From 5166327e3df095d934f51cbe6b125e95ada593d8 Mon Sep 17 00:00:00 2001 From: lkhilton Date: Thu, 14 Nov 2024 12:48:28 -0800 Subject: [PATCH 1/2] repair broken battenberg env --- envs/battenberg/battenberg-1.1.post-deploy.sh | 0 envs/battenberg/battenberg-1.1.yaml | 20 +- .../battenberg/1.1/envs/battenberg-old.yaml | 222 ++++++++++++++++++ 3 files changed, 235 insertions(+), 7 deletions(-) mode change 100644 => 100755 envs/battenberg/battenberg-1.1.post-deploy.sh create mode 100644 modules/battenberg/1.1/envs/battenberg-old.yaml diff --git a/envs/battenberg/battenberg-1.1.post-deploy.sh b/envs/battenberg/battenberg-1.1.post-deploy.sh old mode 100644 new mode 100755 diff --git a/envs/battenberg/battenberg-1.1.yaml b/envs/battenberg/battenberg-1.1.yaml index 29aae570c..337d24fde 100644 --- a/envs/battenberg/battenberg-1.1.yaml +++ b/envs/battenberg/battenberg-1.1.yaml @@ -2,21 +2,26 @@ channels: - conda-forge - bioconda - r - - defaults dependencies: - r-biocmanager=1.30.10 - - binutils_impl_linux-64 - - binutils_linux-64 - bwidget=1.9.14 - bzip2=1.0.8 + - cairo=1.16.0 + - cancerit-allelecount=4.0.2 + - curl=7.69.1 + - fontconfig=2.13.1 + - freetype=2.10.1 + - fribidi=1.0.9 - gettext=0.19.8.1 - graphite2=1.3.13 - gsl=2.6 + - harfbuzz=2.4.0 - htslib=1.9 - icu=64.2 - impute2=2.3.2 - jpeg=9c - krb5=1.17.1 + - make=4.3 - ncurses=6.1 - openssl=1.1.1g - pandoc=2.9.2.1 @@ -24,7 +29,7 @@ dependencies: - parallel=20200322 - pcre=8.44 - perl=5.26.2 - - pip + - pip=20.1 - pixman=0.38.0 - pthread-stubs=0.4 - python=3.8.2 @@ -38,7 +43,7 @@ dependencies: - r-broom=0.5.6 - r-callr=3.4.3 - r-cellranger=1.1.0 - - r-cli + - r-cli=2.0.2 - r-clipr=0.7.0 - r-codetools=0.2_16 - r-colorspace=1.4_1 @@ -86,7 +91,7 @@ dependencies: - r-later=1.0.0 - r-lattice=0.20_41 - r-lazyeval=0.2.2 - - r-lifecycle + - r-lifecycle=0.2.0 - r-lubridate=1.7.8 - r-magrittr=1.5 - r-markdown=1.1 @@ -125,7 +130,7 @@ dependencies: - r-reprex=0.3.0 - r-reshape2=1.4.4 - r-rex=1.2.0 - - r-rlang + - r-rlang=0.4.5 - r-rmarkdown=2.1 - r-roxygen2=7.1.0 - r-rprojroot=1.3_2 @@ -162,4 +167,5 @@ dependencies: - tk=8.6.10 - tktable=2.10 - wheel=0.34.2 + diff --git a/modules/battenberg/1.1/envs/battenberg-old.yaml b/modules/battenberg/1.1/envs/battenberg-old.yaml new file mode 100644 index 000000000..e6f3a0dab --- /dev/null +++ b/modules/battenberg/1.1/envs/battenberg-old.yaml @@ -0,0 +1,222 @@ +channels: + - conda-forge + - bioconda + - r + - defaults +dependencies: + - r-biocmanager=1.30.10 + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - _r-mutex=1.0.1 + - binutils_impl_linux-64=2.34 + - binutils_linux-64=2.34 + - bwidget=1.9.14 + - bzip2=1.0.8 + - ca-certificates=2020.4.5.1 + - cairo=1.16.0 + - cancerit-allelecount=4.0.2 + - certifi=2020.4.5.1 + - curl=7.69.1 + - fontconfig=2.13.1 + - freetype=2.10.1 + - fribidi=1.0.9 + - gcc_impl_linux-64=7.3.0 + - gcc_linux-64=7.3.0 + - gettext=0.19.8.1 + - gfortran_impl_linux-64=7.3.0 + - gfortran_linux-64=7.3.0 + - glib=2.64.2 + - graphite2=1.3.13 + - gsl=2.6 + - gxx_impl_linux-64=7.3.0 + - gxx_linux-64=7.3.0 + - harfbuzz=2.4.0 + - htslib=1.9 + - icu=64.2 + - impute2=2.3.2 + - jpeg=9c + - krb5=1.17.1 + - ld_impl_linux-64=2.34 + - libblas=3.8.0 + - libcblas=3.8.0 + - libcurl=7.69.1 + - libdeflate=1.2 + - libedit=3.1.20170329 + - libffi=3.2.1 + - libgcc-ng=9.2.0 + - libgfortran-ng=7.3.0 + - libgomp=9.2.0 + - libiconv=1.15 + - liblapack=3.8.0 + - libopenblas=0.3.9 + - libpng=1.6.37 + - libssh2=1.8.2 + - libstdcxx-ng=9.2.0 + - libtiff=4.1.0 + - libuuid=2.32.1 + - libwebp-base=1.1.0 + - libxcb=1.13 + - libxml2=2.9.10 + - llvm-openmp=10.0.0 + - lz4-c=1.9.2 + - make=4.3 + - ncurses=6.1 + - openssl=1.1.1g + - pandoc=2.9.2.1 + - pango=1.42.4 + - parallel=20200322 + - pcre=8.44 + - perl=5.26.2 + - pip=20.1 + - pixman=0.38.0 + - pthread-stubs=0.4 + - python=3.8.2 + - python_abi=3.8 + - r-askpass=1.1 + - r-assertthat=0.2.1 + - r-backports=1.1.6 + - r-base=3.6.3 + - r-base64enc=0.1_3 + - r-brew=1.0_6 + - r-broom=0.5.6 + - r-callr=3.4.3 + - r-cellranger=1.1.0 + - r-cli=2.0.2 + - r-clipr=0.7.0 + - r-codetools=0.2_16 + - r-colorspace=1.4_1 + - r-commonmark=1.7 + - r-covr=3.5.0 + - r-crayon=1.3.4 + - r-crosstalk=1.1.0.1 + - r-curl=4.3 + - r-dbi=1.1.0 + - r-dbplyr=1.4.3 + - r-desc=1.2.0 + - r-devtools=2.3.0 + - r-digest=0.6.25 + - r-doparallel=1.0.15 + - r-dplyr=0.8.5 + - r-dt=0.13 + - r-ellipsis=0.3.0 + - r-evaluate=0.14 + - r-fansi=0.4.1 + - r-farver=2.0.3 + - r-forcats=0.5.0 + - r-foreach=1.5.0 + - r-fs=1.4.1 + - r-generics=0.0.2 + - r-getopt=1.20.3 + - r-ggplot2=3.3.0 + - r-gh=1.1.0 + - r-git2r=0.26.1 + - r-glue=1.4.0 + - r-gridextra=2.3 + - r-gtable=0.3.0 + - r-gtools=3.8.2 + - r-haven=2.2.0 + - r-highr=0.8 + - r-hms=0.5.3 + - r-htmltools=0.4.0 + - r-htmlwidgets=1.5.1 + - r-httr=1.4.1 + - r-ini=0.3.1 + - r-isoband=0.2.1 + - r-iterators=1.0.12 + - r-jsonlite=1.6.1 + - r-knitr=1.28 + - r-labeling=0.3 + - r-later=1.0.0 + - r-lattice=0.20_41 + - r-lazyeval=0.2.2 + - r-lifecycle=0.2.0 + - r-lubridate=1.7.8 + - r-magrittr=1.5 + - r-markdown=1.1 + - r-mass=7.3_51.6 + - r-matrix=1.2_18 + - r-memoise=1.1.0 + - r-mgcv=1.8_31 + - r-mime=0.9 + - r-modelr=0.1.6 + - r-munsell=0.5.0 + - r-nlme=3.1_147 + - r-openssl=1.4.1 + - r-optparse=1.6.6 + - r-pillar=1.4.3 + - r-pkgbuild=1.0.7 + - r-pkgconfig=2.0.3 + - r-pkgload=1.0.2 + - r-plogr=0.2.0 + - r-plyr=1.8.6 + - r-praise=1.0.0 + - r-prettyunits=1.1.1 + - r-processx=3.4.2 + - r-progress=1.2.2 + - r-promises=1.1.0 + - r-ps=1.3.2 + - r-purrr=0.3.4 + - r-r6=2.4.1 + - r-rcmdcheck=1.3.3 + - r-rcolorbrewer=1.1_2 + - r-rcpp=1.0.4.6 + - r-readr=1.3.1 + - r-readxl=1.3.1 + - r-rematch=1.0.1 + - r-rematch2=2.1.1 + - r-remotes=2.1.1 + - r-reprex=0.3.0 + - r-reshape2=1.4.4 + - r-rex=1.2.0 + - r-rlang=0.4.5 + - r-rmarkdown=2.1 + - r-roxygen2=7.1.0 + - r-rprojroot=1.3_2 + - r-rstudioapi=0.11 + - r-rversions=2.0.1 + - r-rvest=0.3.5 + - r-scales=1.1.0 + - r-selectr=0.4_2 + - r-sessioninfo=1.1.1 + - r-stringi=1.4.6 + - r-stringr=1.4.0 + - r-sys=3.3 + - r-testthat=2.3.2 + - r-tibble=3.0.1 + - r-tidyr=1.0.2 + - r-tidyselect=1.0.0 + - r-tidyverse=1.3.0 + - r-tinytex=0.22 + - r-usethis=1.6.1 + - r-utf8=1.1.4 + - r-vctrs=0.2.4 + - r-viridislite=0.3.0 + - r-whisker=0.4 + - r-withr=2.2.0 + - r-xfun=0.13 + - r-xml2=1.3.2 + - r-xopen=1.0.0 + - r-yaml=2.2.1 + - r-zeallot=0.1.0 + - readline=8.0 + - sed=4.7 + - setuptools=46.1.3 + - sqlite=3.30.1 + - tk=8.6.10 + - tktable=2.10 + - wheel=0.34.2 + - xorg-kbproto=1.0.7 + - xorg-libice=1.0.10 + - xorg-libsm=1.2.3 + - xorg-libx11=1.6.9 + - xorg-libxau=1.0.9 + - xorg-libxdmcp=1.1.3 + - xorg-libxext=1.3.4 + - xorg-libxrender=0.9.10 + - xorg-renderproto=0.11.1 + - xorg-xextproto=7.3.0 + - xorg-xproto=7.0.31 + - xz=5.2.5 + - zlib=1.2.11 + - zstd=1.4.4 + From cc3d22db179ce79fe61fab906083b12171a95c87 Mon Sep 17 00:00:00 2001 From: lkhilton Date: Thu, 14 Nov 2024 12:48:40 -0800 Subject: [PATCH 2/2] Add missing wget conda env --- modules/battenberg/1.2/battenberg.smk | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/battenberg/1.2/battenberg.smk b/modules/battenberg/1.2/battenberg.smk index 4a64250ef..eed9ed8cf 100644 --- a/modules/battenberg/1.2/battenberg.smk +++ b/modules/battenberg/1.2/battenberg.smk @@ -86,6 +86,7 @@ rule _battenberg_get_reference: **CFG["resources"]["reference"] threads: CFG["threads"]["reference"] + conda: CFG["conda"]["wget"] shell: op.as_one_line(""" wget -qO- {params.url}/battenberg_impute_{params.alt_build}.tar.gz |