https://bioinformaticsonline.com/snippets/view/41672/installing-busco-version-406? https://bioinformaticsonline.com/snippets/view/41672/installing-busco-version-406 Wed, 13 May 2020 11:26:26 -0500 https://bioinformaticsonline.com/snippets/view/41672/installing-busco-version-406 (base) jit@jit-HP-Pro-3335-MT: conda install -c bioconda -c conda-forge busco=4.0.6 Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/jit/anaconda3 added / updated specs: - busco=4.0.6 The following packages will be downloaded: package | build ---------------------------|----------------- _r-mutex-1.0.1 | anacondar_1 3 KB conda-forge augustus-3.2.3 | pl526hcfae127_5 25.8 MB bioconda bamtools-2.4.1 | 1 737 KB bioconda binutils_impl_linux-64-2.34| h53a641e_0 9.2 MB conda-forge binutils_linux-64-2.34 | hc952b39_18 21 KB conda-forge biopython-1.76 | py37h516909a_0 2.6 MB conda-forge blast-2.2.31 | 1 131.2 MB bioconda busco-4.0.6 | pyr36_0 57 KB bioconda bwidget-1.9.14 | 0 119 KB conda-forge dendropy-4.4.0 | py_1 299 KB bioconda findutils-4.6.0 | h14c3975_1000 611 KB conda-forge gcc_impl_linux-64-7.3.0 | habb00fd_1 73.2 MB gcc_linux-64-7.3.0 | h553295d_18 22 KB conda-forge gettext-0.19.8.1 | hc5be6a0_1002 3.6 MB conda-forge gfortran_impl_linux-64-7.3.0| hdf63c60_5 9.4 MB conda-forge gfortran_linux-64-7.3.0 | h553295d_18 21 KB conda-forge gsl-2.2.1 | h0c605f7_3 2.6 MB gxx_impl_linux-64-7.3.0 | hdf63c60_1 18.7 MB gxx_linux-64-7.3.0 | h553295d_18 21 KB conda-forge hmmer-3.1b2 | 3 5.5 MB bioconda ld_impl_linux-64-2.34 | h53a641e_0 616 KB conda-forge libgfortran-3.0.0 | 1 281 KB conda-forge libpng-1.6.37 | hed695b0_1 308 KB conda-forge libssh2-1.9.0 | hab1572f_1 320 KB conda-forge lp_solve-5.5.2.5 | h14c3975_1001 419 KB conda-forge make-4.3 | h516909a_0 505 KB conda-forge metis-5.1.0 | he1b5a44_1005 4.1 MB conda-forge openblas-0.2.20 | 8 17.0 MB conda-forge perl-cpan-meta-2.150010 | pl526_0 5 KB bioconda perl-cpan-meta-requirements-2.140| pl526_0 12 KB bioconda perl-cpan-meta-yaml-0.018 | pl526_0 11 KB bioconda perl-extutils-cbuilder-0.280230| pl526_1 21 KB bioconda perl-extutils-manifest-1.72| pl526_0 13 KB bioconda perl-extutils-parsexs-3.35 | pl526_0 38 KB bioconda perl-json-pp-4.04 | pl526_0 30 KB bioconda perl-module-build-0.4224 | pl526_3 126 KB bioconda perl-text-abbrev-1.02 | pl526_0 5 KB bioconda perl-text-parsewords-3.30 | pl526_0 8 KB bioconda prodigal-2.6.3 | h516909a_2 777 KB bioconda r-assertthat-0.2.1 | r36h6115d3f_2 70 KB conda-forge r-backports-1.1.6 | r36hcdcec82_2 77 KB conda-forge r-base-3.6.0 | hce969dd_0 39.4 MB r-callr-3.4.3 | r36h6115d3f_1 392 KB conda-forge r-cli-2.0.2 | r36h6115d3f_1 395 KB conda-forge r-colorspace-1.4_1 | r36hcdcec82_2 2.4 MB conda-forge r-crayon-1.3.4 | r36h6115d3f_1003 747 KB conda-forge r-desc-1.2.0 | r36h6115d3f_1003 290 KB conda-forge r-digest-0.6.25 | r36h0357c0b_2 199 KB conda-forge r-ellipsis-0.3.0 | r36hcdcec82_1 47 KB conda-forge r-evaluate-0.14 | r36h6115d3f_2 81 KB conda-forge r-fansi-0.4.1 | r36hcdcec82_1 196 KB conda-forge r-farver-2.0.3 | r36h0357c0b_1 1.4 MB conda-forge r-ggplot2-3.3.0 | r36h6115d3f_1 3.9 MB conda-forge r-glue-1.4.0 | r36hcdcec82_1 144 KB conda-forge r-gtable-0.3.0 | r36h6115d3f_3 423 KB conda-forge r-isoband-0.2.1 | r36h0357c0b_1 2.5 MB conda-forge r-labeling-0.3 | r36h6115d3f_1003 67 KB conda-forge r-lattice-0.20_41 | r36hcdcec82_2 1.1 MB conda-forge r-lifecycle-0.2.0 | r36h6115d3f_1 112 KB conda-forge r-magrittr-1.5 | r36h6115d3f_1003 167 KB conda-forge r-mass-7.3_51.6 | r36hcdcec82_2 1.1 MB conda-forge r-matrix-1.2_18 | r36hcdcec82_0 3.8 MB conda-forge r-mgcv-1.8_31 | r36hcdcec82_0 2.7 MB conda-forge r-munsell-0.5.0 | r36h6115d3f_1003 246 KB conda-forge r-nlme-3.1_147 | r36h9bbef5b_1 2.3 MB conda-forge r-pillar-1.4.4 | r36h6115d3f_0 197 KB conda-forge r-pkgbuild-1.0.8 | r36h6115d3f_0 153 KB conda-forge r-pkgconfig-2.0.3 | r36h6115d3f_1 24 KB conda-forge r-pkgload-1.0.2 | r36h0357c0b_1002 162 KB conda-forge r-praise-1.0.0 | r36h6115d3f_1004 23 KB conda-forge r-prettyunits-1.1.1 | r36h6115d3f_1 41 KB conda-forge r-processx-3.4.2 | r36hcdcec82_1 271 KB conda-forge r-ps-1.3.3 | r36hcdcec82_0 235 KB conda-forge r-r6-2.4.1 | r36h6115d3f_1 63 KB conda-forge r-rcolorbrewer-1.1_2 | r36h6115d3f_1003 59 KB conda-forge r-rcpp-1.0.4.6 | r36h0357c0b_1 1.9 MB conda-forge r-rlang-0.4.6 | r36hcdcec82_0 1.0 MB conda-forge r-rprojroot-1.3_2 | r36h6115d3f_1003 94 KB conda-forge r-rstudioapi-0.11 | r36h6115d3f_1 267 KB conda-forge r-scales-1.1.1 | r36h6115d3f_0 558 KB conda-forge r-testthat-2.3.2 | r36h0357c0b_1 1.1 MB conda-forge r-tibble-3.0.1 | r36hcdcec82_1 382 KB conda-forge r-utf8-1.1.4 | r36hcdcec82_1003 161 KB conda-forge r-vctrs-0.3.0 | r36hcdcec82_0 959 KB conda-forge r-viridislite-0.3.0 | r36h6115d3f_1003 64 KB conda-forge r-withr-2.2.0 | r36h6115d3f_1 227 KB conda-forge r-zeallot-0.1.0 | r36h6115d3f_1002 62 KB conda-forge sepp-4.3.10 | py37_0 6.6 MB bioconda suitesparse-5.2.0 | h9e4a6bb_0 2.4 MB tktable-2.10 | h14c3975_0 88 KB ------------------------------------------------------------ Total: 389.5 MB The following NEW packages will be INSTALLED: _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 augustus bioconda/linux-64::augustus-3.2.3-pl526hcfae127_5 bamtools bioconda/linux-64::bamtools-2.4.1-1 binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h53a641e_0 binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.34-hc952b39_18 biopython conda-forge/linux-64::biopython-1.76-py37h516909a_0 blast bioconda/linux-64::blast-2.2.31-1 busco bioconda/noarch::busco-4.0.6-pyr36_0 bwidget conda-forge/linux-64::bwidget-1.9.14-0 dendropy bioconda/noarch::dendropy-4.4.0-py_1 findutils conda-forge/linux-64::findutils-4.6.0-h14c3975_1000 gcc_impl_linux-64 pkgs/main/linux-64::gcc_impl_linux-64-7.3.0-habb00fd_1 gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.3.0-h553295d_18 gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002 gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_5 gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-7.3.0-h553295d_18 gsl pkgs/main/linux-64::gsl-2.2.1-h0c605f7_3 gxx_impl_linux-64 pkgs/main/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_1 gxx_linux-64 conda-forge/linux-64::gxx_linux-64-7.3.0-h553295d_18 hmmer bioconda/linux-64::hmmer-3.1b2-3 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 libgfortran conda-forge/linux-64::libgfortran-3.0.0-1 lp_solve conda-forge/linux-64::lp_solve-5.5.2.5-h14c3975_1001 make conda-forge/linux-64::make-4.3-h516909a_0 metis conda-forge/linux-64::metis-5.1.0-he1b5a44_1005 openblas conda-forge/linux-64::openblas-0.2.20-8 perl-app-cpanminus bioconda/linux-64::perl-app-cpanminus-1.7044-pl526_1 perl-carp bioconda/linux-64::perl-carp-1.38-pl526_3 perl-constant bioconda/linux-64::perl-constant-1.33-pl526_1 perl-cpan-meta bioconda/linux-64::perl-cpan-meta-2.150010-pl526_0 perl-cpan-meta-re~ bioconda/linux-64::perl-cpan-meta-requirements-2.140-pl526_0 perl-cpan-meta-ya~ bioconda/linux-64::perl-cpan-meta-yaml-0.018-pl526_0 perl-data-dumper bioconda/linux-64::perl-data-dumper-2.173-pl526_0 perl-dbi bioconda/linux-64::perl-dbi-1.642-pl526_0 perl-encode bioconda/linux-64::perl-encode-2.88-pl526_1 perl-exporter bioconda/linux-64::perl-exporter-5.72-pl526_1 perl-extutils-cbu~ bioconda/linux-64::perl-extutils-cbuilder-0.280230-pl526_1 perl-extutils-mak~ bioconda/linux-64::perl-extutils-makemaker-7.36-pl526_1 perl-extutils-man~ bioconda/linux-64::perl-extutils-manifest-1.72-pl526_0 perl-extutils-par~ bioconda/linux-64::perl-extutils-parsexs-3.35-pl526_0 perl-file-path bioconda/linux-64::perl-file-path-2.16-pl526_0 perl-file-temp bioconda/linux-64::perl-file-temp-0.2304-pl526_2 perl-getopt-long bioconda/linux-64::perl-getopt-long-2.50-pl526_1 perl-ipc-cmd bioconda/linux-64::perl-ipc-cmd-1.02-pl526_0 perl-json-pp bioconda/noarch::perl-json-pp-4.04-pl526_0 perl-locale-maket~ bioconda/linux-64::perl-locale-maketext-simple-0.21-pl526_2 perl-module-build bioconda/linux-64::perl-module-build-0.4224-pl526_3 perl-module-corel~ bioconda/linux-64::perl-module-corelist-5.20190524-pl526_0 perl-module-load bioconda/linux-64::perl-module-load-0.32-pl526_1 perl-module-load-~ bioconda/linux-64::perl-module-load-conditional-0.68-pl526_2 perl-module-metad~ bioconda/linux-64::perl-module-metadata-1.000036-pl526_0 perl-params-check bioconda/linux-64::perl-params-check-0.38-pl526_1 perl-parent bioconda/linux-64::perl-parent-0.236-pl526_1 perl-perl-ostype bioconda/linux-64::perl-perl-ostype-1.010-pl526_1 perl-scalar-list-~ bioconda/linux-64::perl-scalar-list-utils-1.52-pl526h516909a_0 perl-text-abbrev bioconda/linux-64::perl-text-abbrev-1.02-pl526_0 perl-text-parsewo~ bioconda/linux-64::perl-text-parsewords-3.30-pl526_0 perl-version bioconda/linux-64::perl-version-0.9924-pl526_0 perl-yaml bioconda/noarch::perl-yaml-1.29-pl526_0 prodigal bioconda/linux-64::prodigal-2.6.3-h516909a_2 r-assertthat conda-forge/noarch::r-assertthat-0.2.1-r36h6115d3f_2 r-backports conda-forge/linux-64::r-backports-1.1.6-r36hcdcec82_2 r-base pkgs/r/linux-64::r-base-3.6.0-hce969dd_0 r-callr conda-forge/noarch::r-callr-3.4.3-r36h6115d3f_1 r-cli conda-forge/noarch::r-cli-2.0.2-r36h6115d3f_1 r-colorspace conda-forge/linux-64::r-colorspace-1.4_1-r36hcdcec82_2 r-crayon conda-forge/noarch::r-crayon-1.3.4-r36h6115d3f_1003 r-desc conda-forge/noarch::r-desc-1.2.0-r36h6115d3f_1003 r-digest conda-forge/linux-64::r-digest-0.6.25-r36h0357c0b_2 r-ellipsis conda-forge/linux-64::r-ellipsis-0.3.0-r36hcdcec82_1 r-evaluate conda-forge/noarch::r-evaluate-0.14-r36h6115d3f_2 r-fansi conda-forge/linux-64::r-fansi-0.4.1-r36hcdcec82_1 r-farver conda-forge/linux-64::r-farver-2.0.3-r36h0357c0b_1 r-ggplot2 conda-forge/noarch::r-ggplot2-3.3.0-r36h6115d3f_1 r-glue conda-forge/linux-64::r-glue-1.4.0-r36hcdcec82_1 r-gtable conda-forge/noarch::r-gtable-0.3.0-r36h6115d3f_3 r-isoband conda-forge/linux-64::r-isoband-0.2.1-r36h0357c0b_1 r-labeling conda-forge/noarch::r-labeling-0.3-r36h6115d3f_1003 r-lattice conda-forge/linux-64::r-lattice-0.20_41-r36hcdcec82_2 r-lifecycle conda-forge/noarch::r-lifecycle-0.2.0-r36h6115d3f_1 r-magrittr conda-forge/noarch::r-magrittr-1.5-r36h6115d3f_1003 r-mass conda-forge/linux-64::r-mass-7.3_51.6-r36hcdcec82_2 r-matrix conda-forge/linux-64::r-matrix-1.2_18-r36hcdcec82_0 r-mgcv conda-forge/linux-64::r-mgcv-1.8_31-r36hcdcec82_0 r-munsell conda-forge/noarch::r-munsell-0.5.0-r36h6115d3f_1003 r-nlme conda-forge/linux-64::r-nlme-3.1_147-r36h9bbef5b_1 r-pillar conda-forge/noarch::r-pillar-1.4.4-r36h6115d3f_0 r-pkgbuild conda-forge/noarch::r-pkgbuild-1.0.8-r36h6115d3f_0 r-pkgconfig conda-forge/noarch::r-pkgconfig-2.0.3-r36h6115d3f_1 r-pkgload conda-forge/linux-64::r-pkgload-1.0.2-r36h0357c0b_1002 r-praise conda-forge/noarch::r-praise-1.0.0-r36h6115d3f_1004 r-prettyunits conda-forge/noarch::r-prettyunits-1.1.1-r36h6115d3f_1 r-processx conda-forge/linux-64::r-processx-3.4.2-r36hcdcec82_1 r-ps conda-forge/linux-64::r-ps-1.3.3-r36hcdcec82_0 r-r6 conda-forge/noarch::r-r6-2.4.1-r36h6115d3f_1 r-rcolorbrewer conda-forge/noarch::r-rcolorbrewer-1.1_2-r36h6115d3f_1003 r-rcpp conda-forge/linux-64::r-rcpp-1.0.4.6-r36h0357c0b_1 r-rlang conda-forge/linux-64::r-rlang-0.4.6-r36hcdcec82_0 r-rprojroot conda-forge/noarch::r-rprojroot-1.3_2-r36h6115d3f_1003 r-rstudioapi conda-forge/noarch::r-rstudioapi-0.11-r36h6115d3f_1 r-scales conda-forge/noarch::r-scales-1.1.1-r36h6115d3f_0 r-testthat conda-forge/linux-64::r-testthat-2.3.2-r36h0357c0b_1 r-tibble conda-forge/linux-64::r-tibble-3.0.1-r36hcdcec82_1 r-utf8 conda-forge/linux-64::r-utf8-1.1.4-r36hcdcec82_1003 r-vctrs conda-forge/linux-64::r-vctrs-0.3.0-r36hcdcec82_0 r-viridislite conda-forge/noarch::r-viridislite-0.3.0-r36h6115d3f_1003 r-withr conda-forge/noarch::r-withr-2.2.0-r36h6115d3f_1 r-zeallot conda-forge/noarch::r-zeallot-0.1.0-r36h6115d3f_1002 sepp bioconda/linux-64::sepp-4.3.10-py37_0 suitesparse pkgs/main/linux-64::suitesparse-5.2.0-h9e4a6bb_0 tktable pkgs/main/linux-64::tktable-2.10-h14c3975_0 The following packages will be UPDATED: libpng pkgs/main::libpng-1.6.36-hbc83047_0 --> conda-forge::libpng-1.6.37-hed695b0_1 libssh2 pkgs/main::libssh2-1.8.0-h1ba5d50_4 --> conda-forge::libssh2-1.9.0-hab1572f_1 The following packages will be SUPERSEDED by a higher-priority channel: certifi pkgs/main::certifi-2020.4.5.1-py37_0 --> conda-forge::certifi-2020.4.5.1-py37hc8dfbb8_0 Proceed ([y]/n)? y]]> Jit