From 80fb828bdc86db95fbcb8f105c9ba44f1cb9f39a Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 19 Jan 2021 13:11:13 +0100 Subject: [PATCH 1/3] fix: Add complete conda env to faster solving --- environment.yml | 562 +++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 529 insertions(+), 33 deletions(-) diff --git a/environment.yml b/environment.yml index f16b2d11e..8900046f3 100644 --- a/environment.yml +++ b/environment.yml @@ -6,36 +6,532 @@ channels: - bioconda - defaults dependencies: - - conda-forge::llvm-openmp=8.0.1 - - conda-forge::openmp=8.0.1 - - conda-forge::markdown=3.1.1 - - conda-forge::pymdown-extensions=6.0 - - conda-forge::pygments=2.5.2 - - bioconda::ascat=2.5.2 - - bioconda::bcftools=1.9 - - bioconda::bwa-mem2=2.0 - - bioconda::bwa=0.7.17 - - bioconda::cancerit-allelecount=4.0.2 - - bioconda::cnvkit=0.9.6 - - bioconda::control-freec=11.6 - - bioconda::ensembl-vep=99.2 - - bioconda::fastqc=0.11.9 - - bioconda::fgbio=1.1.0 - - bioconda::freebayes=1.3.2 - - bioconda::gatk4-spark=4.1.7.0 - - bioconda::genesplicer=1.0 - - bioconda::htslib=1.9 - - bioconda::manta=1.6.0 - - bioconda::msisensor=0.5 - - bioconda::multiqc=1.8 - - bioconda::qualimap=2.2.2d - - bioconda::samblaster=0.1.24 - - bioconda::samtools=1.9 - - bioconda::snpeff=4.3.1t - - bioconda::strelka=2.9.10 - - bioconda::tiddit=2.7.1 - - bioconda::trim-galore=0.6.5 - - bioconda::vcfanno=0.3.2 - - bioconda::vcftools=0.1.16 - - conda-forge::pigz=2.3.4 - - conda-forge::r-ggplot2=3.3.0 + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=1_gnu + - _r-mutex=1.0.1=anacondar_1 + - ascat=2.5.2=r40_2 + - backports=1.0=py27_1 + - backports.functools_lru_cache=1.6.1=py_0 + - backports_abc=0.5=py27_0 + - bcftools=1.9=ha228f0b_4 + - binutils_impl_linux-64=2.35.1=h17ad2fc_1 + - binutils_linux-64=2.35=hc3fd857_29 + - bioconductor-biobase=2.50.0=r40h037d062_0 + - bioconductor-biocgenerics=0.36.0=r40_0 + - bioconductor-biocparallel=1.24.0=r40h5f743cb_0 + - bioconductor-biostrings=2.58.0=r40h037d062_0 + - bioconductor-delayedarray=0.16.0=r40h037d062_0 + - bioconductor-dnacopy=1.64.0=r40h323e27b_0 + - bioconductor-genomeinfodb=1.26.0=r40_0 + - bioconductor-genomeinfodbdata=1.2.4=r40_0 + - bioconductor-genomicalignments=1.26.0=r40h037d062_0 + - bioconductor-genomicranges=1.42.0=r40h037d062_0 + - bioconductor-iranges=2.24.0=r40h037d062_0 + - bioconductor-matrixgenerics=1.2.0=r40_0 + - bioconductor-noiseq=2.34.0=r40_0 + - bioconductor-rhtslib=1.22.0=r40h037d062_0 + - bioconductor-rsamtools=2.6.0=r40h5f743cb_0 + - bioconductor-rtracklayer=1.50.0=r40h9bb0e53_1 + - bioconductor-s4vectors=0.28.0=r40h037d062_0 + - bioconductor-summarizedexperiment=1.20.0=r40_0 + - bioconductor-xvector=0.30.0=r40h037d062_0 + - bioconductor-zlibbioc=1.36.0=r40h037d062_0 + - biopython=1.76=py27h516909a_0 + - blas=1.0=mkl + - brotlipy=0.7.0=py27h516909a_1000 + - bwa=0.7.17=hed695b0_7 + - bwa-mem2=2.0=he513fc3_1 + - bwidget=1.9.14=0 + - bz2file=0.98=py_0 + - bzip2=1.0.8=h7f98852_4 + - c-ares=1.17.1=h36c2ea0_0 + - ca-certificates=2020.12.8=h06a4308_0 + - cairo=1.16.0=hcf35c78_1003 + - cancerit-allelecount=4.0.2=ha228f0b_1 + - certifi=2020.6.20=pyhd3eb1b0_3 + - cffi=1.14.0=py27hd463f26_0 + - chardet=3.0.4=py27h8c360ce_1006 + - click=7.1.2=pyh9f0ad1d_0 + - clustalw=2.1=hc9558a2_5 + - cmake=3.17.0=h28c56e5_0 + - cnvkit=0.9.6=py27_1 + - coloredlogs=14.0=py27h8c360ce_1 + - colormath=3.0.0=py_2 + - control-freec=11.6=he1b5a44_0 + - cryptography=2.8=py27h2c19f6a_2 + - curl=7.71.1=he644dc0_8 + - cutadapt=1.18=py27h14c3975_1 + - cycler=0.10.0=py27_0 + - dbus=1.13.18=hb2f20db_0 + - decorator=4.4.2=py_0 + - ensembl-vep=99.2=pl526hecc5488_0 + - enum34=1.1.10=py27h8c360ce_1 + - expat=2.2.10=he6710b0_2 + - fastqc=0.11.9=0 + - fgbio=1.1.0=0 + - font-ttf-dejavu-sans-mono=2.37=hab24e00_0 + - font-ttf-inconsolata=2.001=hab24e00_0 + - font-ttf-source-code-pro=2.030=hab24e00_0 + - font-ttf-ubuntu=0.83=hab24e00_0 + - fontconfig=2.13.1=hba837de_1004 + - fonts-conda-ecosystem=1=0 + - fonts-conda-forge=1=0 + - freebayes=1.3.2=py27h49fb759_2 + - freetype=2.10.4=h0708190_1 + - fribidi=1.0.10=h516909a_0 + - functools32=3.2.3.2=py27_2 + - future=0.18.2=py27h8c360ce_1 + - futures=3.3.0=py27h8c360ce_1 + - gatk4=4.1.7.0=py38_0 + - gatk4-spark=4.1.7.0=0 + - gcc_impl_linux-64=7.5.0=habd7529_18 + - gcc_linux-64=7.5.0=he2a3fca_29 + - genesplicer=1.0=1 + - gettext=0.19.8.1=hf34092f_1004 + - gfortran_impl_linux-64=7.5.0=h56cb351_18 + - gfortran_linux-64=7.5.0=ha081f1e_29 + - giflib=5.2.1=h516909a_2 + - glib=2.66.3=h58526e2_0 + - graphite2=1.3.14=h23475e2_0 + - graphviz=2.42.3=h0511662_0 + - gsl=2.6=he838d99_2 + - gst-plugins-base=1.14.5=h0935bb2_2 + - gstreamer=1.14.5=h36ae1b5_2 + - gxx_impl_linux-64=7.5.0=hd0bb8aa_18 + - gxx_linux-64=7.5.0=h547f3ba_29 + - harfbuzz=2.4.0=h9f30f68_3 + - htslib=1.9=ha228f0b_7 + - humanfriendly=8.1=py27h8c360ce_1 + - icu=64.2=he1b5a44_1 + - idna=2.10=pyh9f0ad1d_0 + - intel-openmp=2020.2=254 + - ipaddress=1.0.23=py_0 + - jinja2=2.11.2=pyh9f0ad1d_0 + - joblib=0.14.1=pyh9f0ad1d_0 + - jpeg=9d=h516909a_0 + - kernel-headers_linux-64=2.6.32=h77966d4_13 + - kiwisolver=1.1.0=py27h9e3301b_1 + - krb5=1.17.2=h926e7f8_0 + - ld_impl_linux-64=2.35.1=hed1e6ac_1 + - libblas=3.8.0=21_mkl + - libcblas=3.8.0=21_mkl + - libclang=9.0.1=default_hde54327_0 + - libcurl=7.71.1=hcdd3856_8 + - libdb=6.2.32=he1b5a44_0 + - libdeflate=1.0=h14c3975_1 + - libedit=3.1.20191231=h46ee950_2 + - libev=4.33=h516909a_1 + - libffi=3.2.1=he1b5a44_1007 + - libgcc=7.2.0=h69d50b8_2 + - libgcc-devel_linux-64=7.5.0=hda03d7c_18 + - libgcc-ng=9.3.0=h2828fa1_18 + - libgd=2.2.5=h307a58e_1007 + - libgfortran-ng=7.5.0=h14aa051_18 + - libgfortran4=7.5.0=h14aa051_18 + - libglib=2.66.3=hbe7bbb4_0 + - libgomp=9.3.0=h2828fa1_18 + - libiconv=1.16=h516909a_0 + - liblapack=3.8.0=21_mkl + - libllvm9=9.0.1=hf817b99_2 + - libnghttp2=1.41.0=h8cfc5f6_2 + - libpng=1.6.37=hed695b0_2 + - libssh2=1.9.0=hab1572f_5 + - libstdcxx-devel_linux-64=7.5.0=hb016644_18 + - libstdcxx-ng=9.3.0=h6de172a_18 + - libtiff=4.1.0=hc3755c2_3 + - libtool=2.4.6=h58526e2_1007 + - libuuid=2.32.1=h14c3975_1000 + - libuv=1.40.0=hd18ef5c_0 + - libwebp=1.0.2=h56121f0_5 + - libxcb=1.14=h7b6447c_0 + - libxkbcommon=0.10.0=he1b5a44_0 + - libxml2=2.9.10=hee79883_0 + - libxslt=1.1.33=h31b3aaa_0 + - llvm-openmp=8.0.1=hc9558a2_0 + - lz4-c=1.9.3=h9c3ff4c_0 + - lzstring=1.0.4=py_1001 + - make=4.3=hd18ef5c_1 + - manta=1.6.0=py27_0 + - markdown=3.1.1=py_0 + - markupsafe=1.1.1=py27hdf8410d_1 + - matplotlib=2.2.5=ha770c72_3 + - matplotlib-base=2.2.5=py27h250f245_1 + - mkl=2020.2=256 + - mkl-service=2.3.0=py27he904b0f_0 + - mkl_fft=1.0.15=py27ha843d7b_0 + - mkl_random=1.1.0=py27hd6b4f25_0 + - monotonic=1.5=py_0 + - msisensor=0.5=h25a10a7_1 + - multiqc=1.8=py_2 + - mysql-connector-c=6.1.11=h6eb9d5d_1007 + - ncurses=6.1=hf484d3e_1002 + - networkx=2.2=py_1 + - nspr=4.29=he1b5a44_1 + - nss=3.55=he751ad9_0 + - numpy=1.16.6=py27hbc911f0_0 + - numpy-base=1.16.6=py27hde5b4d6_0 + - olefile=0.46=pyh9f0ad1d_1 + - openjdk=8.0.265=h516909a_0 + - openmp=8.0.1=0 + - openssl=1.1.1i=h7f98852_0 + - paml=4.9=h516909a_5 + - pandas=0.24.2=py27hf484d3e_0 + - pango=1.42.4=h7062337_4 + - parallel=20201122=ha770c72_0 + - pcre=8.44=he1b5a44_0 + - pcre2=10.35=h032f7d1_2 + - perl=5.26.2=h36c2ea0_1008 + - perl-aceperl=1.92=pl526_2 + - perl-algorithm-diff=1.1903=pl526_2 + - perl-algorithm-munkres=0.08=pl526_1 + - perl-apache-test=1.40=pl526_1 + - perl-app-cpanminus=1.7044=pl526_1 + - perl-appconfig=1.71=pl526_1 + - perl-array-compare=3.0.1=pl526_1 + - perl-autoloader=5.74=pl526_2 + - perl-base=2.23=pl526_1 + - perl-bio-asn1-entrezgene=1.73=pl526_0 + - perl-bio-coordinate=1.007001=pl526_0 + - perl-bio-db-hts=3.01=pl526hed50d52_0 + - perl-bio-featureio=1.6.905=pl526_1 + - perl-bio-phylo=0.58=pl526_1 + - perl-bio-samtools=1.43=pl526h1341992_1 + - perl-bio-tools-phylo-paml=1.7.3=pl526_0 + - perl-bio-tools-run-alignment-clustalw=1.7.4=pl526_0 + - perl-bio-tools-run-alignment-tcoffee=1.7.4=pl526_1 + - perl-bioperl=1.7.2=pl526_10 + - perl-bioperl-core=1.007002=pl526_1 + - perl-bioperl-run=1.007002=pl526_3 + - perl-business-isbn=3.004=pl526_0 + - perl-business-isbn-data=20140910.003=pl526_0 + - 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r-evaluate=0.14=r40h6115d3f_2 + - r-fansi=0.4.2=r40hcfec24a_0 + - r-farver=2.0.3=r40h0357c0b_1 + - r-formatr=1.7=r40h6115d3f_2 + - r-futile.logger=1.4.3=r40h6115d3f_1003 + - r-futile.options=1.0.1=r40h6115d3f_1002 + - r-getopt=1.20.3=r40_2 + - r-ggplot2=3.3.0=r40h6115d3f_1 + - r-glue=1.4.2=r40hcfec24a_0 + - r-gtable=0.3.0=r40h6115d3f_3 + - r-isoband=0.2.3=r40h03ef668_0 + - r-jsonlite=1.7.2=r40hcfec24a_0 + - r-labeling=0.4.2=r40h142f84f_0 + - r-lambda.r=1.2.4=r40h6115d3f_1 + - r-lattice=0.20_41=r40hcfec24a_3 + - r-lifecycle=0.2.0=r40h6115d3f_1 + - r-magrittr=2.0.1=r40hcfec24a_1 + - r-mass=7.3_53=r40hcfec24a_0 + - r-matrix=1.3_2=r40he454529_0 + - r-matrixstats=0.57.0=r40hcfec24a_0 + - r-mgcv=1.8_33=r40h7fa42b6_0 + - r-munsell=0.5.0=r40h6115d3f_1003 + - r-nlme=3.1_150=r40h31ca83e_0 + - r-optparse=1.6.6=r40h6115d3f_1 + - r-pillar=1.4.7=r40hc72bb7e_0 + - r-pkgbuild=1.2.0=r40hc72bb7e_0 + - r-pkgconfig=2.0.3=r40h6115d3f_1 + - r-pkgload=1.1.0=r40h0357c0b_0 + - r-praise=1.0.0=r40h6115d3f_1004 + - r-prettyunits=1.1.1=r40h6115d3f_1 + - r-processx=3.4.5=r40hcfec24a_0 + - r-ps=1.5.0=r40hcfec24a_0 + - r-r.devices=2.16.1=r40h6115d3f_1 + - r-r.methodss3=1.8.1=r40h6115d3f_0 + - r-r.oo=1.24.0=r40h6115d3f_0 + - r-r.utils=2.10.1=r40h6115d3f_0 + - r-r6=2.5.0=r40hc72bb7e_0 + - r-rcolorbrewer=1.1_2=r40h6115d3f_1003 + - r-rcpp=1.0.6=r40h03ef668_0 + - r-rcurl=1.98_1.2=r40hcdcec82_1 + - r-rematch2=2.1.2=r40h6115d3f_1 + - r-rlang=0.4.10=r40hcfec24a_0 + - r-rprojroot=2.0.2=r40hc72bb7e_0 + - r-rstudioapi=0.13=r40hc72bb7e_0 + - r-scales=1.1.1=r40h6115d3f_0 + - r-snow=0.4_3=r40h6115d3f_1002 + - r-testthat=3.0.1=r40h03ef668_0 + - r-tibble=3.0.5=r40hcfec24a_0 + - r-utf8=1.1.4=r40hcdcec82_1003 + - r-vctrs=0.3.6=r40hcfec24a_0 + - r-viridislite=0.3.0=r40h6115d3f_1003 + - r-waldo=0.2.3=r40hc72bb7e_0 + - r-withr=2.4.0=r40hc72bb7e_0 + - r-xml=3.99_0.5=r40hcfec24a_0 + - r-zeallot=0.1.0=r40h6115d3f_1002 + - readline=8.0=h46ee950_1 + - reportlab=3.5.42=py27heca39a3_0 + - requests=2.25.1=pyhd3deb0d_0 + - rhash=1.4.1=h7f98852_0 + - samblaster=0.1.24=hc9558a2_3 + - samtools=1.9=h10a08f8_12 + - scipy=1.2.1=py27h921218d_2 + - sed=4.8=he412f7d_0 + - setuptools=44.0.0=py27_0 + - simplejson=3.17.0=py27hdf8410d_1 + - singledispatch=3.4.0.3=py27_1000 + - six=1.15.0=pyh9f0ad1d_0 + - snpeff=4.3.1t=0 + - spectra=0.0.11=py_1 + - sqlite=3.32.3=hcee41ef_1 + - strelka=2.9.10=0 + - subprocess32=3.5.4=py27h516909a_0 + - sysroot_linux-64=2.12=h77966d4_13 + - t_coffee=11.0.8=py27hea885bf_8 + - tiddit=2.7.1=py27hb3f55d8_1 + - tidyp=1.04=h516909a_2 + - tk=8.6.10=hed695b0_1 + - tktable=2.10=hb7b940f_3 + - tornado=5.1.1=py27h14c3975_1000 + - trim-galore=0.6.5=0 + - unzip=6.0=h516909a_2 + - urllib3=1.26.2=pyhd8ed1ab_0 + - vcfanno=0.3.2=0 + - vcftools=0.1.16=he513fc3_4 + - wheel=0.36.2=pyhd3deb0d_0 + - xopen=0.8.4=py27h8c360ce_1 + - xorg-kbproto=1.0.7=h14c3975_1002 + - xorg-libice=1.0.10=h516909a_0 + - xorg-libsm=1.2.3=h84519dc_1000 + - xorg-libx11=1.6.12=h516909a_0 + - xorg-libxext=1.3.4=h516909a_0 + - xorg-libxpm=3.5.13=h516909a_0 + - xorg-libxrender=0.9.10=h516909a_1002 + - xorg-libxt=1.1.5=h516909a_1003 + - xorg-renderproto=0.11.1=h14c3975_1002 + - xorg-xextproto=7.3.0=h14c3975_1002 + - xorg-xproto=7.0.31=h14c3975_1007 + - xz=5.2.5=h516909a_1 + - yaml=0.2.5=h516909a_0 + - zlib=1.2.11=h516909a_1010 + - zstd=1.4.8=ha95c52a_1 + - pip: + - pyqt5-sip==4.19.18 + - pyqtwebengine==5.12.1 \ No newline at end of file From ed61fae75ebc899bad093e202fafb228538dfcd4 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 19 Jan 2021 13:28:51 +0100 Subject: [PATCH 2/3] fix: remove some package for nf-core lint --- environment.yml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/environment.yml b/environment.yml index 8900046f3..0009ae804 100644 --- a/environment.yml +++ b/environment.yml @@ -45,7 +45,6 @@ dependencies: - bz2file=0.98=py_0 - bzip2=1.0.8=h7f98852_4 - c-ares=1.17.1=h36c2ea0_0 - - ca-certificates=2020.12.8=h06a4308_0 - cairo=1.16.0=hcf35c78_1003 - cancerit-allelecount=4.0.2=ha228f0b_1 - certifi=2020.6.20=pyhd3eb1b0_3 @@ -62,11 +61,9 @@ dependencies: - curl=7.71.1=he644dc0_8 - cutadapt=1.18=py27h14c3975_1 - cycler=0.10.0=py27_0 - - dbus=1.13.18=hb2f20db_0 - decorator=4.4.2=py_0 - ensembl-vep=99.2=pl526hecc5488_0 - enum34=1.1.10=py27h8c360ce_1 - - expat=2.2.10=he6710b0_2 - fastqc=0.11.9=0 - fgbio=1.1.0=0 - font-ttf-dejavu-sans-mono=2.37=hab24e00_0 @@ -92,7 +89,6 @@ dependencies: - gfortran_linux-64=7.5.0=ha081f1e_29 - giflib=5.2.1=h516909a_2 - glib=2.66.3=h58526e2_0 - - graphite2=1.3.14=h23475e2_0 - graphviz=2.42.3=h0511662_0 - gsl=2.6=he838d99_2 - gst-plugins-base=1.14.5=h0935bb2_2 @@ -118,7 +114,6 @@ dependencies: - libclang=9.0.1=default_hde54327_0 - libcurl=7.71.1=hcdd3856_8 - libdb=6.2.32=he1b5a44_0 - - libdeflate=1.0=h14c3975_1 - libedit=3.1.20191231=h46ee950_2 - libev=4.33=h516909a_1 - libffi=3.2.1=he1b5a44_1007 @@ -143,7 +138,6 @@ dependencies: - libuuid=2.32.1=h14c3975_1000 - libuv=1.40.0=hd18ef5c_0 - libwebp=1.0.2=h56121f0_5 - - libxcb=1.14=h7b6447c_0 - libxkbcommon=0.10.0=he1b5a44_0 - libxml2=2.9.10=hee79883_0 - libxslt=1.1.33=h31b3aaa_0 @@ -185,7 +179,6 @@ dependencies: - perl-algorithm-diff=1.1903=pl526_2 - perl-algorithm-munkres=0.08=pl526_1 - perl-apache-test=1.40=pl526_1 - - perl-app-cpanminus=1.7044=pl526_1 - perl-appconfig=1.71=pl526_1 - perl-array-compare=3.0.1=pl526_1 - perl-autoloader=5.74=pl526_2 From de73afc0c5eeca6530bbef673ee49dd06914c1de Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 19 Jan 2021 14:41:52 +0100 Subject: [PATCH 3/3] fix: simplify env --- environment.yml | 555 +++--------------------------------------------- 1 file changed, 33 insertions(+), 522 deletions(-) diff --git a/environment.yml b/environment.yml index 0009ae804..909b79279 100644 --- a/environment.yml +++ b/environment.yml @@ -6,525 +6,36 @@ channels: - bioconda - defaults dependencies: - - _libgcc_mutex=0.1=conda_forge - - _openmp_mutex=4.5=1_gnu - - _r-mutex=1.0.1=anacondar_1 - - ascat=2.5.2=r40_2 - - backports=1.0=py27_1 - - backports.functools_lru_cache=1.6.1=py_0 - - backports_abc=0.5=py27_0 - - bcftools=1.9=ha228f0b_4 - - binutils_impl_linux-64=2.35.1=h17ad2fc_1 - - binutils_linux-64=2.35=hc3fd857_29 - - bioconductor-biobase=2.50.0=r40h037d062_0 - - bioconductor-biocgenerics=0.36.0=r40_0 - - bioconductor-biocparallel=1.24.0=r40h5f743cb_0 - - bioconductor-biostrings=2.58.0=r40h037d062_0 - - bioconductor-delayedarray=0.16.0=r40h037d062_0 - - bioconductor-dnacopy=1.64.0=r40h323e27b_0 - - bioconductor-genomeinfodb=1.26.0=r40_0 - - bioconductor-genomeinfodbdata=1.2.4=r40_0 - - bioconductor-genomicalignments=1.26.0=r40h037d062_0 - - bioconductor-genomicranges=1.42.0=r40h037d062_0 - - bioconductor-iranges=2.24.0=r40h037d062_0 - - bioconductor-matrixgenerics=1.2.0=r40_0 - - bioconductor-noiseq=2.34.0=r40_0 - - bioconductor-rhtslib=1.22.0=r40h037d062_0 - - bioconductor-rsamtools=2.6.0=r40h5f743cb_0 - - bioconductor-rtracklayer=1.50.0=r40h9bb0e53_1 - - bioconductor-s4vectors=0.28.0=r40h037d062_0 - - bioconductor-summarizedexperiment=1.20.0=r40_0 - - bioconductor-xvector=0.30.0=r40h037d062_0 - - bioconductor-zlibbioc=1.36.0=r40h037d062_0 - - biopython=1.76=py27h516909a_0 - 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