=1.0.7
+  - xorg-libice=1.0.10
+  - xorg-libsm=1.2.3
+  - xorg-libx11=1.7.2
+  - xorg-libxt=1.2.1
+  - xorg-xproto=7.0.31
+  - xz=5.2.5
+  - yaml=0.2.5
+  - zipp=3.11.0
+  - zlib=1.2.11
+  - zstd=1.5.2

BALSAMIC/containers/annotate/annotate.sh

@@ -1,2 +1 @@
-conda env update -n base --file ${1}.yaml --prune
-pip install --no-cache-dir genmod==3.7.4
+conda env update -n base --file "${1}".yaml