Phylogenetics tools!

envs/phylowgs/fill_battenberg.yaml

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+name: fill_segments
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - ca-certificates=2020.12.5
+  - certifi=2020.12.5
+  - ld_impl_linux-64=2.35.1
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libffi=3.3
+  - libgcc-ng=9.3.0
+  - libgfortran-ng=9.3.0
+  - libgfortran5=9.3.0
+  - libgomp=9.3.0
+  - liblapack=3.9.0
+  - libopenblas=0.3.12
+  - libstdcxx-ng=9.3.0
+  - ncurses=6.2
+  - numpy=1.19.4
+  - openssl=1.1.1i
+  - pandas=1.2.0
+  - pip=20.3.3
+  - python=3.9.1
+  - python-dateutil=2.8.1
+  - python_abi=3.9
+  - pytz=2020.5
+  - readline=8.0
+  - setuptools=49.6.0
+  - simplejson=3.17.2
+  - six=1.15.0
+  - sqlite=3.34.0
+  - tk=8.6.10
+  - tzdata=2020e
+  - wheel=0.36.2
+  - xz=5.2.5
+  - zlib=1.2.11
+prefix: /home/dreval/miniconda3/envs/fill_segments

envs/phylowgs/phylowgs.yaml

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+name: phylo
+channels:
+  - conda-forge
+  - defaults
+  - bioconda
+  - r
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - binutils_impl_linux-64=2.35.1
+  - binutils_linux-64=2.35
+  - blas=1.1
+  - ca-certificates=2020.12.5
+  - certifi=2019.11.28
+  - dbus=1.13.6
+  - expat=2.2.10
+  - fontconfig=2.13.1
+  - freetype=2.10.4
+  - gcc_impl_linux-64=9.3.0
+  - gcc_linux-64=9.3.0
+  - gettext=0.19.8.1
+  - gfortran_impl_linux-64=9.3.0
+  - gfortran_linux-64=9.3.0
+  - glib=2.58.3
+  - gsl=2.6
+  - gst-plugins-base=1.14.5
+  - gstreamer=1.14.5
+  - gxx_impl_linux-64=9.3.0
+  - gxx_linux-64=9.3.0
+  - icu=64.2
+  - jpeg=9d
+  - kernel-headers_linux-64=2.6.32
+  - ld_impl_linux-64=2.35.1
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libffi=3.2.1
+  - libgcc-devel_linux-64=9.3.0
+  - libgcc-ng=9.3.0
+  - libgfortran=3.0.0
+  - libgfortran-ng=9.3.0
+  - libgfortran5=9.3.0
+  - libgomp=9.3.0
+  - libiconv=1.16
+  - liblapack=3.9.0
+  - libpng=1.6.37
+  - libstdcxx-devel_linux-64=9.3.0
+  - libstdcxx-ng=9.3.0
+  - libuuid=2.32.1
+  - libxcb=1.13
+  - libxml2=2.9.10
+  - libxslt=1.1.33
+  - lxml=3.8.0
+  - mysql-connector-c=6.1.11
+  - mysql-python=1.2.5
+  - ncurses=6.2
+  - numpy=1.15.4
+  - openblas=0.3.3
+  - openssl=1.1.1j
+  - pcre=8.44
+  - phylowgs=20181105
+  - pip=20.1.1
+  - pthread-stubs=0.4
+  - pyqt=5.9.2
+  - python=2.7.15
+  - python_abi=2.7
+  - pyvcf=0.6.8
+  - qt=5.9.7
+  - readline=8.0
+  - setuptools=44.0.0
+  - sip=4.19.8
+  - sqlite=3.34.0
+  - sysroot_linux-64=2.12
+  - tk=8.6.10
+  - wheel=0.36.2
+  - xorg-libxau=1.0.9
+  - xorg-libxdmcp=1.1.3
+  - xz=5.2.5
+  - zlib=1.2.11
+  - pip:
+    - ete2==2.3.10
+    - scipy==0.16.0
+prefix: /home/ssoudi/miniconda3/envs/phylo

envs/phylowgs/phylowgs_results.yaml

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+name: phylowgs_outputs
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - _r-mutex=1.0.1
+  - binutils_impl_linux-64=2.35.1
+  - binutils_linux-64=2.35
+  - bwidget=1.9.14
+  - bzip2=1.0.8
+  - c-ares=1.17.1
+  - ca-certificates=2021.5.30
+  - cairo=1.16.0
+  - curl=7.77.0
+  - font-ttf-dejavu-sans-mono=2.37
+  - font-ttf-inconsolata=3.000
+  - font-ttf-source-code-pro=2.038
+  - font-ttf-ubuntu=0.83
+  - fontconfig=2.13.1
+  - fonts-conda-ecosystem=1
+  - fonts-conda-forge=1
+  - freetype=2.10.4
+  - fribidi=1.0.10
+  - gcc_impl_linux-64=9.3.0
+  - gcc_linux-64=9.3.0
+  - gettext=0.21.0
+  - gfortran_impl_linux-64=9.3.0
+  - gfortran_linux-64=9.3.0
+  - graphite2=1.3.14
+  - gsl=2.6
+  - gxx_impl_linux-64=9.3.0
+  - gxx_linux-64=9.3.0
+  - harfbuzz=2.8.1
+  - icu=68.1
+  - jbig=2.1
+  - jpeg=9d
+  - kernel-headers_linux-64=2.6.32
+  - krb5=1.19.1
+  - ld_impl_linux-64=2.35.1
+  - lerc=2.2.1
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libcurl=7.77.0
+  - libdeflate=1.7
+  - libedit=3.1.20210216
+  - libev=4.33
+  - libffi=3.3
+  - libgcc-devel_linux-64=9.3.0
+  - libgcc-ng=9.3.0
+  - libgfortran-ng=9.3.0
+  - libgfortran5=9.3.0
+  - libglib=2.68.3
+  - libgomp=9.3.0
+  - libiconv=1.16
+  - liblapack=3.9.0
+  - libnghttp2=1.43.0
+  - libopenblas=0.3.15
+  - libpng=1.6.37
+  - libssh2=1.9.0
+  - libstdcxx-devel_linux-64=9.3.0
+  - libstdcxx-ng=9.3.0
+  - libtiff=4.3.0
+  - libuuid=2.32.1
+  - libwebp-base=1.2.0
+  - libxcb=1.14
+  - libxml2=2.9.12
+  - lz4-c=1.9.3
+  - make=4.3
+  - ncurses=6.2
+  - openssl=1.1.1k
+  - pandoc=2.14.0.3
+  - pango=1.48.6
+  - pcre=8.45
+  - pcre2=10.36
+  - pixman=0.40.0
+  - r-askpass=1.1
+  - r-assertthat=0.2.1
+  - r-backports=1.2.1
+  - r-base=4.1.0
+  - r-base64enc=0.1_3
+  - r-blob=1.2.1
+  - r-brio=1.1.2
+  - r-broom=0.7.8
+  - r-callr=3.7.0
+  - r-cellranger=1.1.0
+  - r-cli=3.0.0
+  - r-clipr=0.7.1
+  - r-colorspace=2.0_2
+  - r-cpp11=0.3.1
+  - r-crayon=1.4.1
+  - r-curl=4.3.2
+  - r-data.table=1.14.0
+  - r-dbi=1.1.1
+  - r-dbplyr=2.1.1
+  - r-desc=1.3.0
+  - r-diffobj=0.3.4
+  - r-digest=0.6.27
+  - r-dplyr=1.0.7
+  - r-dtplyr=1.1.0
+  - r-ellipsis=0.3.2
+  - r-evaluate=0.14
+  - r-fansi=0.4.2
+  - r-farver=2.1.0
+  - r-forcats=0.5.1
+  - r-fs=1.5.0
+  - r-gargle=1.1.0
+  - r-generics=0.1.0
+  - r-ggplot2=3.3.5
+  - r-ggrepel=0.9.1
+  - r-glue=1.4.2
+  - r-googledrive=1.0.1
+  - r-googlesheets4=0.3.0
+  - r-gtable=0.3.0
+  - r-haven=2.4.1
+  - r-highr=0.9
+  - r-hms=1.1.0
+  - r-htmltools=0.5.1.1
+  - r-httr=1.4.2
+  - r-ids=1.0.1
+  - r-isoband=0.2.4
+  - r-jsonlite=1.7.2
+  - r-knitr=1.33
+  - r-labeling=0.4.2
+  - r-lattice=0.20_44
+  - r-lifecycle=1.0.0
+  - r-lubridate=1.7.10
+  - r-magrittr=2.0.1
+  - r-markdown=1.1
+  - r-mass=7.3_54
+  - r-matrix=1.3_4
+  - r-mgcv=1.8_36
+  - r-mime=0.11
+  - r-modelr=0.1.8
+  - r-munsell=0.5.0
+  - r-nlme=3.1_152
+  - r-openssl=1.4.4
+  - r-pillar=1.6.1
+  - r-pkgconfig=2.0.3
+  - r-pkgload=1.2.1
+  - r-plyr=1.8.6
+  - r-praise=1.0.0
+  - r-prettyunits=1.1.1
+  - r-processx=3.5.2
+  - r-progress=1.2.2
+  - r-ps=1.6.0
+  - r-purrr=0.3.4
+  - r-r6=2.5.0
+  - r-rappdirs=0.3.3
+  - r-rcolorbrewer=1.1_2
+  - r-rcpp=1.0.6
+  - r-readr=1.4.0
+  - r-readxl=1.3.1
+  - r-rematch=1.0.1
+  - r-rematch2=2.1.2
+  - r-reprex=2.0.0
+  - r-reshape2=1.4.4
+  - r-rjson=0.2.20
+  - r-rlang=0.4.11
+  - r-rmarkdown=2.9
+  - r-rprojroot=2.0.2
+  - r-rstudioapi=0.13
+  - r-rvest=1.0.0
+  - r-scales=1.1.1
+  - r-selectr=0.4_2
+  - r-stringi=1.6.2
+  - r-stringr=1.4.0
+  - r-sys=3.4
+  - r-testthat=3.0.3
+  - r-tibble=3.1.2
+  - r-tidyr=1.1.3
+  - r-tidyselect=1.1.1
+  - r-tidyverse=1.3.1
+  - r-tinytex=0.32
+  - r-utf8=1.2.1
+  - r-uuid=0.1_4
+  - r-vctrs=0.3.8
+  - r-viridislite=0.4.0
+  - r-waldo=0.2.5
+  - r-withr=2.4.2
+  - r-xfun=0.24
+  - r-xml2=1.3.2
+  - r-yaml=2.2.1
+  - readline=8.1
+  - sed=4.8
+  - sysroot_linux-64=2.12
+  - tk=8.6.10
+  - tktable=2.10
+  - xorg-kbproto=1.0.7
+  - xorg-libice=1.0.10
+  - xorg-libsm=1.2.3
+  - xorg-libx11=1.7.2
+  - xorg-libxext=1.3.4
+  - xorg-libxrender=0.9.10
+  - xorg-libxt=1.2.1
+  - xorg-renderproto=0.11.1
+  - xorg-xextproto=7.3.0
+  - xorg-xproto=7.0.31
+  - xz=5.2.5
+  - zlib=1.2.11
+  - zstd=1.5.0
+prefix: /home/lhilton/miniconda3/envs/phylowgs_outputs

modules/phylowgs/1.0/config/default.yaml

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+lcr-modules:
+
+    phylowgs:
+
+        inputs:
+            # Available wildcards: {tumour_id} {normal_id} {pair_status} {genome_build} {sample_id}
+            maf: "__UPDATE__"
+            cellularity: "__UPDATE__" # battenberg/99-outputs/txt/{seq_type}--{genome_build}/{tumour_id}--{normal_id}_subclones.txt
+            subclones: "__UPDATE__" # battenberg/99-outputs/txt/{seq_type}--{genome_build}/{tumour_id}--{normal_id}_cellularity_ploidy.txt
+            drivers: "__UPDATE__" # newline-separated list of driver gene HUGO symbols to be included on plots
+
+        scratch_subdirectories: [] # Recommended: "04-multievolve"
+
+        options:
+            create_inputs:
+                opts:
+                    "-s 5000 --verbose --regions all" # -s controls how many variants should be sub-sampled.
+            multievolve: ""
+            write_results: "--include-ssm-names"
+
+        switches:
+            # NOTE: You must include a "sex" column in the input samples table, formatted with "M" and "F".
+            # If patient sex is unknown, you can leave it empty and phyloWGS will run in "auto" mode.
+            sex:
+                M: "male"
+                F: "female"
+
+        conda_envs:
+            phylowgs: "{MODSDIR}/envs/phylowgs.yaml"
+            phylowgs_results: "{MODSDIR}/envs/phylowgs_results.yaml"
+            fill_battenberg: "{MODSDIR}/envs/fill_battenberg.yaml"
+            vcf2maf: "{MODSDIR}/envs/vcf2maf-1.6.18.yaml"
+            bcftools: "{MODSDIR}/envs/bcftools-1.10.2.yaml"
+            coreutils: "{MODSDIR}/envs/coreutils-8.31.yaml"
+
+        scripts:
+            fill_battenberg: "{MODSDIR}/src/fill_battenberg.py"
+            arm_file: "{MODSDIR}/etc/chromArmFiles/chromArm.{genome_build}.tsv"
+            process_outputs: "src/process_phyloWGS_outputs.R"
+            noncoding: "{MODSDIR}/etc/noncoding.txt"
+
+        threads:
+            create_inputs: 1
+            multievolve: 4
+            write_results: 1
+
+        resources:
+            create_inputs:
+                mem_mb: 10000
+            multievolve:
+                mem_mb: 40000
+                evolve: 1
+            write_results:
+                mem_mb: 20000
+
+        pairing_config:
+            genome:
+                run_paired_tumours: True
+                run_unpaired_tumours_with: None
+                run_paired_tumours_as_unpaired: False

modules/phylowgs/1.0/envs/bcftools-1.10.2.yaml

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+../../../../envs/bcftools/bcftools-1.10.2.yaml

modules/phylowgs/1.0/envs/coreutils-8.31.yaml

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+../../../../envs/coreutils/coreutils-8.31.yaml

modules/phylowgs/1.0/envs/phylowgs.yaml

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+../../../../envs/phylowgs/phylowgs.yaml