<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/1182?offset=50 https://bioinformaticsonline.com/pages/view/33842/awesome-perl-frameworks-libraries-and-software-part-5 Fri, 07 Jul 2017 04:12:47 -0500 https://bioinformaticsonline.com/pages/view/33842/awesome-perl-frameworks-libraries-and-software-part-5 <![CDATA[Awesome perl frameworks, libraries and software - PART 5]]>
  • robelix/sub2srt - subtitle converter
  • reyjrar/graphite-scripts - A Collections of Scripts for Working with Graphite
  • regilero/check_nginx_status - Nagios check for nginx status report
  • omniti-labs/resmon - resmon
  • motemen/App-htmlcat - redirect stdin to web browser
  • moose/Moo - Minimalist Object Orientation (with Moose compatibility)
  • miyagawa/fastpass - Tiny, XS free, standalone and preforking FastCGI daemon for PSGI
  • miyagawa/Filesys-Notify-Simple - Simple and dumb file system watcher
  • mhop/fhem-mirror - Branch 'master' is a read-only-mirror of svn://svn.code.sf.net/p/fhem/code which is updated once a day. On branch 'enocean' I am going to add some Enocean-Devices
  • lopnor/Plack-App-DAV - simple DAV server for Plack
  • kazuho/url_compress - a static PPM-based URL compressor / decompressor
  • jnthn/6model - Just a place that I'm keeping some meta-model prototyping; anything that matters will make it to another repo (e.g. nqp-rx one or Rakudo one) at some point.
  • jasonhancock/nagios-puppetdb - Nagios plugins and pnp4nagios templates related to Puppetlab's PuppetDB project.
  • goccy/p5-Compiler-Parser - Create Abstract Syntax Tree for Perl5
  • cgutteridge/Grinder - Create RDF data from spreadsheets or CSV
  • c9s/Plack-Middleware-OAuth - Plack Middleware for OAuth1 and OAuth2
  • bzip2-cuda/bzip2-cuda - Parallel implementation of bzip2 using cuda
  • alanstevens/ChocoPackages - Chocolatey Nuget Packages
  • SoylentNews/slashcode - The slashcode repository for SoylentNews. The initial code base was uploaded as it appeared on Sourceforge as of the last commit in September 2009
  • Miserlou/XSS-Harvest - XSS Weaponization
    • ]]>     Neel     https://bioinformaticsonline.com/file/view/36952/getoptspl-file Fri, 15 Jun 2018 04:43:03 -0500 https://bioinformaticsonline.com/file/view/36952/getoptspl-file <![CDATA[getopts.pl file]]> SSPACE_longread complain for getopts.pl file.

    To resolve this, download and have in SSPACED-Longreads folder.

    Cheers :)

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/29008/circos-visualize Fri, 02 Sep 2016 08:29:26 -0500 https://bioinformaticsonline.com/bookmarks/view/29008/circos-visualize <![CDATA[CIRCOS Visualize !!]]> Before uploading a data file, check the samples gallery to make sure that your data format is compatible.

    • Your file must be plain text.
    • Your data values must be non-negative integers.
    • Data must be space-separated (one or more tab or space, which will be collapsed).
    • No two rows or columns may have the same name.
    • Column and row names must begin with a letter (e.g. 'A', 'A0', 'A-0') and can only contain letters, numbers and _. No punctuation!
    • Maximum row + column total is 150 — if exceeded, rows and columns are limited to 75.
    • If you are using order, size and color rows/columns in combination they must appear in that order.

    Need help? Post questions to the Circos Google Group.

    http://mkweb.bcgsc.ca/tableviewer/visualize/

    Address of the bookmark: http://mkweb.bcgsc.ca/tableviewer/visualize/

    ]]>     Jit     https://bioinformaticsonline.com/pages/view/9028/linux-for-bioinformatician Thu, 13 Mar 2014 16:59:26 -0500 https://bioinformaticsonline.com/pages/view/9028/linux-for-bioinformatician <![CDATA[Linux for bioinformatician !!!]]> Linux, free operating system for computers, provides several powerful admin tools and utilities which will help you to manage your systems effectively and handle huge amount of genomic/biological data with an ease. The field of bioinformatics relies heavily on Linux-based computers and software. Although most bioinformatics programs can be compiled to run. If you don’t know what these no so user-friendly tools are and how to use them, you could be spending lot of time trying to perform even the basic admin tasks. The focus of this linux series is to help you understand system admin as well as basic tools, which will help you to become an effective bioinformatician and computational biologist.

    For knowledge about Linux and their importance amongst bioinformatician plesae read this article "An introduction to Linux for bioinformatics" by Paul Stothard.

    Linux cheat sheet at http://bioinformaticsonline.com/file/view/87/linux-cheat-sheet

    Please browse for futher useful linux pages on right hand side ...

    ]]>     Rahul Nayak     https://bioinformaticsonline.com/pages/view/11313/linux-sort-commands-for-bioinformatics Sat, 31 May 2014 15:41:16 -0500 https://bioinformaticsonline.com/pages/view/11313/linux-sort-commands-for-bioinformatics <![CDATA[Linux Sort Commands for Bioinformatics]]> Almost all the scripting languages such as Perl, Python etc have built-in sort, but unfortunately none of them are as flexible as sort command. But one when it come to space efficiency GNU sort stands at the top. It can sort a 20Gb file with less than 2Gb memory. It is not trivial to implement so powerful a sort by yourself.

    sort a space-delimited file based on its first column, then the second if the first is the same, and so on:
    sort input.txt

    sort a huge file (GNU sort ONLY):
    sort -S 1500M -t $HOME/tmp input.txt > sorted.txt

    sort starting from the third column, skipping the first two columns:
    sort +2 input.txt

    sort the second column as numbers, descending order; if identical, sort the 3rd as strings, ascending order:
    sort -k2,2nr -k3,3 input.txt

    sort starting from the 4th character at column 2, as numbers:
    sort -k2.4n input.txt

    More Linxu sort command information

    If you have any sort commands you'd like to share, please add them to our comments section below. For more help, you can also type:

    man sort

    or

    sort --help

    on your Unix/Linux system.

    ]]>     Rahul Nayak     https://bioinformaticsonline.com/pages/view/27965/cheatsheet-for-linux Wed, 22 Jun 2016 07:55:06 -0500 https://bioinformaticsonline.com/pages/view/27965/cheatsheet-for-linux <![CDATA[Cheatsheet for Linux !!]]> Linux Commands Cheat Sheet

        File System

        ls — list items in current directory

        ls -l — list items in current directory and show in long format to see perimissions, size, an modification date

        ls -a — list all items in current directory, including hidden files

        ls -F — list all items in current directory and show directories with a slash and executables with a star

        ls dir — list all items in directory dir

        cd dir — change directory to dir

        cd .. — go up one directory

        cd / — go to the root directory

        cd ~ — go to to your home directory

        cd - — go to the last directory you were just in

        pwd — show present working directory

        mkdir dir — make directory dir

        rm file — remove file

        rm -r dir — remove directory dir recursively

        cp file1 file2 — copy file1 to file2

        cp -r dir1 dir2 — copy directory dir1 to dir2 recursively

        mv file1 file2 — move (rename) file1 to file2

        ln -s file link — create symbolic link to file

        touch file — create or update file

        cat file — output the contents of file

        less file — view file with page navigation

        head file — output the first 10 lines of file

        tail file — output the last 10 lines of file

        tail -f file — output the contents of file as it grows, starting with the last 10 lines

        vim file — edit file

        alias name 'command' — create an alias for a command
        System

        shutdown — shut down machine

        reboot — restart machine

        date — show the current date and time

        whoami — who you are logged in as

        finger user — display information about user

        man command — show the manual for command

        df — show disk usage

        du — show directory space usage

        free — show memory and swap usage

        whereis app — show possible locations of app

        which app — show which app will be run by default
        Process Management

        ps — display your currently active processes

        top — display all running processes

        kill pid — kill process id pid

        kill -9 pid — force kill process id pid
        Permissions

        ls -l — list items in current directory and show permissions

        chmod ugo file — change permissions of file to ugo - u is the user's permissions, g is the group's permissions, and o is everyone else's permissions. The values of u, g, and o can be any number between 0 and 7.

        7 — full permissions

        6 — read and write only

        5 — read and execute only

        4 — read only

        3 — write and execute only

        2 — write only

        1 — execute only

        0 — no permissions

        chmod 600 file — you can read and write - good for files

        chmod 700 file — you can read, write, and execute - good for scripts

        chmod 644 file — you can read and write, and everyone else can only read - good for web pages

        chmod 755 file — you can read, write, and execute, and everyone else can read and execute - good for programs that you want to share
        Networking

        wget file — download a file

        curl file — download a file

        scp user@host:file dir — secure copy a file from remote server to the dir directory on your machine

        scp file user@host:dir — secure copy a file from your machine to the dir directory on a remote server

        scp -r user@host:dir dir — secure copy the directory dir from remote server to the directory dir on your machine

        ssh user@host — connect to host as user

        ssh -p port user@host — connect to host on port as user

        ssh-copy-id user@host — add your key to host for user to enable a keyed or passwordless login

        ping host — ping host and output results

        whois domain — get information for domain

        dig domain — get DNS information for domain

        dig -x host — reverse lookup host

        lsof -i tcp:1337 — list all processes running on port 1337
        Searching

        grep pattern files — search for pattern in files

        grep -r pattern dir — search recursively for pattern in dir

        grep -rn pattern dir — search recursively for pattern in dir and show the line number found

        grep -r pattern dir --include='*.ext — search recursively for pattern in dir and only search in files with .ext extension

        command | grep pattern — search for pattern in the output of command

        find file — find all instances of file in real system

        locate file — find all instances of file using indexed database built from the updatedb command. Much faster than find

        sed -i 's/day/night/g' file — find all occurrences of day in a file and replace them with night - s means substitude and g means global - sed also supports regular expressions
        Compression

        tar cf file.tar files — create a tar named file.tar containing files

        tar xf file.tar — extract the files from file.tar

        tar czf file.tar.gz files — create a tar with Gzip compression

        tar xzf file.tar.gz — extract a tar using Gzip

        gzip file — compresses file and renames it to file.gz

        gzip -d file.gz — decompresses file.gz back to file
        Shortcuts

        ctrl+a — move cursor to beginning of line

        ctrl+f — move cursor to end of line

        alt+f — move cursor forward 1 word

        alt+b — move cursor backward 1 word

    ]]>     Jit     https://bioinformaticsonline.com/blog/view/36525/installing-bandage-on-ubunty Tue, 08 May 2018 08:03:21 -0500 https://bioinformaticsonline.com/blog/view/36525/installing-bandage-on-ubunty <![CDATA[Installing Bandage on Ubunty !]]> The following instructions successfully build Bandage (https://github.com/rrwick/Bandage ) on a fresh installation of Ubuntu 14.04:

    1. Ensure the package lists are up-to-date: sudo apt-get update
    2. Install prerequisite packages: sudo apt-get install build-essential git qtbase5-dev libqt5svg5-dev
    3. Download the Bandage code from GitHub: git clone https://github.com/rrwick/Bandage.git
    4. Open a terminal in the Bandage directory.
    5. Set the environment variable to specify that you will be using Qt 5, not Qt 4: export QT_SELECT=5
    6. Run qmake to generate a Makefile: qmake
    7. Build the program: make
    8. Bandage should now be an executable file.
    9. Optionally, copy the program into /usr/local/bin: sudo make install. The Bandage build directory can then be deleted.

    ➜ Tools git:(master) ✗ sudo apt-get update
    [sudo] password for urbe: 
    Hit:1 http://ppa.launchpad.net/webupd8team/atom/ubuntu xenial InRelease
    Get:2 http://security.ubuntu.com/ubuntu xenial-security InRelease [107 kB] 
    Hit:3 http://ppa.launchpad.net/webupd8team/java/ubuntu xenial InRelease 
    Hit:4 http://be.archive.ubuntu.com/ubuntu xenial InRelease 
    Get:5 http://be.archive.ubuntu.com/ubuntu xenial-updates InRelease [109 kB]
    Get:6 http://be.archive.ubuntu.com/ubuntu xenial-backports InRelease [107 kB] 
    Get:7 https://cran.rstudio.com/bin/linux/ubuntu xenial/ InRelease [3.590 B] 
    Hit:8 https://download.docker.com/linux/ubuntu xenial InRelease 
    Ign:9 http://download.opensuse.org/repositories/home:/sionescu/Debian ./ InRelease 
    Hit:10 http://download.opensuse.org/repositories/home:/sionescu/Debian ./ Release 
    Get:11 http://packages.cloud.google.com/apt cloud-sdk-xenial InRelease [6.372 B]
    Get:12 http://security.ubuntu.com/ubuntu xenial-security/main amd64 Packages [484 kB]
    Get:13 http://security.ubuntu.com/ubuntu xenial-security/main i386 Packages [433 kB]
    Get:14 http://security.ubuntu.com/ubuntu xenial-security/main Translation-en [209 kB]
    Get:15 http://security.ubuntu.com/ubuntu xenial-security/main amd64 DEP-11 Metadata [67,5 kB]
    Get:16 http://security.ubuntu.com/ubuntu xenial-security/main DEP-11 64x64 Icons [68,0 kB] 
    Get:17 http://security.ubuntu.com/ubuntu xenial-security/universe amd64 DEP-11 Metadata [107 kB]
    Get:18 http://security.ubuntu.com/ubuntu xenial-security/universe DEP-11 64x64 Icons [147 kB]
    Get:19 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 Packages [769 kB] 
    Get:20 http://be.archive.ubuntu.com/ubuntu xenial-updates/main i386 Packages [710 kB] 
    Get:21 http://be.archive.ubuntu.com/ubuntu xenial-updates/main Translation-en [319 kB]
    Get:22 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 DEP-11 Metadata [319 kB]
    Get:24 http://be.archive.ubuntu.com/ubuntu xenial-updates/main DEP-11 64x64 Icons [228 kB] 
    Get:25 http://be.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 DEP-11 Metadata [246 kB]
    Err:11 http://packages.cloud.google.com/apt cloud-sdk-xenial InRelease 
    The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 6A030B21BA07F4FB
    Get:26 http://be.archive.ubuntu.com/ubuntu xenial-updates/universe DEP-11 64x64 Icons [331 kB]
    Get:27 http://be.archive.ubuntu.com/ubuntu xenial-updates/multiverse amd64 DEP-11 Metadata [5.964 B]
    Get:28 http://be.archive.ubuntu.com/ubuntu xenial-backports/main amd64 DEP-11 Metadata [3.328 B]
    Get:29 http://be.archive.ubuntu.com/ubuntu xenial-backports/universe amd64 DEP-11 Metadata [5.088 B]
    Fetched 4.779 kB in 2s (1.606 kB/s) 
    Reading package lists... Done
    W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://packages.cloud.google.com/apt cloud-sdk-xenial InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 6A030B21BA07F4FB
    W: Failed to fetch http://packages.cloud.google.com/apt/dists/cloud-sdk-xenial/InRelease The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 6A030B21BA07F4FB
    W: Some index files failed to download. They have been ignored, or old ones used instead.
    ➜ Tools git:(master) ✗ sudo apt-get install build-essential git qtbase5-dev libqt5svg5-dev
    Reading package lists... Done
    Building dependency tree 
    Reading state information... Done
    build-essential is already the newest version (12.1ubuntu2).
    git is already the newest version (1:2.7.4-0ubuntu1.3).
    The following packages were automatically installed and are no longer required:
    bridge-utils containerd linux-headers-4.4.0-116 linux-headers-4.4.0-116-generic linux-headers-4.4.0-21 linux-headers-4.4.0-21-generic linux-image-4.4.0-116-generic linux-image-4.4.0-21-generic
    linux-image-extra-4.4.0-116-generic linux-image-extra-4.4.0-21-generic linux-signed-image-4.4.0-116-generic runc ubuntu-fan
    Use 'sudo apt autoremove' to remove them.
    The following additional packages will be installed:
    libdrm-dev libegl1-mesa-dev libgl1-mesa-dev libgles2-mesa libgles2-mesa-dev libglu1-mesa-dev libmirclient-dev libmircommon-dev libmircookie-dev libmircookie2 libmircore-dev libprotobuf-dev libprotobuf9v5
    libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5opengl5 libqt5opengl5-dev libqt5printsupport5 libqt5sql5 libqt5sql5-sqlite libqt5svg5 libqt5test5 libqt5widgets5 libqt5xml5 libwayland-bin
    libwayland-dev libx11-xcb-dev libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present-dev libxcb-randr0 libxcb-randr0-dev libxcb-render-util0 libxcb-render0-dev
    libxcb-shape0-dev libxcb-sync-dev libxcb-xfixes0-dev libxcb-xkb1 libxdamage-dev libxext-dev libxfixes-dev libxkbcommon-dev libxkbcommon-x11-0 libxshmfence-dev libxxf86vm-dev mesa-common-dev qt5-qmake
    qtbase5-dev-tools qttranslations5-l10n x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-xext-dev x11proto-xf86vidmode-dev
    Suggested packages:
    libqt5libqgtk2 qt5-image-formats-plugins qtwayland5 libxext-doc libmysqlclient-dev libpq-dev libsqlite3-dev unixodbc-dev
    The following NEW packages will be installed:
    libdrm-dev libegl1-mesa-dev libgl1-mesa-dev libgles2-mesa libgles2-mesa-dev libglu1-mesa-dev libmirclient-dev libmircommon-dev libmircookie-dev libmircookie2 libmircore-dev libprotobuf-dev libprotobuf9v5
    libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5opengl5 libqt5opengl5-dev libqt5printsupport5 libqt5sql5 libqt5sql5-sqlite libqt5svg5 libqt5svg5-dev libqt5test5 libqt5widgets5 libqt5xml5
    libwayland-bin libwayland-dev libx11-xcb-dev libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present-dev libxcb-randr0 libxcb-randr0-dev libxcb-render-util0
    libxcb-render0-dev libxcb-shape0-dev libxcb-sync-dev libxcb-xfixes0-dev libxcb-xkb1 libxdamage-dev libxext-dev libxfixes-dev libxkbcommon-dev libxkbcommon-x11-0 libxshmfence-dev libxxf86vm-dev mesa-common-dev
    qt5-qmake qtbase5-dev qtbase5-dev-tools qttranslations5-l10n x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-xext-dev x11proto-xf86vidmode-dev
    0 upgraded, 64 newly installed, 0 to remove and 11 not upgraded.
    Need to get 15,2 MB of archives.
    After this operation, 78,5 MB of additional disk space will be used.
    Do you want to continue? [Y/n] Y
    Get:1 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5core5a amd64 5.5.1+dfsg-16ubuntu7.5 [1.817 kB]
    Get:2 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5dbus5 amd64 5.5.1+dfsg-16ubuntu7.5 [175 kB]
    Get:3 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5network5 amd64 5.5.1+dfsg-16ubuntu7.5 [540 kB]
    Get:4 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-icccm4 amd64 0.4.1-1ubuntu1 [10,4 kB]
    Get:5 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-image0 amd64 0.4.0-1build1 [12,3 kB]
    Get:6 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-keysyms1 amd64 0.4.0-1 [8.406 B]
    Get:7 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-randr0 amd64 1.11.1-1ubuntu1 [14,4 kB]
    Get:8 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-render-util0 amd64 0.3.9-1 [9.638 B]
    Get:9 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-xkb1 amd64 1.11.1-1ubuntu1 [29,2 kB]
    Get:10 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxkbcommon-x11-0 amd64 0.5.0-1ubuntu2 [13,5 kB]
    Get:11 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5gui5 amd64 5.5.1+dfsg-16ubuntu7.5 [2.290 kB]
    Get:12 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5widgets5 amd64 5.5.1+dfsg-16ubuntu7.5 [2.252 kB]
    Get:13 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libqt5svg5 amd64 5.5.1-2build1 [128 kB]
    Get:14 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libqt5svg5-dev amd64 5.5.1-2build1 [9.724 B]
    Get:15 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libdrm-dev amd64 2.4.83-1~16.04.1 [229 kB]
    Get:16 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-dri2-dev all 2.8-2 [12,6 kB]
    Get:17 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-gl-dev all 1.4.17-1 [17,9 kB]
    Get:18 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-xext-dev all 7.3.0-1 [212 kB]
    Get:19 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxext-dev amd64 2:1.3.3-1 [82,1 kB]
    Get:20 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-xf86vidmode-dev all 2.3.1-2 [6.116 B]
    Get:21 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxxf86vm-dev amd64 1:1.1.4-1 [13,3 kB]
    Get:22 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-fixes-dev all 1:5.0-2ubuntu2 [14,2 kB]
    Get:23 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxfixes-dev amd64 1:5.0.1-2 [10,9 kB]
    Get:24 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-damage-dev all 1:1.2.1-2 [8.286 B]
    Get:25 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxdamage-dev amd64 1:1.1.4-2 [5.028 B]
    Get:26 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-glx0-dev amd64 1.11.1-1ubuntu1 [26,9 kB]
    Get:27 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-dri2-0-dev amd64 1.11.1-1ubuntu1 [8.384 B]
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    Get:29 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-render0-dev amd64 1.11.1-1ubuntu1 [15,3 kB]
    Get:30 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-randr0-dev amd64 1.11.1-1ubuntu1 [18,2 kB]
    Get:31 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-shape0-dev amd64 1.11.1-1ubuntu1 [6.900 B]
    Get:32 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-xfixes0-dev amd64 1.11.1-1ubuntu1 [11,2 kB]
    Get:33 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-sync-dev amd64 1.11.1-1ubuntu1 [10,1 kB]
    Get:34 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-present-dev amd64 1.11.1-1ubuntu1 [6.618 B]
    Get:35 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxshmfence-dev amd64 1.2-1 [3.676 B]
    Get:36 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libx11-xcb-dev amd64 2:1.6.3-1ubuntu2 [9.730 B]
    Get:37 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libwayland-bin amd64 1.12.0-1~ubuntu16.04.3 [18,4 kB]
    Get:38 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libwayland-dev amd64 1.12.0-1~ubuntu16.04.3 [92,4 kB]
    Get:39 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircore-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [23,7 kB]
    Get:40 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libprotobuf9v5 amd64 2.6.1-1.3 [326 kB]
    Get:41 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libprotobuf-dev amd64 2.6.1-1.3 [473 kB]
    Get:42 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxkbcommon-dev amd64 0.5.0-1ubuntu2 [231 kB]
    Get:43 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircommon-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [14,9 kB]
    Get:44 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircookie2 amd64 0.26.3+16.04.20170605-0ubuntu1.1 [22,5 kB]
    Get:45 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircookie-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [5.152 B]
    Get:46 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmirclient-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [42,6 kB]
    Get:47 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libegl1-mesa-dev amd64 17.2.8-0ubuntu0~16.04.1 [19,9 kB]
    Get:48 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgles2-mesa amd64 17.2.8-0ubuntu0~16.04.1 [13,4 kB]
    Get:49 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgles2-mesa-dev amd64 17.2.8-0ubuntu0~16.04.1 [40,2 kB]
    Get:50 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 mesa-common-dev amd64 17.2.8-0ubuntu0~16.04.1 [525 kB]
    Get:51 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgl1-mesa-dev amd64 17.2.8-0ubuntu0~16.04.1 [4.456 B]
    Get:52 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libglu1-mesa-dev amd64 9.0.0-2.1 [202 kB]
    Get:53 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5concurrent5 amd64 5.5.1+dfsg-16ubuntu7.5 [24,3 kB]
    Get:54 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5opengl5 amd64 5.5.1+dfsg-16ubuntu7.5 [128 kB]
    Get:55 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5printsupport5 amd64 5.5.1+dfsg-16ubuntu7.5 [174 kB]
    Get:56 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5sql5 amd64 5.5.1+dfsg-16ubuntu7.5 [104 kB]
    Get:57 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5test5 amd64 5.5.1+dfsg-16ubuntu7.5 [84,5 kB]
    Get:58 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5xml5 amd64 5.5.1+dfsg-16ubuntu7.5 [91,8 kB]
    Get:59 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qt5-qmake amd64 5.5.1+dfsg-16ubuntu7.5 [1.192 kB]
    Get:60 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qtbase5-dev-tools amd64 5.5.1+dfsg-16ubuntu7.5 [1.056 kB]
    Get:61 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qtbase5-dev amd64 5.5.1+dfsg-16ubuntu7.5 [931 kB]
    Get:62 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5opengl5-dev amd64 5.5.1+dfsg-16ubuntu7.5 [31,5 kB]
    Get:63 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5sql5-sqlite amd64 5.5.1+dfsg-16ubuntu7.5 [33,0 kB]
    Get:64 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 qttranslations5-l10n all 5.5.1-2build1 [1.210 kB]
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    Setting up libmircore-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
    Setting up libprotobuf9v5:amd64 (2.6.1-1.3) ...
    Setting up libprotobuf-dev:amd64 (2.6.1-1.3) ...
    Setting up libxkbcommon-dev (0.5.0-1ubuntu2) ...
    Setting up libmircommon-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
    Setting up libmircookie2:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
    Setting up libmircookie-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
    Setting up libmirclient-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
    Setting up libegl1-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
    Setting up libgles2-mesa:amd64 (17.2.8-0ubuntu0~16.04.1) ...
    Setting up libgles2-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
    Setting up mesa-common-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
    Setting up libgl1-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
    Setting up libglu1-mesa-dev:amd64 (9.0.0-2.1) ...
    Setting up libqt5concurrent5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5opengl5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5printsupport5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5sql5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5test5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5xml5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up qt5-qmake:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up qtbase5-dev-tools (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up qtbase5-dev:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5opengl5-dev:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5sql5-sqlite:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up qttranslations5-l10n (5.5.1-2build1) ...
    Processing triggers for libc-bin (2.23-0ubuntu10) ...
    ➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Bandage.git
    Cloning into 'Bandage'...
    remote: Counting objects: 7813, done.
    remote: Total 7813 (delta 0), reused 0 (delta 0), pack-reused 7813
    Receiving objects: 100% (7813/7813), 27.43 MiB | 16.33 MiB/s, done.
    Resolving deltas: 100% (5973/5973), done.
    Checking connectivity... done.
    ➜ Tools git:(master) ✗ cd Bandage 
    ➜ Bandage git:(master) ls
    Bandage.pro BandageTests.pro blast build_scripts command_line COPYING graph images ogdf program README.md tests ui
    ➜ Bandage git:(master) export QT_SELECT=5
    ➜ Bandage git:(master) qmake
    ➜ Bandage git:(master) ✗ make
    /home/urbe/anaconda3/bin/uic ui/mainwindow.ui -o ui_mainwindow.h
    /home/urbe/anaconda3/bin/uic ui/settingsdialog.ui -o ui_settingsdialog.h
    /home/urbe/anaconda3/bin/uic ui/aboutdialog.ui -o ui_aboutdialog.h
    /home/urbe/anaconda3/bin/uic ui/enteroneblastquerydialog.ui -o ui_enteroneblastquerydialog.h
    /home/urbe/anaconda3/bin/uic ui/blastsearchdialog.ui -o ui_blastsearchdialog.h
    /home/urbe/anaconda3/bin/uic ui/myprogressdialog.ui -o ui_myprogressdialog.h
    /home/urbe/anaconda3/bin/uic ui/pathspecifydialog.ui -o ui_pathspecifydialog.h
    /home/urbe/anaconda3/bin/uic ui/querypathsdialog.ui -o ui_querypathsdialog.h
    /home/urbe/anaconda3/bin/uic ui/blasthitfiltersdialog.ui -o ui_blasthitfiltersdialog.h
    /home/urbe/anaconda3/bin/uic ui/changenodenamedialog.ui -o ui_changenodenamedialog.h
    /home/urbe/anaconda3/bin/uic ui/graphinfodialog.ui -o ui_graphinfodialog.h
    /home/urbe/anaconda3/bin/uic ui/changenodedepthdialog.ui -o ui_changenodedepthdialog.h
    g++ -c -pipe -O2 -std=gnu++0x -Wall -W -D_REENTRANT -fPIC -DQT_NO_DEBUG -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_CORE_LIB -I. -Iui -I/usr/include -I../../anaconda3/include/qt -I../../anaconda3/include/qt/QtSvg -I../../anaconda3/include/qt/QtWidgets -I../../anaconda3/include/qt/QtGui -I../../anaconda3/include/qt/QtCore -I. -I. -I../../anaconda3/mkspecs/linux-g++ -o main.o program/main.cpp
    g++ -c -pipe -O2 -std=gnu++0x -Wall -W -D_REENTRANT -fPIC -DQT_NO_DEBUG -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_CORE_LIB -I. -Iui -I/usr/include -I../../anaconda3/include/qt -I../../anaconda3/include/qt/QtSvg -I../../anaconda3/include/qt/QtWidgets -I../../anaconda3/include/qt/QtGui -I../../anaconda3/include/qt/QtCore -I. -I. -I../../anaconda3/mkspecs/linux-g++ -o settings.o program/settings.cpp
    ....

    ...
    g++ -Wl,-O1 -Wl,-rpath,/home/urbe/anaconda3/lib -o Bandage main.o settings.o globals.o graphlayoutworker.o debruijnnode.o debruijnedge.o graphicsitemnode.o graphicsitemedge.o mainwindow.o graphicsviewzoom.o settingsdialog.o mygraphicsview.o mygraphicsscene.o aboutdialog.o enteroneblastquerydialog.o blasthit.o blastqueries.o blastsearchdialog.o infotextwidget.o assemblygraph.o verticalscrollarea.o myprogressdialog.o nodewidthvisualaid.o verticallabel.o load.o image.o commoncommandlinefunctions.o mytablewidget.o buildblastdatabaseworker.o colourbutton.o blastquery.o runblastsearchworker.o blastsearch.o path.o pathspecifydialog.o graphlocation.o tablewidgetitemint.o tablewidgetitemdouble.o tablewidgetitemshown.o memory.o querypathspushbutton.o querypathsdialog.o blastquerypath.o blasthitfiltersdialog.o scinot.o changenodenamedialog.o querypathsequencecopybutton.o querypaths.o info.o reduce.o Graph.o GraphAttributes.o FMMMLayout.o geometry.o ClusterGraphAttributes.o FruchtermanReingold.o NMM.o GmlParser.o simple_graph_alg.o basic.o XmlParser.o String.o Hashing.o PoolMemoryAllocator.o GraphCopy.o CombinatorialEmbedding.o OgmlParser.o ClusterGraph.o Math.o EdgeAttributes.o NodeAttributes.o MAARPacking.o Multilevel.o numexcept.o Set.o Ogml.o DinoXmlParser.o DinoXmlScanner.o DinoTools.o DinoLineBuffer.o System.o QuadTreeNM.o QuadTreeNodeNM.o Constraint.o MultilevelGraph.o graphinfodialog.o tablewidgetitemname.o changenodedepthdialog.o qrc_images.o moc_graphlayoutworker.o moc_mainwindow.o moc_graphicsviewzoom.o moc_settingsdialog.o moc_mygraphicsview.o moc_mygraphicsscene.o moc_aboutdialog.o moc_enteroneblastquerydialog.o moc_blastquery.o moc_blastsearchdialog.o moc_infotextwidget.o moc_assemblygraph.o moc_verticalscrollarea.o moc_myprogressdialog.o moc_nodewidthvisualaid.o moc_verticallabel.o moc_mytablewidget.o moc_buildblastdatabaseworker.o moc_colourbutton.o moc_runblastsearchworker.o moc_pathspecifydialog.o moc_querypathspushbutton.o moc_querypathsdialog.o moc_blasthitfiltersdialog.o moc_changenodenamedialog.o moc_querypathsequencecopybutton.o moc_graphinfodialog.o moc_changenodedepthdialog.o -L/usr/lib -L/home/urbe/anaconda3/lib -lQt5Svg -lQt5Widgets -lQt5Gui -lQt5Core -lGL -lpthread 
    ➜ Bandage git:(master) ✗ ls 
    aboutdialog.o DinoTools.o Makefile moc_infotextwidget.cpp moc_verticalscrollarea.o scinot.o
    assemblygraph.o DinoXmlParser.o Math.o moc_infotextwidget.o MultilevelGraph.o Set.o
    Bandage DinoXmlScanner.o memory.o moc_mainwindow.cpp Multilevel.o settingsdialog.o
    Bandage.pro EdgeAttributes.o moc_aboutdialog.cpp moc_mainwindow.o mygraphicsscene.o settings.o
    BandageTests.pro enteroneblastquerydialog.o moc_aboutdialog.o moc_mygraphicsscene.cpp mygraphicsview.o simple_graph_alg.o
    basic.o FMMMLayout.o moc_assemblygraph.cpp moc_mygraphicsscene.o myprogressdialog.o String.o
    blast FruchtermanReingold.o moc_assemblygraph.o moc_mygraphicsview.cpp mytablewidget.o System.o
    blasthitfiltersdialog.o geometry.o moc_blasthitfiltersdialog.cpp moc_mygraphicsview.o NMM.o tablewidgetitemdouble.o
    blasthit.o globals.o moc_blasthitfiltersdialog.o moc_myprogressdialog.cpp NodeAttributes.o tablewidgetitemint.o
    blastqueries.o GmlParser.o moc_blastquery.cpp moc_myprogressdialog.o nodewidthvisualaid.o tablewidgetitemname.o
    blastquery.o graph moc_blastquery.o moc_mytablewidget.cpp numexcept.o tablewidgetitemshown.o
    blastquerypath.o GraphAttributes.o moc_blastsearchdialog.cpp moc_mytablewidget.o ogdf tests
    blastsearchdialog.o GraphCopy.o moc_blastsearchdialog.o moc_nodewidthvisualaid.cpp Ogml.o ui
    blastsearch.o graphicsitemedge.o moc_buildblastdatabaseworker.cpp moc_nodewidthvisualaid.o OgmlParser.o ui_aboutdialog.h
    buildblastdatabaseworker.o graphicsitemnode.o moc_buildblastdatabaseworker.o moc_pathspecifydialog.cpp path.o ui_blasthitfiltersdialog.h
    build_scripts graphicsviewzoom.o moc_changenodedepthdialog.cpp moc_pathspecifydialog.o pathspecifydialog.o ui_blastsearchdialog.h
    changenodedepthdialog.o graphinfodialog.o moc_changenodedepthdialog.o moc_querypathsdialog.cpp PoolMemoryAllocator.o ui_changenodedepthdialog.h
    changenodenamedialog.o graphlayoutworker.o moc_changenodenamedialog.cpp moc_querypathsdialog.o program ui_changenodenamedialog.h
    ClusterGraphAttributes.o graphlocation.o moc_changenodenamedialog.o moc_querypathsequencecopybutton.cpp qrc_images.cpp ui_enteroneblastquerydialog.h
    ClusterGraph.o Graph.o moc_colourbutton.cpp moc_querypathsequencecopybutton.o qrc_images.o ui_graphinfodialog.h
    colourbutton.o Hashing.o moc_colourbutton.o moc_querypathspushbutton.cpp QuadTreeNM.o ui_mainwindow.h
    CombinatorialEmbedding.o image.o moc_enteroneblastquerydialog.cpp moc_querypathspushbutton.o QuadTreeNodeNM.o ui_myprogressdialog.h
    command_line images moc_enteroneblastquerydialog.o moc_runblastsearchworker.cpp querypathsdialog.o ui_pathspecifydialog.h
    commoncommandlinefunctions.o info.o moc_graphicsviewzoom.cpp moc_runblastsearchworker.o querypathsequencecopybutton.o ui_querypathsdialog.h
    Constraint.o infotextwidget.o moc_graphicsviewzoom.o moc_settingsdialog.cpp querypaths.o ui_settingsdialog.h
    COPYING load.o moc_graphinfodialog.cpp moc_settingsdialog.o querypathspushbutton.o verticallabel.o
    debruijnedge.o MAARPacking.o moc_graphinfodialog.o moc_verticallabel.cpp README.md verticalscrollarea.o
    debruijnnode.o main.o moc_graphlayoutworker.cpp moc_verticallabel.o reduce.o XmlParser.o
    DinoLineBuffer.o mainwindow.o moc_graphlayoutworker.o moc_verticalscrollarea.cpp runblastsearchworker.o
    ➜ Bandage git:(master) ✗ ./Bandage

    ]]>     Jit     https://bioinformaticsonline.com/pages/view/37677/installing-blat-on-linux Tue, 11 Sep 2018 08:17:35 -0500 https://bioinformaticsonline.com/pages/view/37677/installing-blat-on-linux <![CDATA[Installing BLAT on Linux !]]> It's been a while since I last installed BLAT and when I went to the download directory at UCSC: http://users.soe.ucsc.edu/~kent/src/ I found that the latest blast is now version 35 and that the code to download was: blatSrc35.zip. However, you can also get pre-compiled binaries at: http://hgdownload.cse.ucsc.edu/admin/exe/ and that there was a linux x86_64 executable for my architecture available at: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/. Though YYMV, BLAT can be a little bit of a tricky beast to get going, so I decided to download the source code and compile that.

    I will be compiling this code as 'root' as a system tool in /usr/local/src, so do not scream at me for that.

    First I created an /usr/local/src/blat directory and I copied the blatSrc35.zip file into that.

    Next I used

    unzip blatSrc35.zip

    to unpack the archive. This gives a directory blatSrc now move into that directory.

    #cd blatSrc

    before you begin read the README file that comes with the source code.

    One thing about building blat is that you need to set the MACHTYPE variable so that the BLAT sources know what type of machine you are compiling the software on.

    on most *nix machines, typing

    echo $MACHTYPE

    will return the machine architecture type.

    On my CentOS 6 based system this gave:

    x86_64-redhat-linux-gnu

    However, what BLAT requires is the 'short value' (ie the first part of the MACHTYPE). To correct this, in the bash shell type (change this to the correct MACHTYPE for your system)

    MACHTYPE=x86_64
export MACHTYPE

    now running the command:

    echo $MACHTYPE

    should give the correct short form of the MACHTYPE:

    x86_64

    now create the directory lib/$MACHTYPE in the source tree. ie:

    mkdir lib/$MACHTYPE

    For my machine, lib/x86_64 already existed, so I did not have to do this, but this is not the case for all architectures.

    The BLAT code assumes that you are compiling BLAT as a non-privileged (ie non-root) user. As a result, you must create the directory for the executables to go into:

    mkdir ~/bin/$MACHTYPE

    If you are installing as a normal user, edit your .bashrc to add the following (change the x86_64 to be your MACHTYPE):

    export PATH=~/bin/x86_64::$PATH

    For me, though, this was not good enough. I wanted the executables in /usr/local/bin where all my other code goes. As a result I did some hackery...

    There is a master make template in the inc directory called common.mk and I edited this file with the command:

    vi inc/common.mk

    I replaced the line

        BINDIR=${HOME}/bin/${MACHTYPE}

    with

        BINDIR=/usr/local/bin

    saved and quit (as this is in my path, I do not need to do anything else)

    All the preparation is now done and you can create the blat executables by going into the toplevel of the blat source tree (for me it was /usr/local/src/blat/blatSrc, but change to wherever you unpacked blat into).

    Now simply run the command:

    make

    to compile the code.

    Blat installed cleanly and the executables were all neatly placed in /usr/local/bin/x86_64, just like I wanted.

    now simply running the command:

    blat

    on the command line gives me information on blat and sample usage.

    Blat is installed and it's installed properly in my system code tree!!!

    ]]>     BioStar     https://bioinformaticsonline.com/blog/view/43872/installing-elgg-on-ubuntu Wed, 25 May 2022 02:26:05 -0500 https://bioinformaticsonline.com/blog/view/43872/installing-elgg-on-ubuntu <![CDATA[Installing ELGG on Ubuntu !]]> Elgg is an open-source and highly customizable framework used for building an online social environment. It provides a simple and powerful user interface that helps to manage and build your content through a web browser. Elgg offers a rich set of features including messaging, microblogging, file-sharing, RSS support, access control, groups, and many more.

     

    In this tutorial, we will show you how to install and configure Elgg social networking platform on Ubuntu 20.04.

    Prerequisites

    • A fresh Ubuntu 20.04 VPS on the Atlantic.net Cloud Platform
    • A valid domain name pointed to your server IP
    • A root password configured on your server

    Step 1 – Create Atlantic.Net Cloud Server

    First, log in to your Atlantic.Net Cloud Server. Create a new server, choosing Ubuntu 20.04 as the operating system with at least 2GB RAM. Connect to your Cloud Server via SSH and log in using the credentials highlighted at the top of the page.

    Once you are logged in to your Ubuntu 20.04 server, run the following command to update your base system with the latest available packages.

    apt-get update -y

    Step 2 – Install Apache, MariaDB and PHP

    Elgg runs on Apache web server, is written in PHP, and uses MySQL/MariaDB as a database backend, so you will need to install the Apache, MariaDB, PHP and other required PHP extensions to your server. You can install all of them with the following command:

    apt-get install apache2 mariadb-server php libapache2-mod-php php-common php-sqlite3 php-curl 
php-intl php-mbstring php-xmlrpc php-mysql php-gd php-xml php-cli php-zip unzip wget -y

    After installing all the packages, edit the php.ini file and change some recommended settings.

    nano /etc/php/7.4/apache2/php.ini

    Change the following values:

    max_execution_time = 300
memory_limit = 512M
upload_max_filesize = 100M
date.timezone = Asia/Kolkata

    Save and close the file, then restart the Apache service to apply the configuration changes.

    systemctl restart apache2

    Step 3 – Create a Database for Elgg

    Next, you will need to create a database and user for Elgg. First, log in to MySQL shell with the following command:

    mysql

    Once logged in, create a database and user with the following command:

    CREATE DATABASE elgg;
CREATE USER 'elgg'@'localhost' IDENTIFIED BY 'secure-password';

    Next, grant all the privileges to the elgg database with the following command:

    GRANT ALL ON elgg.* TO 'elgg'@'localhost' IDENTIFIED BY 'secure-password' WITH GRANT 
OPTION;

    Next, flush the privileges and exit from the MariaDB shell with the following command:

    FLUSH PRIVILEGES;
EXIT;

    At this point, the MariaDB database is created for Elgg.

    Step 4 – Install Elgg

    First, download the latest version of Elgg from its official website using the following command:

    wget https://elgg.org/download/elgg-3.3.13.zip

    Once the download is completed, unzip the downloaded file with the following command:

    unzip elgg-3.3.13.zip

    Next, move the extracted directory to the Apache root directory:

    mv elgg-3.3.13 /var/www/html/elgg

    Next, create a data directory and set proper ownership and permissions to the Elgg directory:

    mkdir /var/www/html/data
chown -R www-data:www-data /var/www/html/elgg
chown -R www-data:www-data /var/www/html/data
chmod -R 755 /var/www/html/elgg

    Once you are finished, you can proceed to the next step.

    Step 5 – Configure Apache for Elgg

    Next, you will need to configure Apache to serve Elgg. You can configure it by creating a new Apache virtual host configuration file:

    nano /etc/apache2/sites-available/elgg.conf

    Add the following lines:

    <VirtualHost *:80>
ServerAdmin admin@example.com
DocumentRoot /var/www/html/elgg/
ServerName elgg.example.com
Options FollowSymLinks
AllowOverride All
ErrorLog /var/log/apache2/elgg-error_log
CustomLog /var/log/apache2/elgg-access_log common
</VirtualHost>

    Save and close the file, then enable the virtual host and Apache rewrite module with the following command:

    a2ensite elgg.conf
a2enmod rewrite

    Finally, restart the Apache service to apply the changes:

    systemctl restart apache2

    Step 6 – Access Elgg Web Interface

    Now, open your web browser and access the Elgg web interface using the URL http://elgg.example.com. You should see the Elgg welcome screen:

    ]]>     Neel     https://bioinformaticsonline.com/blog/view/710/how-to-install-perl-modules-manually-using-cpan-command-and-other-quick-ways Fri, 12 Jul 2013 07:20:24 -0500 https://bioinformaticsonline.com/blog/view/710/how-to-install-perl-modules-manually-using-cpan-command-and-other-quick-ways <![CDATA[How to install Perl modules manually, using CPAN command, and other quick ways]]> As a bioinformatics programmer, and crunchy data analyser you need to install several perl modules and dependencies. Installing Perl modules manually by resolving all the dependencies is  tedious and annoying process. Some of the packages like GD is the real pain.

    However, Installing Perl modules using CPAN is a better solution, as it resolves all the dependencies automatically. In this article, let us review how to install Perl modules on Linux ( which is prefereced amonst bioinformatician) using both manual and CPAN method.

    When a Perl module is not installed, application will display the following error message. In this example, XML::Parser Perl module is missing.

    Can't locate XML/parser.pm in @INC (@INC contains:
    /usr/lib/perl5/5.10.0/i386-linux-thread-multi
    /usr/lib/perl5/5.10.0
    /usr/local/lib/perl5/site_perl/5.10.0/i386-linux-thread-multi
    /usr/local/lib/perl5/site_perl/5.10.0
    /usr/lib/perl5/vendor_perl/5.10.0/i386-linux-thread-multi
    /usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl
    /usr/lib/perl5/site_perl/5.10.0 .)

    Manual Method of Perl Module Installation

    • Install Perl Modules Manually

    This manual method is very useful when your computer or server is not connected to the Internet.

    Download Perl module:
    Go to CPAN Search website and search for the module that you wish to download. In this example, let us search, download and install XML::Parser Perl module. I have downloaded the XML-Parser-2.36.tar.gz to /home/download

    # cd /home/download
    # gzip -d XML-Parser-2.36.tar.gz
    # tar xvf XML-Parser-2.36.tar
    # cd XML-Parser-2.36

    Build the perl module:
    Build by running Makefile.PL, remember the case sensitivity, make and make test.

    # perl Makefile.PL
    Checking if your kit is complete...
    Looks good
    Writing Makefile for XML::Parser::Expat
    Writing Makefile for XML::Parser
    # make
    # make test

    Install the perl module:
    Now your package is ready to install.

    # make install

    As a newbie it looks pretty simple, and one go. But, luckily this is a very simple one module with no dependencies. Typically, Perl modules will be dependent on several other modules. Just imagine chasing all these dependencies one-by-one, thinking ... oh ye I got it. That will be very painful and annoying task. I recommend the CPAN method of installation as shown below.

    Install Perl Modules using CPAN automatically

    Logically, you should must have the CPAN perl module installed in your server or computer before you can install any other Perl modules using CPAN. I know you  are laughing, "to install a perl module you need another perl module"  ;)

    Lets verify whether CPAN is already installed:

    To install Perl modules using CPAN, make sure the cpan command is working. Following are the error message when CPAN module is not installed.

    # cpan
    -bash: cpan: command not found

    # perl -MCPAN -e shell
    Can't locate CPAN.pm in @INC (@INC contains:
    /usr/lib/perl5/5.10.0/i386-linux-thread-multi
    /usr/lib/perl5/5.10.0
    /usr/local/lib/perl5/site_perl/5.10.0/i386-linux-thread-multi
    /usr/local/lib/perl5/site_perl/5.10.0
    /usr/lib/perl5/vendor_perl/5.10.0/i386-linux-thread-multi
    /usr/lib/perl5/vendor_perl/5.10.0
    /usr/lib/perl5/vendor_perl /usr/lib/perl5/site_perl/5.10.0 .).
    BEGIN failed--compilation aborted.

    Install the CPAN module using yum:
    If CPAN in not installed in your system, you can use "yum" for the rescue. Dont worry biological data cruncher, this is true we are now dependent all these tiny magicians :).

    # yum install perl-CPAN

    Output of yum install perl-CPAN command:

    Loaded plugins: refresh-packagekit
    updates-newkey                       | 2.3 kB     00:00
    primary.sqlite.bz2                   | 2.4 MB     00:00
    Setting up Install Process
    Parsing package install arguments

    Resolving Dependencies
    Transaction Summary
    =============================================================================
    Install      5 Package(s)
    Update       0 Package(s)
    Remove       0 Package(s)

    Total download size: 1.0 M
    Is this ok [y/N]: y
    Downloading Packages:
    (1/5): perl-ExtUtils-ParseXS-2.18-31.fc9.i386.rpm     |  30 kB     00:00
    (2/5): perl-Test-Harness-2.64-31.fc9.i386.rpm         |  70 kB     00:00
    (3/5): perl-CPAN-1.9205-31.fc9.i386.rpm               | 217 kB     00:00
    (4/5): perl-ExtUtils-MakeMaker-6.36-31.fc9.i386.rpm   | 284 kB     00:00
    (5/5): perl-devel-5.10.0-31.fc9.i386.rpm              | 408 kB     00:00

    Installing     : perl-ExtUtils-ParseXS                             [1/5]
    Installing     : perl-devel                                        [2/5]
    Installing     : perl-Test-Harness                                 [3/5]
    Installing     : perl-ExtUtils-MakeMaker                           [4/5]
    Installing     : perl-CPAN                                         [5/5]


    Installed: perl-CPAN.i386 0:1.9205-31.fc9
    Dependency Installed:
      perl-ExtUtils-MakeMaker.i386 0:6.36-31.fc9
      perl-ExtUtils-ParseXS.i386 1:2.18-31.fc9
      perl-Test-Harness.i386 0:2.64-31.fc9
      perl-devel.i386 4:5.10.0-31.fc9
    Complete!

    Configure cpan the first time:
    Once the CPAN is installed, you need to configure it by executing cpan, you should set some configuration parameters as shown below. I have shown only the important configuration parameters below. Accept all the default values by pressing enter.

    Note: Make sure to execute “o conf commit” in the cpan prompt after the configuration to save the settings.

    # cpan

    Sorry, we have to rerun the configuration dialog for CPAN.pm due
    to some missing parameters...

    CPAN build and cache directory? [/root/.cpan]
    Download target directory? [/root/.cpan/sources]
    Directory where the build process takes place? [/root/.cpan/build]

    Always commit changes to config variables to disk? [no]
    Cache size for build directory (in MB)? [100]
    Let the index expire after how many days? [1]

    Perform cache scanning (atstart or never)? [atstart]
    Cache metadata (yes/no)? [yes]
    Policy on building prerequisites (follow, ask or ignore)? [ask]

    Parameters for the 'perl Makefile.PL' command? []
    Parameters for the 'perl Build.PL' command? []

    Your ftp_proxy? []
    Your http_proxy? []
    Your no_proxy? []
    Is it OK to try to connect to the Internet? [yes]

    First, pick a nearby continent and country by typing in the number(s)
    (1) Africa
    (2) Asia
    (3) Central America
    (4) Europe
    (5) North America
    (6) Oceania
    (7) South America
    Select your continent (or several nearby continents) [] 5

    (1) Bahamas
    (2) Canada
    (3) Mexico
    (4) United States
    Select your country (or several nearby countries) [] 4

    (2) ftp://carroll.cac.psu.edu/pub/CPAN/
    (3) ftp://cpan-du.viaverio.com/pub/CPAN/
    (4) ftp://cpan-sj.viaverio.com/pub/CPAN/
    (5) ftp://cpan.calvin.edu/pub/CPAN
    (6) ftp://cpan.cs.utah.edu/pub/CPAN/
    e.g. '1 4 5' or '7 1-4 8' [] 2-16

    cpan[1]> o conf commit
    commit: wrote '/usr/lib/perl5/5.10.0/CPAN/Config.pm'

    cpan[2]> quit
    No history written (no histfile specified).
    Lockfile removed.

    • Install Perl Modules using CPAN

    Hey smile please, now you are ready with CPAN and can download modules in one line command.

    You can use one of the following method to install a Perl module using cpan:

    # perl -MCPAN -e 'install Bundle::BioPerl'

    (or)

    # cpan
    cpan shell -- CPAN exploration and modules installation (v1.9205)
    ReadLine support available (maybe install Bundle::CPAN or Bundle::CPANxxl?)

    cpan[1]> install "Bundle::BioPerl"

    In the example above, CPAN will check for Bundle::BioPerl dependencies and automatically resolves and installs Bundle::BioPerl with all the dependent Perl modules.

    • Quick Ways

    Oh, look at your face.. smily hmm :). This is what your are looking for, a quick and best way to install Perl modules, Bioperl. Following are the the steps to download BioPerl in your server/computer.

    # sudo apt-cache search perl BioPerl

    Output will be like as follows:

    bioperl - Perl tools for computational molecular biology
    bioperl-run - BioPerl wrappers: scripts
    libbio-perl-perl - BioPerl core perl modules
    libbio-perl-run-perl - BioPerl wrappers: modules
    libbio-samtools-perl - Perl interface to SamTools library for DNA sequencing
    libbiojava-java - Java API to biological data and applications (default version)
    libbiojava3-java - Java API to biological data and applications (default version)
    python-biopython-sql - Biopython support for the BioSQL database schema
    libbtlib-perl - library for basic sequence manipulation

    # sudo apt-get install bioperl

    If it is installed then flash the following message:

    Reading package lists... Done
    Building dependency tree      
    Reading state information... Done
    bioperl is already the newest version.
    0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.

    In it is found not installed in your server or system them install all with dependencies.

    You can use the same approach to install all the modules, and packages if required.

    Thanks for reading. Best of luck for your research.

    ]]>     Jit