https://bioinformaticsonline.com/snippets/owner/neelam?offset=20 https://bioinformaticsonline.com/snippets/view/43099/install-odgi-using-conda Thu, 24 Jun 2021 04:41:34 -0500 https://bioinformaticsonline.com/snippets/view/43099/install-odgi-using-conda conda install -c bioconda odgi Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/anaconda3/envs/ added / updated specs: - odgi The following packages will be downloaded: package | build ---------------------------|----------------- jemalloc-5.2.1 | h2531618_5 1.0 MB odgi-0.6 | py37hfecc14a_1 236.6 MB bioconda ------------------------------------------------------------ Total: 237.6 MB The following NEW packages will be INSTALLED: odgi bioconda/linux-64::odgi-0.6-py37hfecc14a_1 The following packages will be UPDATED: jemalloc bioconda::jemalloc-4.5.0-0 --> pkgs/main::jemalloc-5.2.1-h2531618_5 Proceed ([y]/n)? y Downloading and Extracting Packages odgi-0.6 | 236.6 MB | ################################################################################################################################################################################### | 100% jemalloc-5.2.1 | 1.0 MB | ################################################################################################################################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Neel https://bioinformaticsonline.com/snippets/view/43098/install-kat-using-conda Thu, 24 Jun 2021 04:31:31 -0500 https://bioinformaticsonline.com/snippets/view/43098/install-kat-using-conda conda install -c bioconda kat Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/anaconda3/envs/ added / updated specs: - kat The following packages will be downloaded: package | build ---------------------------|----------------- boost-1.73.0 | py37h06a4308_11 25 KB jellyfish-2.2.10 | h6bb024c_1 393 KB bioconda jemalloc-4.5.0 | 0 6.2 MB bioconda kat-2.0.8 | 0 7.5 MB bioconda libboost-1.73.0 | h3ff78a5_11 13.9 MB lz4-c-1.9.3 | h2531618_0 186 KB py-boost-1.73.0 | py37ha9443f7_11 204 KB zstd-1.4.9 | haebb681_0 480 KB ------------------------------------------------------------ Total: 28.8 MB The following NEW packages will be INSTALLED: boost pkgs/main/linux-64::boost-1.73.0-py37h06a4308_11 jellyfish bioconda/linux-64::jellyfish-2.2.10-h6bb024c_1 jemalloc bioconda/linux-64::jemalloc-4.5.0-0 kat bioconda/linux-64::kat-2.0.8-0 libboost pkgs/main/linux-64::libboost-1.73.0-h3ff78a5_11 lz4-c pkgs/main/linux-64::lz4-c-1.9.3-h2531618_0 py-boost pkgs/main/linux-64::py-boost-1.73.0-py37ha9443f7_11 zstd pkgs/main/linux-64::zstd-1.4.9-haebb681_0 The following packages will be UPDATED: libxslt conda-forge::libxslt-1.1.33-h15afd5d_2 --> pkgs/main::libxslt-1.1.34-hc22bd24_0 The following packages will be SUPERSEDED by a higher-priority channel: icu conda-forge::icu-68.1-h58526e2_0 --> pkgs/main::icu-58.2-he6710b0_3 libxml2 conda-forge::libxml2-2.9.12-h72842e0_0 --> pkgs/main::libxml2-2.9.10-hb55368b_3 Proceed ([y]/n)? y Downloading and Extracting Packages libboost-1.73.0 | 13.9 MB | ################################################################################################################################################################################### | 100% zstd-1.4.9 | 480 KB | ################################################################################################################################################################################### | 100% lz4-c-1.9.3 | 186 KB | ################################################################################################################################################################################### | 100% py-boost-1.73.0 | 204 KB | ################################################################################################################################################################################### | 100% kat-2.0.8 | 7.5 MB | ################################################################################################################################################################################### | 100% jellyfish-2.2.10 | 393 KB | ################################################################################################################################################################################### | 100% jemalloc-4.5.0 | 6.2 MB | ################################################################################################################################################################################### | 100% boost-1.73.0 | 25 KB | ################################################################################################################################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Neel https://bioinformaticsonline.com/snippets/view/43097/install-megahit-using-conda Thu, 24 Jun 2021 04:28:38 -0500 https://bioinformaticsonline.com/snippets/view/43097/install-megahit-using-conda conda install -c bioconda megahit Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/anaconda3/envs/ added / updated specs: - megahit The following packages will be downloaded: package | build ---------------------------|----------------- megahit-1.2.9 | h2e03b76_1 2.9 MB bioconda ------------------------------------------------------------ Total: 2.9 MB The following NEW packages will be INSTALLED: megahit bioconda/linux-64::megahit-1.2.9-h2e03b76_1 Proceed ([y]/n)? y Downloading and Extracting Packages megahit-1.2.9 | 2.9 MB | ################################################################################################################################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Neel https://bioinformaticsonline.com/snippets/view/43052/download-genome-using-ncbi-esearch-command-line Fri, 30 Apr 2021 00:31:09 -0500 https://bioinformaticsonline.com/snippets/view/43052/download-genome-using-ncbi-esearch-command-line #Download using command line "NC_005956.1" / "CP003784.1" esearch -db nucleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -query "CP003784.1" | efetch -format fasta > seq2.fa #fastANI for alignment free comparision #conda install -c bioconda fastani fastANI -q seq1.fa -r seq2.fa --visualize -o fastani.out #Plot using sequences Rscript plotSeq.R seq1.fa seq2.fa fastani.out.visual]]> Neel https://bioinformaticsonline.com/snippets/view/43051/install-ncbi-entrez-direct-and-esearch-using-conda Fri, 30 Apr 2021 00:25:35 -0500 https://bioinformaticsonline.com/snippets/view/43051/install-ncbi-entrez-direct-and-esearch-using-conda $ conda install -c bioconda entrez-direct Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.10.1 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/MetaENV added / updated specs: - entrez-direct The following packages will be downloaded: package | build ---------------------------|----------------- entrez-direct-13.9 | pl5262he881be0_2 5.2 MB bioconda ------------------------------------------------------------ Total: 5.2 MB The following packages will be UPDATED: entrez-direct 13.9-pl526h375a9b1_0 --> 13.9-pl5262he881be0_2 Proceed ([y]/n)? y Downloading and Extracting Packages entrez-direct-13.9 | 5.2 MB | ############################################################################# | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Neel https://bioinformaticsonline.com/snippets/view/42944/install-htop-in-elementaryubuntu-os Wed, 10 Mar 2021 08:18:27 -0600 https://bioinformaticsonline.com/snippets/view/42944/install-htop-in-elementaryubuntu-os neelam@neelam-Lenovo-ideapad-320-15ISK:~$ sudo apt-get install htop Reading package lists... Done Building dependency tree Reading state information... Done The following packages were automatically installed and are no longer required: gir1.2-vte-2.91 libido3-0.1-0 libllvm6.0 libwayland-egl1-mesa Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: htop 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 80.0 kB of archives. After this operation, 221 kB of additional disk space will be used. Get:1 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 htop amd64 2.1.0-3 [80.0 kB] Fetched 80.0 kB in 0s (239 kB/s) Selecting previously unselected package htop. (Reading database ... 176684 files and directories currently installed.) Preparing to unpack .../htop_2.1.0-3_amd64.deb ... Unpacking htop (2.1.0-3) ... Setting up htop (2.1.0-3) ... Processing triggers for desktop-file-utils (0.23-1ubuntu3.18.04.2+elementary2~ubuntu5.0.1) ... Processing triggers for bamfdaemon (0.5.3+18.04.20180207.2-0ubuntu1) ... Rebuilding /usr/share/applications/bamf-2.index... Processing triggers for man-db (2.8.3-2ubuntu0.1) ... Processing triggers for gnome-menus (3.13.3-11ubuntu1.1) ... Processing triggers for mime-support (3.60ubuntu1) ...]]> Neel https://bioinformaticsonline.com/snippets/view/42920/perl-script-to-run-awk-inside-perl Sat, 27 Feb 2021 01:40:25 -0600 https://bioinformaticsonline.com/snippets/view/42920/perl-script-to-run-awk-inside-perl #!/usr/local/bin/perl eval 'exec /usr/local/bin/perl -S $0 ${1+"$@"}' if $running_under_some_shell; # this emulates #! processing on NIH machines. # (remove #! line above if indigestible) eval '$'.$1.'$2;' while $ARGV[0] =~ /^([A-Za-z_0-9]+=)(.*)/ && shift; # process any FOO=bar switches $, = ' '; # set output field separator $\ = "\n"; # set output record separator while (<>) { chomp; # strip record separator @Fld = split(' ', $_, -1); if ($awk) { $Fld[(1)-1] = ''; $Fld[(2)-1] = ''; print join($,,@Fld); } print join($,,@Fld) if $f1 . . $txt; }]]> Neel https://bioinformaticsonline.com/snippets/view/42919/perl-ipcopen2-module Sat, 27 Feb 2021 01:29:04 -0600 https://bioinformaticsonline.com/snippets/view/42919/perl-ipcopen2-module syntax: $output = open2(\*CHLD_OUT, \*CHLD_IN, 'command arg1 arg2'); It runs a process for both reading and writing and creates a pipe to both STDIN and STDOUT. It can be used in both ways: $output = open2(my $out, my $in, 'command arg1 arg2'); OR without using the shell $output = open2(my $out, my $in, 'command', 'arg1', 'arg2'); You can read about it more in the documentation: IPC::Open2.]]> Neel https://bioinformaticsonline.com/snippets/view/42656/command-to-create-conda-environment Thu, 21 Jan 2021 04:39:56 -0600 https://bioinformaticsonline.com/snippets/view/42656/command-to-create-conda-environment # using pip pip install -r requirements.txt # using Conda conda create --name <env_name> --file requirements.txt #Using yaml conda env create -f environment.yml #Listing env conda env list #Create env with python36 conda create -n myenv python=3.6]]> Neel https://bioinformaticsonline.com/snippets/view/42193/picard-tools-command-to-get-some-insert-statistics Sun, 06 Sep 2020 10:23:15 -0500 https://bioinformaticsonline.com/snippets/view/42193/picard-tools-command-to-get-some-insert-statistics #picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $PICARD_HOME/picard.jar CollectInsertSizeMetrics MINIMUM_PCT=0 HISTOGRAM_FILE=<assembly name>.pdf INPUT=<sorted-bam-filename> OUTPUT=<assembly name>.sorted.collectInseSize HISTOGRAM_WIDTH=500]]> Neel