<![CDATA[BOL: Owner]]> https://bioinformaticsonline.com/snippets/owner/rahul?offset=10 https://bioinformaticsonline.com/snippets/view/41350/install-conda-on-remote-server Sat, 07 Mar 2020 00:52:01 -0600 https://bioinformaticsonline.com/snippets/view/41350/install-conda-on-remote-server <![CDATA[Install conda on remote server !]]> Please take a look at the Anaconda repo archive page https://repo.continuum.io/archive/ and select an appropriate version that you like to install. $ wget -c https://repo.continuum.io/archive/Anaconda3-vers.num-Linux-x86_64.sh $ bash Anaconda3-version.num-Linux-x86_64.sh $ wget -c https://repo.continuum.io/archive/Anaconda3-5.0.1-Linux-x86_64.sh $ bash Anaconda3-5.0.1-Linux-x86_64.sh OR try this # Go to home directory cd ~ # You can change what anaconda version you want at # https://repo.continuum.io/archive/ wget https://repo.continuum.io/archive/Anaconda3-4.2.0-Linux-x86_64.sh bash Anaconda3-4.2.0-Linux-x86_64.sh -b -p ~/anaconda rm Anaconda3-4.2.0-Linux-x86_64.sh echo 'export PATH="~/anaconda/bin:$PATH"' >> ~/.bashrc # Refresh basically source .bashrc conda update conda]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/41326/circos-with-circosjs Mon, 02 Mar 2020 23:29:38 -0600 https://bioinformaticsonline.com/snippets/view/41326/circos-with-circosjs <![CDATA[Circos with circosJS]]> <!DOCTYPE html> <html> <head> <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/4.11.0/d3.js"></script> <script src='https://cdn.rawgit.com/nicgirault/circosJS/v2/dist/circos.js'></script> </head> <body> <script> let width = $(window).width() - 20, height = $(window).height() - 20 let svg = d3.select("body") .append("svg") .attr('id', 'chart') .attr("width", width) .attr("height", height) let instance = new Circos({ container: '#chart', width: width, height: height, }) let layout_data = [ {"len": 31, "color": "#8dd3c7", "label": "January", "id": "january"}, {"len": 28, "color": "#ffffb3", "label": "February", "id": "february"}, {"len": 31, "color": "#bebada", "label": "March", "id": "march"}, {"len": 30, "color": "#fb8072", "label": "April", "id": "april"}, {"len": 31, "color": "#80b1d3", "label": "May", "id": "may"}, {"len": 30, "color": "#fdb462", "label": "June", "id": "june"}, {"len": 31, "color": "#b3de69", "label": "July", "id": "july"}, {"len": 31, "color": "#fccde5", "label": "August", "id": "august"}, {"len": 30, "color": "#d9d9d9", "label": "September", "id": "september"}, {"len": 31, "color": "#bc80bd", "label": "October", "id": "october"}, {"len": 30, "color": "#ccebc5", "label": "November", "id": "november"}, {"len": 31, "color": "#ffed6f", "label": "December", "id": "december"}, ]; let layout_data2 = [ { source: { id: 'january', start: 1, end: 12 }, target: { id: 'april', start: 18, end: 20 }}, { source: { id: 'february', start: 20, end: 28}, target: { id: 'december', start: 1, end: 13}} ]; let configuration = { innerRadius: 250, outerRadius: 300, cornerRadius: 10, gap: 0.04, // in radian labels: { display: true, position: 'center', size: '14px', color: '#000000', radialOffset: 20, }, ticks: { display: true, color: 'grey', spacing: 10000000, labels: true, labelSpacing: 10, labelSuffix: 'Mb', labelDenominator: 1000000, labelDisplay0: true, labelSize: '10px', labelColor: '#000000', labelFont: 'default', majorSpacing: 5, size: { minor: 2, major: 5, } }, clickCallback: null } instance.layout(layout_data, configuration) instance.render() </script> </body> </html>]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/41142/check-your-linux-os Tue, 18 Feb 2020 01:35:23 -0600 https://bioinformaticsonline.com/snippets/view/41142/check-your-linux-os <![CDATA[Check your Linux OS]]> (py36) [wsu29@bladeamd-2 lofreq]$ lsb_release -a LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: CentOS Description: CentOS release 6.7 (Final) Release: 6.7 Codename: Final]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/41037/install-python-numpy-python-scipy-python-matplotlib-on-ubuntu Sat, 15 Feb 2020 05:57:22 -0600 https://bioinformaticsonline.com/snippets/view/41037/install-python-numpy-python-scipy-python-matplotlib-on-ubuntu <![CDATA[Install python-numpy python-scipy python-matplotlib on Ubuntu !]]> $MT:~/Downloads/chaos$ sudo apt-get install python-numpy python-scipy python-matplotlib Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: blt fonts-lyx libjs-jquery-ui python-backports.functools-lru-cache python-cycler python-dateutil python-decorator python-matplotlib-data python-olefile python-pil python-subprocess32 python-tk python-tz tk8.6-blt2.5 ttf-bitstream-vera Suggested packages: blt-demo libjs-jquery-ui-docs python-cycler-doc dvipng ffmpeg inkscape ipython python-cairocffi python-configobj python-excelerator python-gobject python-matplotlib-doc python-nose python-qt4 python-sip python-tornado python-traits python-wxgtk3.0 texlive-extra-utils texlive-latex-extra ttf-staypuft python-numpy-dbg python-numpy-doc python-pil-doc python-pil-dbg python-scipy-doc tix python-tk-dbg The following NEW packages will be installed: blt fonts-lyx libjs-jquery-ui python-backports.functools-lru-cache python-cycler python-dateutil python-decorator python-matplotlib python-matplotlib-data python-numpy python-olefile python-pil python-scipy python-subprocess32 python-tk python-tz tk8.6-blt2.5 ttf-bitstream-vera 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. Need to get 21.1 MB/21.1 MB of archives. After this operation, 83.2 MB of additional disk space will be used. Do you want to continue? [Y/n] Y Get:1 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4 [572 kB] Get:2 http://in.archive.ubuntu.com/ubuntu bionic-updates/universe amd64 fonts-lyx all 2.2.4-0ubuntu0.18.04.1 [155 kB] Get:3 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get:4 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 python-backports.functools-lru-cache all 1.4-2 [5,960 B] Get:5 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 python-cycler all 0.10.0-1 [7,520 B] Get:6 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-dateutil all 2.6.1-1 [60.6 kB] Get:7 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-decorator all 4.1.2-1 [9,300 B] Get:8 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 ttf-bitstream-vera all 1.10-8 [352 kB] Get:9 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 python-matplotlib-data all 2.1.1-2ubuntu3 [3,774 kB] Get:10 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-tz all 2018.3-2 [31.6 kB] Get:11 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-numpy amd64 1:1.13.3-2ubuntu1 [1,938 kB] Get:12 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 python-subprocess32 amd64 3.2.7-3 [27.2 kB] Get:13 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 python-matplotlib amd64 2.1.1-2ubuntu3 [3,901 kB] Get:14 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-olefile all 0.45.1-1 [33.2 kB] Get:15 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python-pil amd64 5.1.0-1ubuntu0.2 [329 kB] Get:16 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 python-scipy amd64 0.19.1-2ubuntu1 [9,689 kB] Fetched 21.1 MB in 14s (1,460 kB/s) Selecting previously unselected package tk8.6-blt2.5. (Reading database ... 190390 files and directories currently installed.) Preparing to unpack .../00-tk8.6-blt2.5_2.5.3+dfsg-4_amd64.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-4) ... Selecting previously unselected package blt. Preparing to unpack .../01-blt_2.5.3+dfsg-4_amd64.deb ... Unpacking blt (2.5.3+dfsg-4) ... Selecting previously unselected package fonts-lyx. Preparing to unpack .../02-fonts-lyx_2.2.4-0ubuntu0.18.04.1_all.deb ... Unpacking fonts-lyx (2.2.4-0ubuntu0.18.04.1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../03-libjs-jquery-ui_1.12.1+dfsg-5_all.deb ... Unpacking libjs-jquery-ui (1.12.1+dfsg-5) ... Selecting previously unselected package python-backports.functools-lru-cache. Preparing to unpack .../04-python-backports.functools-lru-cache_1.4-2_all.deb ... Unpacking python-backports.functools-lru-cache (1.4-2) ... Selecting previously unselected package python-cycler. Preparing to unpack .../05-python-cycler_0.10.0-1_all.deb ... Unpacking python-cycler (0.10.0-1) ... Selecting previously unselected package python-dateutil. Preparing to unpack .../06-python-dateutil_2.6.1-1_all.deb ... Unpacking python-dateutil (2.6.1-1) ... Selecting previously unselected package python-decorator. Preparing to unpack .../07-python-decorator_4.1.2-1_all.deb ... Unpacking python-decorator (4.1.2-1) ... Selecting previously unselected package ttf-bitstream-vera. Preparing to unpack .../08-ttf-bitstream-vera_1.10-8_all.deb ... Unpacking ttf-bitstream-vera (1.10-8) ... Selecting previously unselected package python-matplotlib-data. Preparing to unpack .../09-python-matplotlib-data_2.1.1-2ubuntu3_all.deb ... Unpacking python-matplotlib-data (2.1.1-2ubuntu3) ... Selecting previously unselected package python-tz. Preparing to unpack .../10-python-tz_2018.3-2_all.deb ... Unpacking python-tz (2018.3-2) ... Selecting previously unselected package python-numpy. Preparing to unpack .../11-python-numpy_1%3a1.13.3-2ubuntu1_amd64.deb ... Unpacking python-numpy (1:1.13.3-2ubuntu1) ... Selecting previously unselected package python-subprocess32. Preparing to unpack .../12-python-subprocess32_3.2.7-3_amd64.deb ... Unpacking python-subprocess32 (3.2.7-3) ... Selecting previously unselected package python-matplotlib. Preparing to unpack .../13-python-matplotlib_2.1.1-2ubuntu3_amd64.deb ... Unpacking python-matplotlib (2.1.1-2ubuntu3) ... Selecting previously unselected package python-olefile. Preparing to unpack .../14-python-olefile_0.45.1-1_all.deb ... Unpacking python-olefile (0.45.1-1) ... Selecting previously unselected package python-pil:amd64. Preparing to unpack .../15-python-pil_5.1.0-1ubuntu0.2_amd64.deb ... Unpacking python-pil:amd64 (5.1.0-1ubuntu0.2) ... Selecting previously unselected package python-tk. Preparing to unpack .../16-python-tk_2.7.17-1~18.04_amd64.deb ... Unpacking python-tk (2.7.17-1~18.04) ... Selecting previously unselected package python-scipy. Preparing to unpack .../17-python-scipy_0.19.1-2ubuntu1_amd64.deb ... Unpacking python-scipy (0.19.1-2ubuntu1) ... Setting up python-backports.functools-lru-cache (1.4-2) ... Setting up python-tz (2018.3-2) ... Setting up python-cycler (0.10.0-1) ... Setting up python-numpy (1:1.13.3-2ubuntu1) ... Setting up python-dateutil (2.6.1-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4) ... Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up python-olefile (0.45.1-1) ... Setting up ttf-bitstream-vera (1.10-8) ... Setting up python-decorator (4.1.2-1) ... Setting up python-subprocess32 (3.2.7-3) ... Setting up python-pil:amd64 (5.1.0-1ubuntu0.2) ... Setting up blt (2.5.3+dfsg-4) ... Setting up fonts-lyx (2.2.4-0ubuntu0.18.04.1) ... Setting up python-matplotlib-data (2.1.1-2ubuntu3) ... Setting up python-scipy (0.19.1-2ubuntu1) ... Setting up python-matplotlib (2.1.1-2ubuntu3) ... Setting up python-tk (2.7.17-1~18.04) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Processing triggers for man-db (2.8.3-2ubuntu0.1) ... Processing triggers for fontconfig (2.12.6-0ubuntu2) ...]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/41036/install-gnuplot-in-ubuntu Sat, 15 Feb 2020 05:38:06 -0600 https://bioinformaticsonline.com/snippets/view/41036/install-gnuplot-in-ubuntu <![CDATA[Install gnuplot in Ubuntu !]]> $MT:~/Downloads/cgr-perl$ sudo apt-get install gnuplot [sudo] password for jit: Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: aglfn gnuplot-data gnuplot-qt libdouble-conversion1 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5printsupport5 libqt5svg5 libqt5widgets5 libwxbase3.0-0v5 libwxgtk3.0-0v5 libxcb-xinerama0 qt5-gtk-platformtheme qttranslations5-l10n Suggested packages: gnuplot-doc qt5-image-formats-plugins qtwayland5 The following NEW packages will be installed: aglfn gnuplot gnuplot-data gnuplot-qt libdouble-conversion1 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5printsupport5 libqt5svg5 libqt5widgets5 libwxbase3.0-0v5 libwxgtk3.0-0v5 libxcb-xinerama0 qt5-gtk-platformtheme qttranslations5-l10n 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. Need to get 15.8 MB/15.8 MB of archives. After this operation, 65.0 MB of additional disk space will be used. Do you want to continue? [Y/n] Y Get:1 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libdouble-conversion1 amd64 2.0.1-4ubuntu1 [33.0 kB] Get:2 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libqt5core5a amd64 5.9.5+dfsg-0ubuntu2.5 [2,036 kB] Get:3 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libqt5dbus5 amd64 5.9.5+dfsg-0ubuntu2.5 [195 kB] Get:4 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libqt5network5 amd64 5.9.5+dfsg-0ubuntu2.5 [635 kB] Get:5 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libqt5gui5 amd64 5.9.5+dfsg-0ubuntu2.5 [2,568 kB] Get:6 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libqt5widgets5 amd64 5.9.5+dfsg-0ubuntu2.5 [2,203 kB] Get:7 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libqt5svg5 amd64 5.9.5-0ubuntu1 [128 kB] Get:8 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 aglfn all 1.7-3 [29.4 kB] Get:9 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 gnuplot-data all 5.2.2+dfsg1-2ubuntu1 [56.7 kB] Get:10 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libqt5printsupport5 amd64 5.9.5+dfsg-0ubuntu2.5 [178 kB] Get:11 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libwxbase3.0-0v5 amd64 3.0.4+dfsg-3 [954 kB] Get:12 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libwxgtk3.0-0v5 amd64 3.0.4+dfsg-3 [4,182 kB] Get:13 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 gnuplot-qt amd64 5.2.2+dfsg1-2ubuntu1 [1,013 kB] Get:14 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 gnuplot all 5.2.2+dfsg1-2ubuntu1 [3,816 B] Get:15 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 qt5-gtk-platformtheme amd64 5.9.5+dfsg-0ubuntu2.5 [117 kB] Get:16 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 qttranslations5-l10n all 5.9.5-0ubuntu1 [1,485 kB] Fetched 15.8 MB in 9s (1,720 kB/s) Selecting previously unselected package libdouble-conversion1:amd64. (Reading database ... 189871 files and directories currently installed.) Preparing to unpack .../00-libdouble-conversion1_2.0.1-4ubuntu1_amd64.deb ... Unpacking libdouble-conversion1:amd64 (2.0.1-4ubuntu1) ... Selecting previously unselected package libqt5core5a:amd64. Preparing to unpack .../01-libqt5core5a_5.9.5+dfsg-0ubuntu2.5_amd64.deb ... Unpacking libqt5core5a:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Selecting previously unselected package libqt5dbus5:amd64. Preparing to unpack .../02-libqt5dbus5_5.9.5+dfsg-0ubuntu2.5_amd64.deb ... Unpacking libqt5dbus5:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Selecting previously unselected package libqt5network5:amd64. Preparing to unpack .../03-libqt5network5_5.9.5+dfsg-0ubuntu2.5_amd64.deb ... Unpacking libqt5network5:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Selecting previously unselected package libxcb-xinerama0:amd64. Preparing to unpack .../04-libxcb-xinerama0_1.13-2~ubuntu18.04_amd64.deb ... Unpacking libxcb-xinerama0:amd64 (1.13-2~ubuntu18.04) ... Selecting previously unselected package libqt5gui5:amd64. Preparing to unpack .../05-libqt5gui5_5.9.5+dfsg-0ubuntu2.5_amd64.deb ... Unpacking libqt5gui5:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Selecting previously unselected package libqt5widgets5:amd64. Preparing to unpack .../06-libqt5widgets5_5.9.5+dfsg-0ubuntu2.5_amd64.deb ... Unpacking libqt5widgets5:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Selecting previously unselected package libqt5svg5:amd64. Preparing to unpack .../07-libqt5svg5_5.9.5-0ubuntu1_amd64.deb ... Unpacking libqt5svg5:amd64 (5.9.5-0ubuntu1) ... Selecting previously unselected package aglfn. Preparing to unpack .../08-aglfn_1.7-3_all.deb ... Unpacking aglfn (1.7-3) ... Selecting previously unselected package gnuplot-data. Preparing to unpack .../09-gnuplot-data_5.2.2+dfsg1-2ubuntu1_all.deb ... Unpacking gnuplot-data (5.2.2+dfsg1-2ubuntu1) ... Selecting previously unselected package libqt5printsupport5:amd64. Preparing to unpack .../10-libqt5printsupport5_5.9.5+dfsg-0ubuntu2.5_amd64.deb ... Unpacking libqt5printsupport5:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Selecting previously unselected package libwxbase3.0-0v5:amd64. Preparing to unpack .../11-libwxbase3.0-0v5_3.0.4+dfsg-3_amd64.deb ... Unpacking libwxbase3.0-0v5:amd64 (3.0.4+dfsg-3) ... Selecting previously unselected package libwxgtk3.0-0v5:amd64. Preparing to unpack .../12-libwxgtk3.0-0v5_3.0.4+dfsg-3_amd64.deb ... Unpacking libwxgtk3.0-0v5:amd64 (3.0.4+dfsg-3) ... Selecting previously unselected package gnuplot-qt. Preparing to unpack .../13-gnuplot-qt_5.2.2+dfsg1-2ubuntu1_amd64.deb ... Unpacking gnuplot-qt (5.2.2+dfsg1-2ubuntu1) ... Selecting previously unselected package gnuplot. Preparing to unpack .../14-gnuplot_5.2.2+dfsg1-2ubuntu1_all.deb ... Unpacking gnuplot (5.2.2+dfsg1-2ubuntu1) ... Selecting previously unselected package qt5-gtk-platformtheme:amd64. Preparing to unpack .../15-qt5-gtk-platformtheme_5.9.5+dfsg-0ubuntu2.5_amd64.deb ... Unpacking qt5-gtk-platformtheme:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Selecting previously unselected package qttranslations5-l10n. Preparing to unpack .../16-qttranslations5-l10n_5.9.5-0ubuntu1_all.deb ... Unpacking qttranslations5-l10n (5.9.5-0ubuntu1) ... Setting up libxcb-xinerama0:amd64 (1.13-2~ubuntu18.04) ... Setting up libdouble-conversion1:amd64 (2.0.1-4ubuntu1) ... Setting up libwxbase3.0-0v5:amd64 (3.0.4+dfsg-3) ... Setting up qttranslations5-l10n (5.9.5-0ubuntu1) ... Setting up aglfn (1.7-3) ... Setting up libqt5core5a:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Setting up libqt5dbus5:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Setting up libqt5network5:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Setting up libwxgtk3.0-0v5:amd64 (3.0.4+dfsg-3) ... Setting up gnuplot-data (5.2.2+dfsg1-2ubuntu1) ... Setting up libqt5gui5:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Setting up qt5-gtk-platformtheme:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Setting up libqt5widgets5:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Setting up libqt5printsupport5:amd64 (5.9.5+dfsg-0ubuntu2.5) ... Setting up libqt5svg5:amd64 (5.9.5-0ubuntu1) ... Setting up gnuplot-qt (5.2.2+dfsg1-2ubuntu1) ... update-alternatives: using /usr/bin/gnuplot-qt to provide /usr/bin/gnuplot (gnuplot) in auto mode Setting up gnuplot (5.2.2+dfsg1-2ubuntu1) ... Processing triggers for man-db (2.8.3-2ubuntu0.1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ...]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/41025/to-convert-just-one-specific-read-group-to-fastq Fri, 14 Feb 2020 03:35:22 -0600 https://bioinformaticsonline.com/snippets/view/41025/to-convert-just-one-specific-read-group-to-fastq <![CDATA[To convert just one specific read group to fastq]]> # Stop script on error. set -uex # The SRR BioProject number for the sequencing data. PROJECT=PRJNA257197 # The number of datasets to subselect from the project. N=5 # Get the project run information. esearch -db sra -query $PROJECT | efetch -format runinfo > runinfo.txt # Select the first N elements. Keep only valid SRR numbers. cat runinfo.txt | cut -f 1 -d , | grep SRR | head -$N > selected.txt # Store the data in the reads folder. mkdir -p reads # Download the SRR data for each cat selected.txt | parallel fastq-dump -O reads -X 1000 --split-files {} # Create a directory for bam files mkdir -p bam # Generate a separate BAM file for each SAMPLE. cat selected.txt | parallel "picard FastqToSam F1=reads/{}_1.fastq F2=reads/{}_1.fastq O=bam/{}.bam RG=GROUP-{} LB=LIB-{} SM=SAMPLE_{} QUIET=true 2>> log.txt" # Merge all the BAM files into one. samtools merge -f all.bam bam/*.bam # Investigate the readgroups in the header. echo "" echo "SAM file header:" samtools view -H all.bam echo "" echo "Number of alignments with read group: GROUP-SRR1972919" samtools view -c -r GROUP-SRR1972919 all.bam # Reverting the process is to extract reads, tagged with readgroups to paired files. samtools fastq -t -1 all1.fq -2 all2.fq all.bam # To convert just one specific read group. samtools view -r GROUP-SRR1972919 all.bam | samtools fastq -t -1 all_SRR1972919_1.fq -2 all_SRR1972919_2fq -]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40976/update-conda Mon, 10 Feb 2020 04:06:25 -0600 https://bioinformaticsonline.com/snippets/view/40976/update-conda <![CDATA[Update conda !]]> (my_GATK) [wsu29@bladeamd-2 testGATK]$ conda update -n base -c defaults conda Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/miniconda3 added / updated specs: - conda The following packages will be downloaded: package | build ---------------------------|----------------- asn1crypto-1.3.0 | py37_0 164 KB ca-certificates-2020.1.1 | 0 125 KB certifi-2019.11.28 | py37_0 153 KB cffi-1.13.2 | py37h2e261b9_0 224 KB conda-4.8.2 | py37_0 2.8 MB pip-20.0.2 | py37_1 1.7 MB pycosat-0.6.3 | py37h7b6447c_0 82 KB pyopenssl-19.1.0 | py37_0 87 KB requests-2.22.0 | py37_1 92 KB ruamel_yaml-0.15.87 | py37h7b6447c_0 256 KB setuptools-45.1.0 | py37_0 511 KB six-1.14.0 | py37_0 27 KB sqlite-3.31.1 | h7b6447c_0 1.1 MB tqdm-4.42.0 | py_0 55 KB urllib3-1.25.8 | py37_0 169 KB wheel-0.34.2 | py37_0 51 KB ------------------------------------------------------------ Total: 7.5 MB The following packages will be UPDATED: asn1crypto 1.2.0-py37_0 --> 1.3.0-py37_0 ca-certificates 2019.10.16-0 --> 2020.1.1-0 certifi 2019.9.11-py37_0 --> 2019.11.28-py37_0 cffi 1.13.0-py37h2e261b9_0 --> 1.13.2-py37h2e261b9_0 conda 4.7.12-py37_0 --> 4.8.2-py37_0 pip 19.3.1-py37_0 --> 20.0.2-py37_1 pyopenssl 19.0.0-py37_0 --> 19.1.0-py37_0 requests 2.22.0-py37_0 --> 2.22.0-py37_1 ruamel_yaml 0.15.46-py37h14c3975_0 --> 0.15.87-py37h7b6447c_0 setuptools 41.4.0-py37_0 --> 45.1.0-py37_0 six 1.12.0-py37_0 --> 1.14.0-py37_0 sqlite 3.30.0-h7b6447c_0 --> 3.31.1-h7b6447c_0 tqdm 4.36.1-py_0 --> 4.42.0-py_0 urllib3 1.24.2-py37_0 --> 1.25.8-py37_0 wheel 0.33.6-py37_0 --> 0.34.2-py37_0 The following packages will be DOWNGRADED: pycosat 0.6.3-py37h14c3975_0 --> 0.6.3-py37h7b6447c_0 Proceed ([y]/n)? Y Downloading and Extracting Packages six-1.14.0 | 27 KB | ####################################################################################################### | 100% ruamel_yaml-0.15.87 | 256 KB | ####################################################################################################### | 100% ca-certificates-2020 | 125 KB | ####################################################################################################### | 100% conda-4.8.2 | 2.8 MB | ####################################################################################################### | 100% sqlite-3.31.1 | 1.1 MB | ####################################################################################################### | 100% certifi-2019.11.28 | 153 KB | ####################################################################################################### | 100% urllib3-1.25.8 | 169 KB | ####################################################################################################### | 100% pyopenssl-19.1.0 | 87 KB | ####################################################################################################### | 100% asn1crypto-1.3.0 | 164 KB | ####################################################################################################### | 100% pip-20.0.2 | 1.7 MB | ####################################################################################################### | 100% wheel-0.34.2 | 51 KB | ####################################################################################################### | 100% setuptools-45.1.0 | 511 KB | ####################################################################################################### | 100% tqdm-4.42.0 | 55 KB | ####################################################################################################### | 100% pycosat-0.6.3 | 82 KB | ####################################################################################################### | 100% cffi-1.13.2 | 224 KB | ####################################################################################################### | 100% requests-2.22.0 | 92 KB | ####################################################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40910/perl-script-to-delete-the-adjacent-repeats Wed, 05 Feb 2020 23:09:15 -0600 https://bioinformaticsonline.com/snippets/view/40910/perl-script-to-delete-the-adjacent-repeats <![CDATA[Perl script to delete the adjacent repeats !]]> /usr/bin/perl #Mostly the interview question for bioinfomatician ! #Write a code to delete the adjacent repeated character .... $string='ATTTTTTGGC'; # This should be converted to ATGC $string =~ s/(\w)\1/$1/g; print $string; #For more helps ... check out this #This bit of code will do the job: $string =~ s/(.)\1/$1/g #Alternatively, if you want to ignore case when comparing, you could use: $string =~ s/(.)\1/$1/gi #And finally, if you wanted to trim any number of duplicates down to a single letter, this would work: $string =~ s/(.)\1+/$1/gi]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40879/install-npm Mon, 03 Feb 2020 07:02:07 -0600 https://bioinformaticsonline.com/snippets/view/40879/install-npm <![CDATA[Install NPM !]]> $ sudo apt install npm Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: gyp javascript-common libjs-async libjs-inherits libjs-jquery libjs-node-uuid libjs-underscore libssl1.0-dev libuv1-dev node-abbrev node-ansi node-ansi-color-table node-archy node-async node-balanced-match node-block-stream node-brace-expansion node-builtin-modules node-combined-stream node-concat-map node-cookie-jar node-delayed-stream node-forever-agent node-form-data node-fs.realpath node-fstream node-fstream-ignore node-github-url-from-git node-glob node-graceful-fs node-gyp node-hosted-git-info node-inflight node-inherits node-ini node-is-builtin-module node-isexe node-json-stringify-safe node-lockfile node-lru-cache node-mime node-minimatch node-mkdirp node-mute-stream node-node-uuid node-nopt node-normalize-package-data node-npmlog node-once node-osenv node-path-is-absolute node-pseudomap node-qs node-read node-read-package-json node-request node-retry node-rimraf node-semver node-sha node-slide node-spdx-correct node-spdx-expression-parse node-spdx-license-ids node-tar node-tunnel-agent node-underscore node-validate-npm-package-license node-which node-wrappy node-yallist nodejs-dev Suggested packages: apache2 | lighttpd | httpd node-hawk node-aws-sign node-oauth-sign node-http-signature The following NEW packages will be installed: gyp javascript-common libjs-async libjs-inherits libjs-jquery libjs-node-uuid libjs-underscore libssl1.0-dev libuv1-dev node-abbrev node-ansi node-ansi-color-table node-archy node-async node-balanced-match node-block-stream node-brace-expansion node-builtin-modules node-combined-stream node-concat-map node-cookie-jar node-delayed-stream node-forever-agent node-form-data node-fs.realpath node-fstream node-fstream-ignore node-github-url-from-git node-glob node-graceful-fs node-gyp node-hosted-git-info node-inflight node-inherits node-ini node-is-builtin-module node-isexe node-json-stringify-safe node-lockfile node-lru-cache node-mime node-minimatch node-mkdirp node-mute-stream node-node-uuid node-nopt node-normalize-package-data node-npmlog node-once node-osenv node-path-is-absolute node-pseudomap node-qs node-read node-read-package-json node-request node-retry node-rimraf node-semver node-sha node-slide node-spdx-correct node-spdx-expression-parse node-spdx-license-ids node-tar node-tunnel-agent node-underscore node-validate-npm-package-license node-which node-wrappy node-yallist nodejs-dev npm 0 upgraded, 73 newly installed, 0 to remove and 387 not upgraded. Need to get 4,335 kB of archives. After this operation, 24.2 MB of additional disk space will be used. Do you want to continue? [Y/n] Y Get:1 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 gyp all 0.1+20150913git1f374df9-1ubuntu1 [265 kB] Get:2 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 javascript-common all 11 [6,066 B] Get:3 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-async all 0.8.0-3 [25.4 kB] Get:4 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libjs-jquery all 3.2.1-1 [152 kB] Get:5 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-node-uuid all 1.4.7-5 [11.5 kB] Get:6 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libjs-underscore all 1.8.3~dfsg-1 [59.9 kB] Get:7 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libssl1.0-dev amd64 1.0.2n-1ubuntu5.3 [1,365 kB] Get:8 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libuv1-dev amd64 1.18.0-3 [82.0 kB] Get:9 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-async all 0.8.0-3 [2,840 B] Get:10 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 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http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-pseudomap all 1.0.2-1 [3,534 B] Get:21 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-spdx-license-ids all 1.2.2-1 [4,792 B] Get:22 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-spdx-correct all 1.0.2-1 [3,718 B] Get:23 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-spdx-expression-parse all 1.0.4-1 [12.1 kB] Get:24 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-underscore all 1.8.3~dfsg-1 [3,790 B] Get:25 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-validate-npm-package-license all 3.0.1-1 [3,488 B] Get:26 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-yallist all 2.0.0-1 [5,398 B] Get:27 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-inherits all 2.0.3-1 [2,792 B] Get:28 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-abbrev all 1.0.9-1 [3,708 B] Get:29 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-ansi all 0.3.0-2ubuntu1 [8,720 B] Get:30 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-ansi-color-table all 1.0.0-1 [4,478 B] Get:31 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-archy all 1.0.0-1ubuntu1 [4,264 B] Get:32 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-balanced-match all 0.4.2-1 [4,030 B] Get:33 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-inherits all 2.0.3-1 [3,092 B] Get:34 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-block-stream all 0.0.9-1ubuntu1 [4,736 B] Get:35 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-concat-map all 0.0.1-1 [3,502 B] Get:36 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-brace-expansion all 1.1.8-1 [5,840 B] Get:37 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-delayed-stream all 0.0.5-1 [4,750 B] Get:38 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-combined-stream all 0.0.5-1 [4,958 B] Get:39 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-cookie-jar all 0.3.1-1 [3,746 B] Get:40 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-forever-agent all 0.5.1-1 [3,194 B] Get:41 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-mime all 1.3.4-1 [11.9 kB] Get:42 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-form-data all 0.1.0-1 [6,412 B] Get:43 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-minimatch all 3.0.4-3 [13.5 kB] Get:44 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-glob all 7.1.2-4 [17.7 kB] Get:45 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-rimraf all 2.6.2-1 [8,152 B] Get:46 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-mkdirp all 0.5.1-1 [4,848 B] Get:47 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-graceful-fs all 4.1.11-1 [10.8 kB] Get:48 http://in.archive.ubuntu.com/ubuntu bionic-updates/universe amd64 node-fstream all 1.0.10-1ubuntu0.18.04.1 [18.4 kB] Get:49 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-fstream-ignore all 0.0.6-2 [5,586 B] Get:50 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-github-url-from-git all 1.4.0-1 [3,782 B] Get:51 http://in.archive.ubuntu.com/ubuntu bionic-updates/universe amd64 nodejs-dev amd64 8.10.0~dfsg-2ubuntu0.4 [351 kB] Get:52 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-nopt all 3.0.6-3 [9,572 B] Get:53 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-npmlog all 0.0.4-1 [5,844 B] Get:54 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-osenv all 0.1.4-1 [4,212 B] Get:55 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-tunnel-agent all 0.3.1-1 [4,018 B] Get:56 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-json-stringify-safe all 5.0.0-1 [3,544 B] Get:57 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-qs all 2.2.4-1ubuntu1 [7,680 B] Get:58 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-request all 2.26.1-1 [14.5 kB] Get:59 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-semver all 5.4.1-1 [22.6 kB] Get:60 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-tar all 2.2.1-1 [17.7 kB] Get:61 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-which all 1.3.0-1 [4,504 B] Get:62 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-gyp all 3.6.2-1ubuntu1 [29.4 kB] Get:63 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-ini all 1.3.4-1 [5,588 B] Get:64 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-lockfile all 0.4.1-1 [5,450 B] Get:65 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-lru-cache all 4.1.1-1 [8,228 B] Get:66 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-mute-stream all 0.0.7-1 [4,372 B] Get:67 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-normalize-package-data all 2.3.5-2 [10.6 kB] Get:68 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-read all 1.0.7-1 [4,572 B] Get:69 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-read-package-json all 1.2.4-1 [7,780 B] Get:70 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-retry all 0.10.1-1 [8,016 B] Get:71 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-sha all 1.2.3-1 [4,272 B] Get:72 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 node-slide all 1.1.6-1 [6,212 B] Get:73 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 npm all 3.5.2-0ubuntu4 [1,586 kB] Fetched 4,335 kB in 15s (297 kB/s) Extracting templates from packages: 100% Selecting previously unselected package gyp. (Reading database ... 180389 files and directories currently installed.) Preparing to unpack .../00-gyp_0.1+20150913git1f374df9-1ubuntu1_all.deb ... Unpacking gyp (0.1+20150913git1f374df9-1ubuntu1) ... Selecting previously unselected package javascript-common. Preparing to unpack .../01-javascript-common_11_all.deb ... Unpacking javascript-common (11) ... Selecting previously unselected package libjs-async. Preparing to unpack .../02-libjs-async_0.8.0-3_all.deb ... Unpacking libjs-async (0.8.0-3) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../03-libjs-jquery_3.2.1-1_all.deb ... Unpacking libjs-jquery (3.2.1-1) ... Selecting previously unselected package libjs-node-uuid. Preparing to unpack .../04-libjs-node-uuid_1.4.7-5_all.deb ... Unpacking libjs-node-uuid (1.4.7-5) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../05-libjs-underscore_1.8.3~dfsg-1_all.deb ... Unpacking libjs-underscore (1.8.3~dfsg-1) ... 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Setting up npm (3.5.2-0ubuntu4) ...]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40876/cuda-toolkit-102-download Mon, 03 Feb 2020 04:12:32 -0600 https://bioinformaticsonline.com/snippets/view/40876/cuda-toolkit-102-download <![CDATA[CUDA Toolkit 10.2 Download]]> #More at https://developer.nvidia.com/cuda-downloads?target_os=Linux&target_arch=x86_64&target_distro=Ubuntu&target_version=1804&target_type=deblocal $ wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin --2020-02-03 15:15:56-- https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin Resolving developer.download.nvidia.com (developer.download.nvidia.com)... 192.229.232.112, 2606:2800:247:2063:46e:21d:825:102e Connecting to developer.download.nvidia.com (developer.download.nvidia.com)|192.229.232.112|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 56 [application/octet-stream] Saving to: ‘cuda-ubuntu1804.pin’ cuda-ubuntu1804.pin 100%[===========================================================>] 56 --.-KB/s in 0s 2020-02-03 15:15:56 (1.48 MB/s) - ‘cuda-ubuntu1804.pin’ saved [56/56] $ sudo mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600 $ wget http://developer.download.nvidia.com/compute/cuda/10.2/Prod/local_installers/cuda-repo-ubuntu1804-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb --2020-02-03 15:19:22-- http://developer.download.nvidia.com/compute/cuda/10.2/Prod/local_installers/cuda-repo-ubuntu1804-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb Resolving developer.download.nvidia.com (developer.download.nvidia.com)... 192.229.232.112, 2606:2800:247:2063:46e:21d:825:102e Connecting to developer.download.nvidia.com (developer.download.nvidia.com)|192.229.232.112|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 1896270068 (1.8G) [application/x-deb] Saving to: ‘cuda-repo-ubuntu1804-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb’ cuda-repo-ubuntu1804-10-2-local-1 100%[===========================================================>] 1.77G 4.90MB/s in 6m 27s 2020-02-03 15:25:50 (4.67 MB/s) - ‘cuda-repo-ubuntu1804-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb’ saved [1896270068/1896270068] $ sudo dpkg -i cuda-repo-ubuntu1804-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb $ sudo apt-key add /var/cuda-repo-10-2-local-10.2.89-440.33.01/7fa2af80.pub $ sudo apt-get update $ apt-get -y install cuda]]> Rahul Nayak