https://bioinformaticsonline.com/snippets?offset=260 https://bioinformaticsonline.com/snippets/view/40805/bash-command-to-install-gatk-bedtools-and-snpeff Sat, 01 Feb 2020 02:29:09 -0600 https://bioinformaticsonline.com/snippets/view/40805/bash-command-to-install-gatk-bedtools-and-snpeff (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install gatk Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - gatk The following packages will be downloaded: package | build ---------------------------|----------------- certifi-2019.11.28 | py38_0 156 KB gatk-3.8 | 7 8 KB bioconda pip-20.0.2 | py38_1 1.9 MB python-3.8.1 | h0371630_1 57.8 MB r-assertthat-0.2.1 | r36h6115d3f_0 74 KB r-bitops-1.0_6 | r36h96ca727_4 34 KB r-catools-1.17.1.2 | r36h29659fb_0 223 KB r-cli-1.1.0 | r36h6115d3f_0 189 KB r-colorspace-1.4_1 | r36h96ca727_0 2.5 MB r-crayon-1.3.4 | r36h6115d3f_0 757 KB r-dichromat-2.0_0 | r36h6115d3f_4 163 KB r-digest-0.6.18 | r36h96ca727_0 155 KB r-fansi-0.4.0 | r36h96ca727_0 193 KB r-gdata-2.18.0 | r36h6115d3f_0 1.1 MB r-ggplot2-3.1.1 | r36h6115d3f_0 3.6 MB r-glue-1.3.1 | r36h96ca727_0 165 KB r-gplots-3.0.1.1 | r36h6115d3f_0 699 KB r-gsalib-2.1 | r36h6115d3f_0 31 KB r-gtable-0.3.0 | r36h6115d3f_0 425 KB r-gtools-3.8.1 | r36h96ca727_0 325 KB r-kernsmooth-2.23_15 | r36ha65eedd_4 102 KB r-labeling-0.3 | r36h6115d3f_4 71 KB r-lattice-0.20_38 | r36h96ca727_0 1.1 MB r-lazyeval-0.2.2 | r36h96ca727_0 164 KB r-magrittr-1.5 | r36h6115d3f_4 173 KB r-mass-7.3_51.3 | r36h96ca727_0 1.1 MB r-matrix-1.2_17 | r36h96ca727_0 3.8 MB r-mgcv-1.8_28 | r36h96ca727_0 2.6 MB r-munsell-0.5.0 | r36h6115d3f_0 254 KB r-nlme-3.1_139 | r36ha65eedd_0 2.2 MB r-pillar-1.3.1 | r36h6115d3f_0 180 KB r-pkgconfig-2.0.2 | r36h6115d3f_0 25 KB r-plyr-1.8.4 | r36h29659fb_0 815 KB r-r6-2.4.0 | r36h6115d3f_0 68 KB r-rcolorbrewer-1.1_2 | r36h6115d3f_0 62 KB r-rcpp-1.0.1 | r36h29659fb_0 3.3 MB r-reshape-0.8.8 | r36h6115d3f_0 174 KB r-reshape2-1.4.3 | r36h29659fb_0 129 KB r-rlang-0.3.4 | r36h96ca727_0 1.0 MB r-scales-1.0.0 | r36h29659fb_0 580 KB r-stringi-1.4.3 | r36h29659fb_0 773 KB r-stringr-1.4.0 | r36h6115d3f_0 221 KB r-tibble-2.1.1 | r36h96ca727_0 316 KB r-utf8-1.1.4 | r36h96ca727_0 159 KB r-viridislite-0.3.0 | r36h6115d3f_0 66 KB r-withr-2.1.2 | r36h6115d3f_0 181 KB setuptools-45.1.0 | py38_0 657 KB sqlite-3.30.1 | h7b6447c_0 1.9 MB wheel-0.34.1 | py38_0 49 KB ------------------------------------------------------------ Total: 92.5 MB The following NEW packages will be INSTALLED: certifi pkgs/main/linux-64::certifi-2019.11.28-py38_0 gatk bioconda/noarch::gatk-3.8-7 pip pkgs/main/linux-64::pip-20.0.2-py38_1 python pkgs/main/linux-64::python-3.8.1-h0371630_1 r-assertthat pkgs/r/noarch::r-assertthat-0.2.1-r36h6115d3f_0 r-bitops pkgs/r/linux-64::r-bitops-1.0_6-r36h96ca727_4 r-catools pkgs/r/linux-64::r-catools-1.17.1.2-r36h29659fb_0 r-cli pkgs/r/noarch::r-cli-1.1.0-r36h6115d3f_0 r-colorspace pkgs/r/linux-64::r-colorspace-1.4_1-r36h96ca727_0 r-crayon pkgs/r/noarch::r-crayon-1.3.4-r36h6115d3f_0 r-dichromat pkgs/r/noarch::r-dichromat-2.0_0-r36h6115d3f_4 r-digest pkgs/r/linux-64::r-digest-0.6.18-r36h96ca727_0 r-fansi pkgs/r/linux-64::r-fansi-0.4.0-r36h96ca727_0 r-gdata pkgs/r/noarch::r-gdata-2.18.0-r36h6115d3f_0 r-ggplot2 pkgs/r/noarch::r-ggplot2-3.1.1-r36h6115d3f_0 r-glue pkgs/r/linux-64::r-glue-1.3.1-r36h96ca727_0 r-gplots pkgs/r/noarch::r-gplots-3.0.1.1-r36h6115d3f_0 r-gsalib pkgs/r/noarch::r-gsalib-2.1-r36h6115d3f_0 r-gtable pkgs/r/noarch::r-gtable-0.3.0-r36h6115d3f_0 r-gtools pkgs/r/linux-64::r-gtools-3.8.1-r36h96ca727_0 r-kernsmooth pkgs/r/linux-64::r-kernsmooth-2.23_15-r36ha65eedd_4 r-labeling pkgs/r/noarch::r-labeling-0.3-r36h6115d3f_4 r-lattice pkgs/r/linux-64::r-lattice-0.20_38-r36h96ca727_0 r-lazyeval pkgs/r/linux-64::r-lazyeval-0.2.2-r36h96ca727_0 r-magrittr pkgs/r/noarch::r-magrittr-1.5-r36h6115d3f_4 r-mass pkgs/r/linux-64::r-mass-7.3_51.3-r36h96ca727_0 r-matrix pkgs/r/linux-64::r-matrix-1.2_17-r36h96ca727_0 r-mgcv pkgs/r/linux-64::r-mgcv-1.8_28-r36h96ca727_0 r-munsell pkgs/r/noarch::r-munsell-0.5.0-r36h6115d3f_0 r-nlme pkgs/r/linux-64::r-nlme-3.1_139-r36ha65eedd_0 r-pillar pkgs/r/noarch::r-pillar-1.3.1-r36h6115d3f_0 r-pkgconfig pkgs/r/noarch::r-pkgconfig-2.0.2-r36h6115d3f_0 r-plyr pkgs/r/linux-64::r-plyr-1.8.4-r36h29659fb_0 r-r6 pkgs/r/noarch::r-r6-2.4.0-r36h6115d3f_0 r-rcolorbrewer pkgs/r/noarch::r-rcolorbrewer-1.1_2-r36h6115d3f_0 r-rcpp pkgs/r/linux-64::r-rcpp-1.0.1-r36h29659fb_0 r-reshape pkgs/r/linux-64::r-reshape-0.8.8-r36h6115d3f_0 r-reshape2 pkgs/r/linux-64::r-reshape2-1.4.3-r36h29659fb_0 r-rlang pkgs/r/linux-64::r-rlang-0.3.4-r36h96ca727_0 r-scales pkgs/r/linux-64::r-scales-1.0.0-r36h29659fb_0 r-stringi pkgs/r/linux-64::r-stringi-1.4.3-r36h29659fb_0 r-stringr pkgs/r/noarch::r-stringr-1.4.0-r36h6115d3f_0 r-tibble pkgs/r/linux-64::r-tibble-2.1.1-r36h96ca727_0 r-utf8 pkgs/r/linux-64::r-utf8-1.1.4-r36h96ca727_0 r-viridislite pkgs/r/noarch::r-viridislite-0.3.0-r36h6115d3f_0 r-withr pkgs/r/noarch::r-withr-2.1.2-r36h6115d3f_0 setuptools pkgs/main/linux-64::setuptools-45.1.0-py38_0 sqlite pkgs/main/linux-64::sqlite-3.30.1-h7b6447c_0 wheel pkgs/main/linux-64::wheel-0.34.1-py38_0 Proceed ([y]/n)? y Downloading and Extracting Packages pip-20.0.2 | 1.9 MB | ############################################################ | 100% r-glue-1.3.1 | 165 KB | ############################################################ | 100% r-cli-1.1.0 | 189 KB | ############################################################ | 100% r-gsalib-2.1 | 31 KB | ############################################################ | 100% r-munsell-0.5.0 | 254 KB | ############################################################ | 100% r-bitops-1.0_6 | 34 KB | ############################################################ | 100% r-reshape2-1.4.3 | 129 KB | ############################################################ | 100% r-rcpp-1.0.1 | 3.3 MB | ############################################################ | 100% r-lattice-0.20_38 | 1.1 MB | ############################################################ | 100% r-colorspace-1.4_1 | 2.5 MB | ############################################################ | 100% r-gdata-2.18.0 | 1.1 MB | ############################################################ | 100% r-scales-1.0.0 | 580 KB | ############################################################ | 100% r-withr-2.1.2 | 181 KB | ############################################################ | 100% r-matrix-1.2_17 | 3.8 MB | ############################################################ | 100% r-mass-7.3_51.3 | 1.1 MB | ############################################################ | 100% r-mgcv-1.8_28 | 2.6 MB | ############################################################ | 100% setuptools-45.1.0 | 657 KB | ############################################################ | 100% r-labeling-0.3 | 71 KB | ############################################################ | 100% r-lazyeval-0.2.2 | 164 KB | ############################################################ | 100% gatk-3.8 | 8 KB | ############################################################ | 100% certifi-2019.11.28 | 156 KB | ############################################################ | 100% r-dichromat-2.0_0 | 163 KB | ############################################################ | 100% r-gtable-0.3.0 | 425 KB | ############################################################ | 100% r-r6-2.4.0 | 68 KB | ############################################################ | 100% r-tibble-2.1.1 | 316 KB | ############################################################ | 100% r-reshape-0.8.8 | 174 KB | ############################################################ | 100% r-kernsmooth-2.23_15 | 102 KB | ############################################################ | 100% r-plyr-1.8.4 | 815 KB | ############################################################ | 100% r-fansi-0.4.0 | 193 KB | ############################################################ | 100% r-rcolorbrewer-1.1_2 | 62 KB | ############################################################ | 100% r-viridislite-0.3.0 | 66 KB | ############################################################ | 100% r-magrittr-1.5 | 173 KB | ############################################################ | 100% wheel-0.34.1 | 49 KB | ############################################################ | 100% r-pkgconfig-2.0.2 | 25 KB | ############################################################ | 100% python-3.8.1 | 57.8 MB | ############################################################ | 100% sqlite-3.30.1 | 1.9 MB | ############################################################ | 100% r-rlang-0.3.4 | 1.0 MB | ############################################################ | 100% r-assertthat-0.2.1 | 74 KB | ############################################################ | 100% r-utf8-1.1.4 | 159 KB | ############################################################ | 100% r-stringr-1.4.0 | 221 KB | ############################################################ | 100% r-catools-1.17.1.2 | 223 KB | ############################################################ | 100% r-gplots-3.0.1.1 | 699 KB | ############################################################ | 100% r-ggplot2-3.1.1 | 3.6 MB | ############################################################ | 100% r-gtools-3.8.1 | 325 KB | ############################################################ | 100% r-pillar-1.3.1 | 180 KB | ############################################################ | 100% r-nlme-3.1_139 | 2.2 MB | ############################################################ | 100% r-digest-0.6.18 | 155 KB | ############################################################ | 100% r-stringi-1.4.3 | 773 KB | ############################################################ | 100% r-crayon-1.3.4 | 757 KB | ############################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install bedtools Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - bedtools The following packages will be downloaded: package | build ---------------------------|----------------- bedtools-2.29.2 | hc088bd4_0 13.8 MB bioconda ------------------------------------------------------------ Total: 13.8 MB The following NEW packages will be INSTALLED: bedtools bioconda/linux-64::bedtools-2.29.2-hc088bd4_0 Proceed ([y]/n)? y Downloading and Extracting Packages bedtools-2.29.2 | 13.8 MB | ############################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install SnpEff Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - snpeff The following packages will be downloaded: package | build ---------------------------|----------------- snpeff-4.3.1t | 3 19.7 MB bioconda ------------------------------------------------------------ Total: 19.7 MB The following NEW packages will be INSTALLED: snpeff bioconda/noarch::snpeff-4.3.1t-3 Proceed ([y]/n)? t Invalid choice: t Proceed ([y]/n)? y Downloading and Extracting Packages snpeff-4.3.1t | 19.7 MB | ############################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40804/bash-command-to-install-bwa-samtools-picard Sat, 01 Feb 2020 01:55:04 -0600 https://bioinformaticsonline.com/snippets/view/40804/bash-command-to-install-bwa-samtools-picard (base) [wsu29@bladeamd-2 tmp]$ conda install bwa Collecting package metadata (repodata.json): done Solving environment: - The environment is inconsistent, please check the package plan carefully The following packages are causing the inconsistency: - defaults/linux-64::numba==0.43.1=py37h962f231_0 - defaults/linux-64::anaconda==2019.03=py37_0 done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/anaconda3 added / updated specs: - bwa The following packages will be downloaded: package | build ---------------------------|----------------- _anaconda_depends-2019.03 | py37_0 5 KB anaconda-custom | py37_1 3 KB bwa-0.7.17 | hed695b0_7 523 KB bioconda ca-certificates-2020.1.1 | 0 132 KB certifi-2019.11.28 | py37_0 156 KB openssl-1.1.1d | h7b6447c_3 3.7 MB perl-5.26.2 | h14c3975_0 15.9 MB tbb-2019.8 | hfd86e86_0 1.4 MB ------------------------------------------------------------ Total: 21.8 MB The following NEW packages will be INSTALLED: _anaconda_depends pkgs/main/linux-64::_anaconda_depends-2019.03-py37_0 bwa bioconda/linux-64::bwa-0.7.17-hed695b0_7 perl pkgs/main/linux-64::perl-5.26.2-h14c3975_0 tbb pkgs/main/linux-64::tbb-2019.8-hfd86e86_0 The following packages will be UPDATED: ca-certificates 2019.1.23-0 --> 2020.1.1-0 certifi 2019.3.9-py37_0 --> 2019.11.28-py37_0 openssl 1.1.1b-h7b6447c_1 --> 1.1.1d-h7b6447c_3 The following packages will be DOWNGRADED: anaconda 2019.03-py37_0 --> custom-py37_1 Proceed ([y]/n)? y Downloading and Extracting Packages certifi-2019.11.28 | 156 KB | ############################################################ | 100% ca-certificates-2020 | 132 KB | ############################################################ | 100% perl-5.26.2 | 15.9 MB | ############################################################ | 100% bwa-0.7.17 | 523 KB | ############################################################ | 100% anaconda-custom | 3 KB | ############################################################ | 100% openssl-1.1.1d | 3.7 MB | ############################################################ | 100% _anaconda_depends-20 | 5 KB | ############################################################ | 100% tbb-2019.8 | 1.4 MB | ############################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install samtools Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - samtools The following packages will be downloaded: package | build ---------------------------|----------------- bzip2-1.0.8 | h7b6447c_0 105 KB curl-7.67.0 | hbc83047_0 145 KB htslib-1.9 | h4da6232_3 1.2 MB bioconda krb5-1.16.4 | h173b8e3_0 1.4 MB libcurl-7.67.0 | h20c2e04_0 576 KB libdeflate-1.2 | h516909a_1 63 KB bioconda libssh2-1.8.2 | h1ba5d50_0 250 KB libstdcxx-ng-9.1.0 | hdf63c60_0 4.0 MB samtools-1.9 | h10a08f8_12 299 KB bioconda ------------------------------------------------------------ Total: 8.0 MB The following NEW packages will be INSTALLED: bzip2 pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0 ca-certificates pkgs/main/linux-64::ca-certificates-2020.1.1-0 curl pkgs/main/linux-64::curl-7.67.0-hbc83047_0 htslib bioconda/linux-64::htslib-1.9-h4da6232_3 krb5 pkgs/main/linux-64::krb5-1.16.4-h173b8e3_0 libcurl pkgs/main/linux-64::libcurl-7.67.0-h20c2e04_0 libdeflate bioconda/linux-64::libdeflate-1.2-h516909a_1 libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0 libssh2 pkgs/main/linux-64::libssh2-1.8.2-h1ba5d50_0 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 ncurses pkgs/main/linux-64::ncurses-6.1-he6710b0_1 openssl pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3 samtools bioconda/linux-64::samtools-1.9-h10a08f8_12 tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0 xz pkgs/main/linux-64::xz-5.2.4-h14c3975_4 Proceed ([y]/n)? y Downloading and Extracting Packages libstdcxx-ng-9.1.0 | 4.0 MB | ############################################################ | 100% libdeflate-1.2 | 63 KB | ############################################################ | 100% bzip2-1.0.8 | 105 KB | ############################################################ | 100% libssh2-1.8.2 | 250 KB | ############################################################ | 100% samtools-1.9 | 299 KB | ############################################################ | 100% krb5-1.16.4 | 1.4 MB | ############################################################ | 100% libcurl-7.67.0 | 576 KB | ############################################################ | 100% curl-7.67.0 | 145 KB | ############################################################ | 100% htslib-1.9 | 1.2 MB | ############################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install picard Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - picard The following packages will be downloaded: package | build ---------------------------|----------------- _r-mutex-1.0.0 | anacondar_1 2 KB binutils_impl_linux-64-2.33.1| he6710b0_7 8.6 MB binutils_linux-64-2.33.1 | h9595d00_15 24 KB bwidget-1.9.11 | 1 113 KB gcc_impl_linux-64-7.3.0 | habb00fd_1 73.2 MB gcc_linux-64-7.3.0 | h553295d_15 25 KB gfortran_impl_linux-64-7.3.0| hdf63c60_1 9.0 MB gfortran_linux-64-7.3.0 | h553295d_15 25 KB glib-2.63.1 | h5a9c865_0 3.4 MB gsl-2.4 | h14c3975_4 2.6 MB gxx_impl_linux-64-7.3.0 | hdf63c60_1 18.7 MB gxx_linux-64-7.3.0 | h553295d_15 25 KB ld_impl_linux-64-2.33.1 | h53a641e_7 645 KB libpng-1.6.37 | hbc83047_0 364 KB libtiff-4.1.0 | h2733197_0 589 KB libxml2-2.9.9 | hea5a465_1 2.0 MB make-4.2.1 | h1bed415_1 429 KB openjdk-8.0.152 | h46b5887_1 128.6 MB picard-2.21.7 | 0 14.7 MB bioconda r-base-3.6.1 | h9bb98a2_1 39.7 MB tktable-2.10 | h14c3975_0 88 KB ------------------------------------------------------------ Total: 302.7 MB The following NEW packages will be INSTALLED: _r-mutex pkgs/r/linux-64::_r-mutex-1.0.0-anacondar_1 binutils_impl_lin~ pkgs/main/linux-64::binutils_impl_linux-64-2.33.1-he6710b0_7 binutils_linux-64 pkgs/main/linux-64::binutils_linux-64-2.33.1-h9595d00_15 bwidget pkgs/main/linux-64::bwidget-1.9.11-1 cairo pkgs/main/linux-64::cairo-1.14.12-h8948797_3 fontconfig pkgs/main/linux-64::fontconfig-2.13.0-h9420a91_0 freetype pkgs/main/linux-64::freetype-2.9.1-h8a8886c_1 fribidi pkgs/main/linux-64::fribidi-1.0.5-h7b6447c_0 gcc_impl_linux-64 pkgs/main/linux-64::gcc_impl_linux-64-7.3.0-habb00fd_1 gcc_linux-64 pkgs/main/linux-64::gcc_linux-64-7.3.0-h553295d_15 gfortran_impl_lin~ pkgs/main/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_1 gfortran_linux-64 pkgs/main/linux-64::gfortran_linux-64-7.3.0-h553295d_15 glib pkgs/main/linux-64::glib-2.63.1-h5a9c865_0 graphite2 pkgs/main/linux-64::graphite2-1.3.13-h23475e2_0 gsl pkgs/main/linux-64::gsl-2.4-h14c3975_4 gxx_impl_linux-64 pkgs/main/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_1 gxx_linux-64 pkgs/main/linux-64::gxx_linux-64-7.3.0-h553295d_15 harfbuzz pkgs/main/linux-64::harfbuzz-1.8.8-hffaf4a1_0 icu pkgs/main/linux-64::icu-58.2-h9c2bf20_1 jpeg pkgs/main/linux-64::jpeg-9b-h024ee3a_2 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7 libffi pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4 libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0 libpng pkgs/main/linux-64::libpng-1.6.37-hbc83047_0 libtiff pkgs/main/linux-64::libtiff-4.1.0-h2733197_0 libuuid pkgs/main/linux-64::libuuid-1.0.3-h1bed415_2 libxcb pkgs/main/linux-64::libxcb-1.13-h1bed415_1 libxml2 pkgs/main/linux-64::libxml2-2.9.9-hea5a465_1 make pkgs/main/linux-64::make-4.2.1-h1bed415_1 openjdk pkgs/main/linux-64::openjdk-8.0.152-h46b5887_1 pango pkgs/main/linux-64::pango-1.42.4-h049681c_0 pcre pkgs/main/linux-64::pcre-8.43-he6710b0_0 picard bioconda/noarch::picard-2.21.7-0 pixman pkgs/main/linux-64::pixman-0.38.0-h7b6447c_0 r-base pkgs/r/linux-64::r-base-3.6.1-h9bb98a2_1 readline pkgs/main/linux-64::readline-7.0-h7b6447c_5 tktable pkgs/main/linux-64::tktable-2.10-h14c3975_0 zstd pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0 Proceed ([y]/n)? y Downloading and Extracting Packages tktable-2.10 | 88 KB | ############################################################ | 100% gcc_linux-64-7.3.0 | 25 KB | ############################################################ | 100% openjdk-8.0.152 | 128.6 MB | ############################################################ | 100% gfortran_impl_linux- | 9.0 MB | ############################################################ | 100% libpng-1.6.37 | 364 KB | ############################################################ | 100% libxml2-2.9.9 | 2.0 MB | ############################################################ | 100% gcc_impl_linux-64-7. | 73.2 MB | ############################################################ | 100% picard-2.21.7 | 14.7 MB | ############################################################ | 100% gsl-2.4 | 2.6 MB | ############################################################ | 100% r-base-3.6.1 | 39.7 MB | ############################################################ | 100% ld_impl_linux-64-2.3 | 645 KB | ############################################################ | 100% _r-mutex-1.0.0 | 2 KB | ############################################################ | 100% bwidget-1.9.11 | 113 KB | ############################################################ | 100% make-4.2.1 | 429 KB | ############################################################ | 100% glib-2.63.1 | 3.4 MB | ############################################################ | 100% gxx_linux-64-7.3.0 | 25 KB | ############################################################ | 100% binutils_linux-64-2. | 24 KB | ############################################################ | 100% gxx_impl_linux-64-7. | 18.7 MB | ############################################################ | 100% gfortran_linux-64-7. | 25 KB | ############################################################ | 100% libtiff-4.1.0 | 589 KB | ############################################################ | 100% binutils_impl_linux- | 8.6 MB | ############################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40803/bash-command-to-install-miniconda Sat, 01 Feb 2020 01:46:31 -0600 https://bioinformaticsonline.com/snippets/view/40803/bash-command-to-install-miniconda (base) [wsu29@bladeamd-2 tmp]$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh --2020-02-01 13:25:25-- https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh Resolving repo.anaconda.com... 104.16.130.3, 104.16.131.3, 2606:4700::6810:8303, ... Connecting to repo.anaconda.com|104.16.130.3|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 71785000 (68M) [application/x-sh] Saving to: `Miniconda3-latest-Linux-x86_64.sh' 100%[=============================================================>] 7,17,85,000 2.07M/s in 33s 2020-02-01 13:25:59 (2.06 MB/s) - `Miniconda3-latest-Linux-x86_64.sh' saved [71785000/71785000] (base) [wsu29@bladeamd-2 tmp]$ sh Miniconda3-latest-Linux-x86_64.sh Welcome to Miniconda3 4.7.12 In order to continue the installation process, please review the license agreement. Please, press ENTER to continue >>> ... ... ... Please answer 'yes' or 'no':' >>> yes Miniconda3 will now be installed into this location: /data/sata_data/workshop/wsu29/miniconda3 - Press ENTER to confirm the location - Press CTRL-C to abort the installation - Or specify a different location below [/data/sata_data/workshop/wsu29/miniconda3] >>> Miniconda3 will now be installed into this location: /data/sata_data/workshop/wsu29/miniconda3 - Press ENTER to confirm the location - Press CTRL-C to abort the installation - Or specify a different location below [/data/sata_data/workshop/wsu29/miniconda3] >>> PREFIX=/data/sata_data/workshop/wsu29/miniconda3 Unpacking payload ... Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/miniconda3 added / updated specs: - _libgcc_mutex==0.1=main - asn1crypto==1.2.0=py37_0 - ca-certificates==2019.10.16=0 - certifi==2019.9.11=py37_0 - cffi==1.13.0=py37h2e261b9_0 - chardet==3.0.4=py37_1003 - conda-package-handling==1.6.0=py37h7b6447c_0 - conda==4.7.12=py37_0 - cryptography==2.8=py37h1ba5d50_0 - idna==2.8=py37_0 - libedit==3.1.20181209=hc058e9b_0 - libffi==3.2.1=hd88cf55_4 - libgcc-ng==9.1.0=hdf63c60_0 - libstdcxx-ng==9.1.0=hdf63c60_0 - ncurses==6.1=he6710b0_1 - openssl==1.1.1d=h7b6447c_3 - pip==19.3.1=py37_0 - pycosat==0.6.3=py37h14c3975_0 - pycparser==2.19=py37_0 - pyopenssl==19.0.0=py37_0 - pysocks==1.7.1=py37_0 - python==3.7.4=h265db76_1 - readline==7.0=h7b6447c_5 - requests==2.22.0=py37_0 - ruamel_yaml==0.15.46=py37h14c3975_0 - setuptools==41.4.0=py37_0 - six==1.12.0=py37_0 - sqlite==3.30.0=h7b6447c_0 - tk==8.6.8=hbc83047_0 - tqdm==4.36.1=py_0 - urllib3==1.24.2=py37_0 - wheel==0.33.6=py37_0 - xz==5.2.4=h14c3975_4 - yaml==0.1.7=had09818_2 - zlib==1.2.11=h7b6447c_3 The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main asn1crypto pkgs/main/linux-64::asn1crypto-1.2.0-py37_0 ca-certificates pkgs/main/linux-64::ca-certificates-2019.10.16-0 certifi pkgs/main/linux-64::certifi-2019.9.11-py37_0 cffi pkgs/main/linux-64::cffi-1.13.0-py37h2e261b9_0 chardet pkgs/main/linux-64::chardet-3.0.4-py37_1003 conda pkgs/main/linux-64::conda-4.7.12-py37_0 conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0 cryptography pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0 idna pkgs/main/linux-64::idna-2.8-py37_0 libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0 libffi pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4 libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 ncurses pkgs/main/linux-64::ncurses-6.1-he6710b0_1 openssl pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3 pip pkgs/main/linux-64::pip-19.3.1-py37_0 pycosat pkgs/main/linux-64::pycosat-0.6.3-py37h14c3975_0 pycparser pkgs/main/linux-64::pycparser-2.19-py37_0 pyopenssl pkgs/main/linux-64::pyopenssl-19.0.0-py37_0 pysocks pkgs/main/linux-64::pysocks-1.7.1-py37_0 python pkgs/main/linux-64::python-3.7.4-h265db76_1 readline pkgs/main/linux-64::readline-7.0-h7b6447c_5 requests pkgs/main/linux-64::requests-2.22.0-py37_0 ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.46-py37h14c3975_0 setuptools pkgs/main/linux-64::setuptools-41.4.0-py37_0 six pkgs/main/linux-64::six-1.12.0-py37_0 sqlite pkgs/main/linux-64::sqlite-3.30.0-h7b6447c_0 tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0 tqdm pkgs/main/noarch::tqdm-4.36.1-py_0 urllib3 pkgs/main/linux-64::urllib3-1.24.2-py37_0 wheel pkgs/main/linux-64::wheel-0.33.6-py37_0 xz pkgs/main/linux-64::xz-5.2.4-h14c3975_4 yaml pkgs/main/linux-64::yaml-0.1.7-had09818_2 zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3 Preparing transaction: done Executing transaction: done installation finished. Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no] [no] >>> yes no change /data/sata_data/workshop/wsu29/miniconda3/condabin/conda no change /data/sata_data/workshop/wsu29/miniconda3/bin/conda no change /data/sata_data/workshop/wsu29/miniconda3/bin/conda-env no change /data/sata_data/workshop/wsu29/miniconda3/bin/activate no change /data/sata_data/workshop/wsu29/miniconda3/bin/deactivate no change /data/sata_data/workshop/wsu29/miniconda3/etc/profile.d/conda.sh no change /data/sata_data/workshop/wsu29/miniconda3/etc/fish/conf.d/conda.fish no change /data/sata_data/workshop/wsu29/miniconda3/shell/condabin/Conda.psm1 no change /data/sata_data/workshop/wsu29/miniconda3/shell/condabin/conda-hook.ps1 no change /data/sata_data/workshop/wsu29/miniconda3/lib/python3.7/site-packages/xontrib/conda.xsh no change /data/sata_data/workshop/wsu29/miniconda3/etc/profile.d/conda.csh modified /data/sata_data/workshop/wsu29/.bashrc ==> For changes to take effect, close and re-open your current shell. <== If you'd prefer that conda's base environment not be activated on startup, set the auto_activate_base parameter to false: conda config --set auto_activate_base false Thank you for installing Miniconda3!]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40802/bash-commandline-to-install-anaconda Sat, 01 Feb 2020 01:36:00 -0600 https://bioinformaticsonline.com/snippets/view/40802/bash-commandline-to-install-anaconda #The line begins with $ are the commands $ mkdir tmp $ cd tmp/ $ curl -O https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 654M 100 654M 0 0 940k 0 0:11:52 0:11:52 --:--:-- 2059k $ sha256sum Anaconda3-2019.03-Linux-x86_64.sh 45c851b7497cc14d5ca060064394569f724b67d9b5f98a926ed49b834a6bb73a Anaconda3-2019.03-Linux-x86_64.sh $ bash Anaconda3-2019.03-Linux-x86_64.sh In order to continue the installation process, please review the license agreement. Please, press ENTER to continue >>> =================================== Anaconda End User License Agreement =================================== ...... ...... ...... Do you accept the license terms? [yes|no] Please answer 'yes' or 'no':' >>> yes Anaconda3 will now be installed into this location: /data/sata_data/workshop/wsu29/anaconda3 - Press ENTER to confirm the location - Press CTRL-C to abort the installation - Or specify a different location below [/data/sata_data/workshop/wsu29/anaconda3] >>> PREFIX=/data/sata_data/workshop/wsu29/anaconda3 installing: python-3.7.3-h0371630_0 ... Python 3.7.3 installing: conda-env-2.6.0-1 ... installing: blas-1.0-mkl ... installing: ca-certificates-2019.1.23-0 ... installing: intel-openmp-2019.3-199 ... installing: libgcc-ng-8.2.0-hdf63c60_1 ... installing: libgfortran-ng-7.3.0-hdf63c60_0 ... installing: libstdcxx-ng-8.2.0-hdf63c60_1 ... installing: bzip2-1.0.6-h14c3975_5 ... installing: expat-2.2.6-he6710b0_0 ... installing: fribidi-1.0.5-h7b6447c_0 ... installing: gmp-6.1.2-h6c8ec71_1 ... installing: graphite2-1.3.13-h23475e2_0 ... installing: icu-58.2-h9c2bf20_1 ... installing: jbig-2.1-hdba287a_0 ... installing: jpeg-9b-h024ee3a_2 ... installing: libffi-3.2.1-hd88cf55_4 ... installing: liblief-0.9.0-h7725739_2 ... installing: libsodium-1.0.16-h1bed415_0 ... installing: libtool-2.4.6-h7b6447c_5 ... installing: libuuid-1.0.3-h1bed415_2 ... installing: libxcb-1.13-h1bed415_1 ... installing: lz4-c-1.8.1.2-h14c3975_0 ... installing: lzo-2.10-h49e0be7_2 ... installing: mkl-2019.3-199 ... installing: ncurses-6.1-he6710b0_1 ... installing: openssl-1.1.1b-h7b6447c_1 ... installing: patchelf-0.9-he6710b0_3 ... installing: pcre-8.43-he6710b0_0 ... installing: pixman-0.38.0-h7b6447c_0 ... installing: snappy-1.1.7-hbae5bb6_3 ... installing: xz-5.2.4-h14c3975_4 ... installing: yaml-0.1.7-had09818_2 ... installing: zlib-1.2.11-h7b6447c_3 ... installing: blosc-1.15.0-hd408876_0 ... installing: glib-2.56.2-hd408876_0 ... installing: hdf5-1.10.4-hb1b8bf9_0 ... installing: libedit-3.1.20181209-hc058e9b_0 ... installing: libpng-1.6.36-hbc83047_0 ... installing: libssh2-1.8.0-h1ba5d50_4 ... installing: libxml2-2.9.9-he19cac6_0 ... installing: mpfr-4.0.1-hdf1c602_3 ... installing: pandoc-2.2.3.2-0 ... installing: readline-7.0-h7b6447c_5 ... installing: tk-8.6.8-hbc83047_0 ... installing: zeromq-4.3.1-he6710b0_3 ... installing: zstd-1.3.7-h0b5b093_0 ... installing: dbus-1.13.6-h746ee38_0 ... installing: freetype-2.9.1-h8a8886c_1 ... installing: gstreamer-1.14.0-hb453b48_1 ... installing: krb5-1.16.1-h173b8e3_7 ... installing: libarchive-3.3.3-h5d8350f_5 ... installing: libtiff-4.0.10-h2733197_2 ... installing: libxslt-1.1.33-h7d1a2b0_0 ... installing: mpc-1.1.0-h10f8cd9_1 ... installing: sqlite-3.27.2-h7b6447c_0 ... installing: unixodbc-2.3.7-h14c3975_0 ... installing: fontconfig-2.13.0-h9420a91_0 ... installing: gst-plugins-base-1.14.0-hbbd80ab_1 ... installing: libcurl-7.64.0-h20c2e04_2 ... installing: alabaster-0.7.12-py37_0 ... installing: asn1crypto-0.24.0-py37_0 ... installing: atomicwrites-1.3.0-py37_1 ... installing: attrs-19.1.0-py37_1 ... installing: backcall-0.1.0-py37_0 ... installing: backports-1.0-py37_1 ... installing: bitarray-0.8.3-py37h14c3975_0 ... installing: boto-2.49.0-py37_0 ... installing: cairo-1.14.12-h8948797_3 ... installing: certifi-2019.3.9-py37_0 ... installing: chardet-3.0.4-py37_1 ... installing: click-7.0-py37_0 ... installing: cloudpickle-0.8.0-py37_0 ... installing: colorama-0.4.1-py37_0 ... installing: contextlib2-0.5.5-py37_0 ... installing: curl-7.64.0-hbc83047_2 ... installing: dask-core-1.1.4-py37_1 ... installing: decorator-4.4.0-py37_1 ... installing: defusedxml-0.5.0-py37_1 ... installing: docutils-0.14-py37_0 ... installing: entrypoints-0.3-py37_0 ... installing: et_xmlfile-1.0.1-py37_0 ... installing: fastcache-1.0.2-py37h14c3975_2 ... installing: filelock-3.0.10-py37_0 ... installing: future-0.17.1-py37_0 ... installing: glob2-0.6-py37_1 ... installing: gmpy2-2.0.8-py37h10f8cd9_2 ... installing: greenlet-0.4.15-py37h7b6447c_0 ... installing: heapdict-1.0.0-py37_2 ... installing: idna-2.8-py37_0 ... installing: imagesize-1.1.0-py37_0 ... installing: ipython_genutils-0.2.0-py37_0 ... installing: itsdangerous-1.1.0-py37_0 ... installing: jdcal-1.4-py37_0 ... installing: jeepney-0.4-py37_0 ... installing: kiwisolver-1.0.1-py37hf484d3e_0 ... installing: lazy-object-proxy-1.3.1-py37h14c3975_2 ... installing: llvmlite-0.28.0-py37hd408876_0 ... installing: locket-0.2.0-py37_1 ... installing: lxml-4.3.2-py37hefd8a0e_0 ... installing: markupsafe-1.1.1-py37h7b6447c_0 ... installing: mccabe-0.6.1-py37_1 ... installing: mistune-0.8.4-py37h7b6447c_0 ... installing: mkl-service-1.1.2-py37he904b0f_5 ... installing: more-itertools-6.0.0-py37_0 ... installing: mpmath-1.1.0-py37_0 ... installing: msgpack-python-0.6.1-py37hfd86e86_1 ... installing: numpy-base-1.16.2-py37hde5b4d6_0 ... installing: olefile-0.46-py37_0 ... installing: pandocfilters-1.4.2-py37_1 ... installing: parso-0.3.4-py37_0 ... installing: pep8-1.7.1-py37_0 ... installing: pickleshare-0.7.5-py37_0 ... installing: pkginfo-1.5.0.1-py37_0 ... installing: pluggy-0.9.0-py37_0 ... installing: ply-3.11-py37_0 ... installing: prometheus_client-0.6.0-py37_0 ... installing: psutil-5.6.1-py37h7b6447c_0 ... installing: ptyprocess-0.6.0-py37_0 ... installing: py-1.8.0-py37_0 ... installing: py-lief-0.9.0-py37h7725739_2 ... installing: pycodestyle-2.5.0-py37_0 ... installing: pycosat-0.6.3-py37h14c3975_0 ... installing: pycparser-2.19-py37_0 ... installing: pycrypto-2.6.1-py37h14c3975_9 ... installing: pycurl-7.43.0.2-py37h1ba5d50_0 ... installing: pyflakes-2.1.1-py37_0 ... installing: pyodbc-4.0.26-py37he6710b0_0 ... installing: pyparsing-2.3.1-py37_0 ... installing: pysocks-1.6.8-py37_0 ... installing: python-libarchive-c-2.8-py37_6 ... installing: pytz-2018.9-py37_0 ... installing: pyyaml-5.1-py37h7b6447c_0 ... installing: pyzmq-18.0.0-py37he6710b0_0 ... installing: qt-5.9.7-h5867ecd_1 ... installing: qtpy-1.7.0-py37_1 ... installing: rope-0.12.0-py37_0 ... installing: ruamel_yaml-0.15.46-py37h14c3975_0 ... installing: send2trash-1.5.0-py37_0 ... installing: simplegeneric-0.8.1-py37_2 ... installing: sip-4.19.8-py37hf484d3e_0 ... installing: six-1.12.0-py37_0 ... installing: snowballstemmer-1.2.1-py37_0 ... installing: sortedcontainers-2.1.0-py37_0 ... installing: soupsieve-1.8-py37_0 ... installing: sphinxcontrib-1.0-py37_1 ... installing: sqlalchemy-1.3.1-py37h7b6447c_0 ... installing: tblib-1.3.2-py37_0 ... installing: testpath-0.4.2-py37_0 ... installing: toolz-0.9.0-py37_0 ... installing: tornado-6.0.2-py37h7b6447c_0 ... installing: tqdm-4.31.1-py37_1 ... installing: unicodecsv-0.14.1-py37_0 ... installing: wcwidth-0.1.7-py37_0 ... installing: webencodings-0.5.1-py37_1 ... installing: werkzeug-0.14.1-py37_0 ... installing: wrapt-1.11.1-py37h7b6447c_0 ... installing: wurlitzer-1.0.2-py37_0 ... installing: xlrd-1.2.0-py37_0 ... installing: xlsxwriter-1.1.5-py37_0 ... installing: xlwt-1.3.0-py37_0 ... installing: zipp-0.3.3-py37_1 ... installing: babel-2.6.0-py37_0 ... installing: backports.os-0.1.1-py37_0 ... installing: backports.shutil_get_terminal_size-1.0.0-py37_2 ... installing: beautifulsoup4-4.7.1-py37_1 ... installing: cffi-1.12.2-py37h2e261b9_1 ... installing: cycler-0.10.0-py37_0 ... installing: cytoolz-0.9.0.1-py37h14c3975_1 ... installing: harfbuzz-1.8.8-hffaf4a1_0 ... installing: html5lib-1.0.1-py37_0 ... installing: importlib_metadata-0.8-py37_0 ... installing: jedi-0.13.3-py37_0 ... 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Do you wish the installer to initialize Anaconda3 by running conda init? [yes|no] [no] >>> yes WARNING: The conda.compat module is deprecated and will be removed in a future release. no change /data/sata_data/workshop/wsu29/anaconda3/condabin/conda no change /data/sata_data/workshop/wsu29/anaconda3/bin/conda no change /data/sata_data/workshop/wsu29/anaconda3/bin/conda-env no change /data/sata_data/workshop/wsu29/anaconda3/bin/activate no change /data/sata_data/workshop/wsu29/anaconda3/bin/deactivate no change /data/sata_data/workshop/wsu29/anaconda3/etc/profile.d/conda.sh no change /data/sata_data/workshop/wsu29/anaconda3/etc/fish/conf.d/conda.fish no change /data/sata_data/workshop/wsu29/anaconda3/shell/condabin/Conda.psm1 no change /data/sata_data/workshop/wsu29/anaconda3/shell/condabin/conda-hook.ps1 no change /data/sata_data/workshop/wsu29/anaconda3/lib/python3.7/site-packages/xonsh/conda.xsh no change /data/sata_data/workshop/wsu29/anaconda3/etc/profile.d/conda.csh modified /data/sata_data/workshop/wsu29/.bashrc ==> For changes to take effect, close and re-open your current shell. <== If you'd prefer that conda's base environment not be activated on startup, set the auto_activate_base parameter to false: conda config --set auto_activate_base false Thank you for installing Anaconda3! =========================================================================== Anaconda and JetBrains are working together to bring you Anaconda-powered environments tightly integrated in the PyCharm IDE. PyCharm for Anaconda is available at: https://www.anaconda.com/pycharm #Ativate now $ source ~/.bashrc #Check/Test $ conda list # Python 3 environment named my_env can be created with the following command: $ conda create --name my_env python=3 #Activate env $ conda activate my_env #To update conda $ conda update -n base -c defaults conda]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40763/perl-subroutine-for-kmer Thu, 30 Jan 2020 04:38:48 -0600 https://bioinformaticsonline.com/snippets/view/40763/perl-subroutine-for-kmer sub kmers { my $seq = shift or return; my $len = length $seq; my @kmers; for (my $i = 0; ($i + $KMER_SIZE) <= $len; $i++) { my $kmer = substr($seq, $i, $KMER_SIZE); print "$kmer\n"; push @kmers, substr($seq, $i, $KMER_SIZE); } return \@kmers; }]]> BioStar https://bioinformaticsonline.com/snippets/view/40756/install-samtools-bcftools-and-htslib-on-ubuntu Wed, 29 Jan 2020 06:47:15 -0600 https://bioinformaticsonline.com/snippets/view/40756/install-samtools-bcftools-and-htslib-on-ubuntu #Inspired from online search sudo apt-get update sudo apt-get install gcc sudo apt-get install make sudo apt-get install libbz2-dev sudo apt-get install zlib1g-dev sudo apt-get install libncurses5-dev sudo apt-get install libncursesw5-dev sudo apt-get install liblzma-dev cd /usr/bin wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 tar -vxjf htslib-1.9.tar.bz2 cd htslib-1.9 make cd .. wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 tar -vxjf samtools-1.9.tar.bz2 cd samtools-1.9 make cd .. wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 tar -vxjf bcftools-1.9.tar.bz2 cd bcftools-1.9 make export PATH="$PATH:/usr/bin/bcftools-1.9" export PATH="$PATH:/usr/bin/samtools-1.9" export PATH="$PATH:/usr/bin/htslib-1.9" source ~/.profile echo "All done"]]> Neel https://bioinformaticsonline.com/snippets/view/40726/perl6-script-to-count-atgc Tue, 28 Jan 2020 05:45:48 -0600 https://bioinformaticsonline.com/snippets/view/40726/perl6-script-to-count-atgc use v6; my $default-input = "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"; sub MAIN($input = $default-input) { "{<A C G T>.map({ +$input.comb(/$_/) })}".say; } #I love perl v6]]> Poonam Mahapatra https://bioinformaticsonline.com/snippets/view/40719/bash-script-to-alignment-of-short-reads-against-reference-genome Tue, 28 Jan 2020 04:21:43 -0600 https://bioinformaticsonline.com/snippets/view/40719/bash-script-to-alignment-of-short-reads-against-reference-genome bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1770413_2.fastq.gz \ | samtools view -b - >SRR1770413.raw.bam sambamba sort SRR1770413.raw.bam sambamba markdup SRR1770413.raw.sorted.bam SRR1770413.bam ##Breaking it down by line: #alignment with bwa: bwa mem -t $threads -R '@RG\tID:K12\tSM:K12' --- this says "align using so many threads" and also "give the reads the read group K12 and the sample name K12" #reference and FASTQs E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1770413_2.fastq.gz --- this just specifies the base reference file name (bwa finds the indexes using this) and the input alignment files. The first file should contain the first mate, the second file the second mate. #conversion to BAM: samtools view -b - --- this reads SAM from stdin (the - specifier in place of the file name indicates this) and converts to BAM. #sorting the BAM file: sambamba sort SRR1770413.raw.bam --- sort the BAM file, writing it to .sorted.bam. #marking PCR duplicates: sambamba markdup SRR1770413.raw.sorted.bam SRR1770413.bam --- this marks reads which appear to be redundant PCR duplicates based on their read mapping position. It uses the same criteria for marking duplicates as picard. minimap2 -ax sr -t 40 -R '@RG\tID:O104_H4\tSM:O104_H4' \ E.coli_K12_MG1655.fa SRR341549_1.fastq.gz SRR341549_2.fastq.gz \ | samtools view -b - >SRR341549.raw.minimap2.bam sambamba sort SRR341549.raw.minimap2.bam sambamba markdup SRR341549.raw.sorted.minimap2.bam SRR341549.minimap2.bam #The only major change from bwa mem is that we'll tell it we're working with short read data using -ax sr:]]> Neel https://bioinformaticsonline.com/snippets/view/40717/bash-script-to-download-sra-file Tue, 28 Jan 2020 04:15:52 -0600 https://bioinformaticsonline.com/snippets/view/40717/bash-script-to-download-sra-file #We can use the sratoolkit to directly pull the sequence data (in paired FASTQ format) from the archive. fastq-dump is in the SRA toolkit. It allows directly downloading data from a particular sequencing run ID fastq-dump --split-files SRR1770413 #SRA stores data in a particular compressed format (SRA!) that isn't directly compatible with any downstream tools, so it's necessary to put things into FASTQ for further processing. The --split-files part of the command ensures we get two files, one for the first and second mate in each pair. We'll use them in this format when aligning. wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra instant/reads/ByRun/sra/SRR/SRR177/SRR1770413/SRR1770413.sra sra-dump --split-files SRR1770413.sra]]> Jit https://bioinformaticsonline.com/snippets/view/40623/perl-script-to-remove-duplicated-lines Mon, 27 Jan 2020 04:48:56 -0600 https://bioinformaticsonline.com/snippets/view/40623/perl-script-to-remove-duplicated-lines #!/usr/bin/perl use strict; use warnings; { $_ = <DATA>; my $next_line; while( $next_line = <DATA> ) { #print "current line: $_ -- next line: $next_line$/"; print $_ if $_ ne $next_line; } continue { $_ = $next_line; } print $_ if eof; } __DATA__ apple apple plum vinegar apple banana banana banana apple]]> Rahul Nayak