<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/33839? https://bioinformaticsonline.com/pages/view/33837/awesome-perl-frameworks-libraries-and-software-part-1 Fri, 07 Jul 2017 04:06:59 -0500 https://bioinformaticsonline.com/pages/view/33837/awesome-perl-frameworks-libraries-and-software-part-1 <![CDATA[Awesome perl frameworks, libraries and software - PART 1]]> A curated list of awesome Perl frameworks, libraries and software.

]]> Neel https://bioinformaticsonline.com/pages/view/33841/awesome-perl-frameworks-libraries-and-software-part-4 Fri, 07 Jul 2017 04:11:54 -0500 https://bioinformaticsonline.com/pages/view/33841/awesome-perl-frameworks-libraries-and-software-part-4 <![CDATA[Awesome perl frameworks, libraries and software - PART 4]]>
  • tjstein/php5-fpm-munin-plugins - A set of Munin plugins for PHP5-FPM
  • perusio/nginx-munin - A set of plugins for monitoring nginx with Munin
  • openresty/lua-resty-memcached - Lua memcached client driver for the ngx_lua based on the cosocket API
  • jayjanssen/myq_gadgets - Various iostat style scripts for MySQL
  • apt-mirror/apt-mirror - Official apt-mirror source.
  • kentaro/cinnamon - a simple deploy tool
  • mdom/dategrep - print lines matching a date range
  • kazuho/jailing - super-easy chroot jail builder/runner for Linux
  • teleshoes/tpacpi-bat - ThinkPad ACPI Battery Util
  • hechtus/squeezebox-googlemusic - Squeezebox (Logitech Media Server) Plugin for Google Play Music
  • hexchat/hexchat-addons - Plugins and scripts made for HexChat
  • berekuk/Ubic - Polymorphic service manager.
  • deryckoe/Wordpress-Syntax-Mode-for-Coda-2 - Wordpress Syntax Mode working on Coda 2.0.2
  • squentin/gmusicbrowser - jukebox for large collections of music
  • autodl-community/autodl-irssi - A community-driven fork of autodl-irssi
  • yoshiki/markdown2impress - markdown2impress is script to convert markdown into presentation using impress.js.
  • pagespeed/cpanel - mod_pagespeed module for CPanel WHM
  • liyanage/xcode-text-macros - Some XCode text macros plus a macro overview HTML page generator
  • erlang/eep - Erlang Enhancement ProposalS
  • Koha-Community/Koha - Koha is a free software integrated library system (ILS). Koha is distributed under the GNU GPL version 3 or later. Note: this is a synced mirror of the official Koha repo.
  • vti/bootylicious - LIghtweight blog engine on Mojo steroids!
  • tokuhirom/Furl - pretty fast http client library for perl5
  • miyagawa/Carmel - CPAN Artifact Repository Manager
  • combinatorylogic/clike - A simple C-like language compiler with an extensible syntax and typed macros support
  • cloudflare/CloudFlare-Tools - Tools which enable you to get the full benefit of using the CloudFlare service.
  • untoldwind/alfred2-layout - Alfred 2 Layout workflow
  • nothingmuch/kiokudb - KiokuDB Core
  • katzgrau/chip - A log file multiplexer and monitor. Tail multiple remote or local log files, set actions, and more. A friend to every developer and system admin. Alpha.
  • SethRobertson/git-what-branch - Discover what branch a commit is on, or how it got to a named branch
  • shabble/irssi-docs - In-depth documentation of the Irssi IRC Client
  • kappa/yadisk-sync - Linux syncronizer for Yandex.Disk
  • dotse/dnscheck - DNSCheck code, DNS delegation quality checker.
  • darold/pgcluu - PostgreSQL Cluster performances monitoring and auditing tool
  • cfengine/design-center - CFEngine community-contributed content
  • bestpractical/sd - A distributed issue tracker; upstream is now http://gitorious.org/prophet
  • masak/proto - A a hyper-lightweight dependency tracking and project installation system
  • liblime/LibLime-Koha - LibLime Koha is the most mature of the open source ILS applications. Based on the ground-breaking 3.0 platform (derived from the original Koha offering of 1999), LibLime Koha is a completely web-based open source ILS, with library staff, systems librarians, and library users all accessing LibLime Koha through a web browser. Relying on the MySQL relational database, all LibLime Koha data is readily accessible.
  • ingydotnet/... - Dot Dot Dot
  • gusmaskowitz/apachebuddy.pl - Not written by me, maintained by me : Apachebuddy.pl
  • zaf/asterisk-googletts - Asterisk AGI script that uses Google's translate text to speech service.
  • openresty/lua-resty-core - New FFI-based API for lua-nginx-module
  • openSUSE/kiwi - KIWI OS Image builder
  • FastVPSEestiOu/Antidoto - Linux antimalware and antirootkit tool
  • sorin-ionescu/dotfiles - My command line life.
  • oetiker/smokeping-3.x - reengineered SmokePing, using Extopus as its frontend
  • nekokak/p5-Teng - simple DBI wrapper/ORMapper
  • faiproject/fai - non-interactive system to install, customize and manage Linux systems
  • abh/ntppool - NTP Pool Project
  • willixix/naglio-plugins - Monitoring Plugins by William Leibzon
  • stealth/troubleshooter - setroubleshootd xSports
  • openresty/lua-resty-string - String utilities and common hash functions for ngx_lua and LuaJIT
  • mdxp/cookbooks - My custom Cookbooks for Chef
  • ingydotnet/vroom-pm - Vim Based Slideshow Presentations
  • iamcal/Flickr-StatsD - Mirror of code.flickr.com: Flickr-StatsD
  • ernstsson/Arqua - Architectural quality analysis tool for GCC project
  • qiaoxueshi/FLEXLoader - A jailbreak iOS device tweak which can load FLEX dynamiclly
  • punchdrunker/iOSEmoji - information about unicode6 emoji used in iOS5
  • openresty/replace-filter-nginx-module - Streaming regular expression replacement in response bodies
  • djabberd/DJabberd - The main DJabberd source
  • darold/pgFormatter - A PostgreSQL SQL syntax beautifier that can work as a console program or as a CGI. Download from https://sourceforge.net/p/pgformatter/ and demo site at http://sqlformat.darold.net/
  • aspiers/mysqldiff - tool and CPAN suite backend for comparing MySQL database schemas
  • michaeldexter/vmrc - Virtual Machine rc script
  • keydet89/RegRipper2.8 - RegRipper version 2.8
  • kazuho/kaztools - shellscripts and utilities for myself
  • gknops/adHocGenerate - Wireless ad hoc distribution of iOS applications
  • book/Act - A Conference Toolkit (Git conversion of the Subversion repository)
  • turingou/docor - a smart and tiny README maker using default manifest package.json
  • rjbs/Soviet-Minecraft - a gross hack for chatty control of Minecraft
  • osklil/hls-fetch - Download and decrypt videos served by the HTTP Live Streaming (HLS) protocol.
  • alestic/ec2-expire-snapshots - Delete expired EBS snapshots in Amazon EC2. Install on Ubuntu with: sudo add-apt-repository -y ppa:alestic && sudo apt-get update && sudo apt-get install -y ec2-expire-snapshots
  • rpetrich/objc_api_visibility - Private API checker for iOS. Requires class-dump-z to be in the PATH
  • mojombo/gollum-demo - Gollum test repo
  • mikecardwell/gpgit - Encrypt Email using GnuPG and a pipe
  • lxctl/lxctl - vzctl like utilities for lxc
  • justone/dfm - dotfiles manager
  • miyagawa/cpanfile - Yet another way to declare CPAN dependencies
  • imatix/gitdown - Turn github into your publishing platform
  • grayhemp/pgtoolkit - Tools for PostgreSQL maintenance
  • domm/App-TimeTracker - distributed timetracking from the commandline
  • xaicron/mysqlenv - mysql binary manager
  • tagomoris/fluent-agent-lite - Lightweight log delivery agent works w/ fluentd
  • openresty/lua-resty-upstream-healthcheck - Health Checker for Nginx Upstream Servers in Pure Lua
  • niXman/mingw-builds - Scripts for building the dual-target(32 & 64 bit) MinGW-W64 compilers for 32 and 64 bit Windows
  • lvc/abi-compliance-checker - A tool for checking backward API/ABI compatibility of a C/C++ library
  • chilts/cil - DVCS backed issue tracking system
  • TooTallNate/node-cgi - An http/stack/connect layer to invoke and serve CGI executables.
  • CityGenerator/CityGenerator - CityGenerator is a tool for generating a setting for Fantasy Roleplaying games.
  • yoshinorim/mha4mysql-node - Development tree of Master High Availability Manager and tools for MySQL (MHA), Node (MySQL Server) part
  • Netflix-Skunkworks/jenkins-cli - Simple Jenkins Command Line Interface
  • vrtadmin/clamav-faq - ClamAV FAQ
  • ssinyagin/gerty - A universal framework for device management automation. Eventually a replacement for RANCID... and much more
  • quran/quran.com-images - images using fonts from King Fahed Complex / qurancomplex.com
  • matschaffer/profile - My Bash profile
  • jigish/dotfiles - My configs
  • darold/ora2pg - Ora2Pg is a free tool used to migrate an Oracle database to a PostgreSQL compatible schema. It connects your Oracle database, scan it automaticaly and extracts its structure or data, it then generates SQL scripts that you can load into PostgreSQL.
  • castaway/dbix-class-book - DBIx::Class book
  • brucemiller/LaTeXML - LaTeXML is a TeX and LaTeX to XML translator.
  • OpenDDRdotORG/OpenDDR-Resources - OpenDDR resources
  • revmischa/rtsp-server - Lightweight RTSP/RTP streaming media server
  • oetiker/znapzend - zfs backup with remote capabilities and mbuffer integration.
  • cardinal/cardinal - Cardinal - Ruby compiler for Parrot
  • LibreCat/Catmandu - https://metacpan.org/pod/Catmandu
  • rdvn/zabbix-templates - Various Zabbix templates
  • mischat/shareNice - An ethical way of adding social sharing features to your website, without compromising your users' privacy by dropping tracking cookies on them.
  • kayac/isucon3 - ISUCON3
  • coryarcangel/Pizza-Party-0.1.b - Order pizza over the commandline (circa 2004)
  • msparks/irssiscripts - Scripts for the Irssi IRC client
  • mogui/MDWamp - MDWamp is a client side objective-C implementation of the WebSocket subprotocol WAMP.
  • michaeljamesfitzgerald/Introducing-Regular-Expressions - Example code and target text files for the O'Reilly book Introducing Regular Expressions
  • jeffreykegler/Marpa--R2 - Parse any language you can describe in BNF -- Release 2
  • glensc/nagios-plugin-check_raid - Nagios/Icinga plugin to check current server's RAID status
  • futuretap/iTunesFeaturedCheck - Scrapes the App Store and finds out whether an app is featured on either the App Store homepage or in a specific category
  • yepher/RaZBerry - Notes About ZWave and RazBerry
  • tokuhirom/Minilla - Authorizing tool for CPAN modules
  • rgeissert/http-redirector - Debian mirrors HTTP redirector
  • oetiker/rrdtool-2.x - RRDtool 2.x - The Time Series Database
  • mindreframer/nginx-lua-stuff - some libs for NginX-Lua integration
  • crowbar/barclamp-nagios - [UNMAINTAINED] Crowbar Nagios: System Monitoring
  • andk/cpanpm - CPAN.pm
  • moritz/ilbot - IRC logging bot and web frontend
  • meso-cacase/difff - Webベースのテキスト比較ツール difff《ﾃﾞｭﾌﾌ》
  • elliotchance/mbzdb - Port of the MusicBrainz database to run on other RDBMSs with replication (previously named MB_MySQL.)
  • trapd00r/vidir - edit directory in $EDITOR (better than vim . with netrw)
  • evalEmpire/gitpan - Git repositories for all of CPAN
  • pagekite/Colormake - A simple wrapper around make to colorize the output.
  • manuelkasper/AS-Stats - A simple tool to generate per-AS traffic graphs from NetFlow/sFlow records
  • kazeburo/Monoceros - PSGI/Plack server with event driven connection manager, preforking workers
  • justintime/nagios-plugins - Collection of some handy Nagios plugins
  • justingit/dada-mail - Dada Mail is a simple, web-based mailing list manager. It totally rules.
  • grantm/bcvi - Back-channel vi
  • JeremyJones/Apachetop - apachetop is a console-based tool for monitoring the threads and overall performance of a set of Apache web servers.
  • garu/tweetylicious - a Twitter-like microblogging app in just one file
  • doujiang24/lua-resty-kafka - Lua kafka client driver for the ngx_lua based on the cosocket API
  • HikariKnight/rsu-client - A git repository for the RuneScape Linux/Unix Client Project
  • wimpunk/ddclient - Fork of the original ddclient code
  • tokuhirom/tora - Tora! Tora! Tora!
  • stepb/urxvt-tabbedex - Tabbed plugin for rxvt-unicode with many enhancements
  • rafl/moosex-declare - Declarative syntax for Moose
  • pobox/Moonpig - the moonpig billing system
  • fink/fink - The fink package manager
  • theiostream/theos-ref - Theos Docs! (because there never was a chapter 2)
  • robinbowes/flac2mp3 - flac2mp3 is a tool to convert audio files from flac to mp3 format including the copying of tags.
  • rayman813/coda2-mode-wordpress - Wordpress Syntax Mode/Highlight/Autocomplete for Coda 2
  • hackman/linux-sysadmin-course - Linux System Administration 101
  • deepakdaswani/whatsapp_discover - "Whatsapp Discover" is a tool for getting phone numbers of devices using Whatsapp by real time sniffing from an interface (disabled in this first version) or from a list of pcap files, which can be processed in batch
  • calio/form-input-nginx-module - This is a nginx module that reads HTTP POST and PUT request body encoded in "application/x-www-form-urlencoded", and parse the arguments in request body into nginx variables.
  • bloonix/awesant - Awesant is a log shipper for logstash.
  • AndriiGrytsenko/openssh-ldap-publickey - Wrapper for OpenSSH to store public keys inside the OpenLDAP entry.
  • nikyoudale/symbolicatecrash-mac - A version of the symbolicatecrash script that works for Mac app crash logs
  • mhwest13/Memcached-Munin-Plugin - Memcached Munin Plugins
  • knmnyn/ParsCit - An open-source CRF Reference String Parsing Package
  • c9s/App-gh - GitHub Command-line Utility.
  • bradfitz/shipit - Software Release Tool
  • sukria/WebKeePass - Web interface over a KeePass database
  • naturalist/kelp - A web framework light, yet rich in nutrients.
  • kirei/catt - Certification Authority Trust Tracker
  • kazuho/Starlet - a Plack Server, formerly known as Plack::Server::Standalone::Prefork::Server::Starter
  • dolmen/github-keygen - Easy creation of secure SSH configuration for your Github account(s)
  • bigplum/nginx-tcp-lua-module - A TCP server with lua supporting based on nginx
  • baohaojun/ajoke - Abducting Java Onto Emacs, K is silent.
  • apache/spamassassin - Read-only mirror of Apache SpamAssassin. Submit patches to https://bz.apache.org/SpamAssassin/. Do not send pull requests
  • tsee/Games-Lacuna-Client - A client for the Lacuna Expanse
  • sitaramc/gitpod - local caching server for git when the actual server is on the other side of a (possibly slow) WAN link
  • mjdominus/git-util - Miscellaneous git scripts and utilities
  • kevina/wordlist - SCOWL (and friends).
  • franckcuny/jitterbug - Cross Language Continuous Integration for Git
  • fastmail/towncrier - A status dashboard
  • collectiveintel/cif-v1 - the fastest way to consume threat intelligence.
  • anestisb/WeBaCoo - Web Backdoor Cookie Script-Kit
  • Tarrasch/zsh-autoenv - Autoenv for zsh
  • xme/hoover - Wireless Probe Requests Sniffer
  • spencertipping/caterwaul - A Javascript-to-Javascript compiler
  • openresty/lua-redis-parser - Lua module for parsing raw redis responses
  • mpeters/smolder - Web-based Continuous Integration Smoke Server
  • madscientist/msjnc - MadScientist Juniper Network Connect Session Manager
  • kfdm/irssi-growl - Growl notification script for irssi
  • jimsalterjrs/sanoid - Policy-driven snapshot management and replication tools. Currently using ZFS for underlying next-gen storage, with explicit plans to support btrfs when btrfs becomes more reliable. Primarily intended for Linux, but BSD use is supported and reasonably frequently tested.
  • duritong/puppet-nagios - a nagios module for puppet
  • szabgab/screencasts - The translated captions of my screencasts
  • openresty/resty-cli - Fancy command-line utilities for OpenResty
  • kre/Kinetic-Rules-Engine - Source code for KRE
  • helloandre/cr48 - my programs that i've put on cr48
  • csirtgadgets/massive-octo-spice - the fastest way to consume threat intelligence
  • agentzh/sshbatch - SSH::Batch for cluster operations
  • SPORE/api-description - SPORE description for API
  • xilinus/prototypeui - Prototype UI
  • tagomoris/isucon - isucon web applications and tools
  • perl6/doc - Perl 6 documentation (tools and docs)
  • hirose31/redis-traffic-stats - Redis query analyzer for counting, traffic stats by command
  • gjreda/pydata2014nyc - Materials for my pandas tutorial at PyData 2014, NYC
  • genaev/vmd - vkontakte music downloader
  • dalibo/sqlserver2pgsql - Migration tool to convert a Microsoft SQL Server Database into a PostgreSQL database, as automatically as possible
  • symkat/Stalker - Records and correlates nick!user@host information
  • lvc/japi-compliance-checker - A tool for checking backward API/ABI compatibility of a Java library
  • justinabrahms/jlilly-bashy-dotfiles - This is a collection of my dotfiles not related to either vim or emacs. Mostly just bashy stuff.
  • interchange/interchange - Interchange
  • ingydotnet/jemplate - Industrial strength JavaScript template framework
  • depesz/explain.depesz.com - Webpage for showing easier to read version of PostgreSQL explains
  • Webconverger/webc - Webconverger's curated chroot from which updates originate
  • SSLMate/sslmate - The SSLMate Client - Buy and Manage SSL Certs from the Command Line
  • stayradiated/dotfiles - Just my configs for CRUX and OS X
  • openresty/lua-resty-lock - Simple nonblocking lock API for ngx_lua based on shared memory dictionaries
  • nickspacek/Net-Google-Tasks - Interface to Google Tasks
  • jdavis/dotfiles - Config files for various things
  • evadne/LESS.mode - LESS syntax mode for SubEthaEdit and Coda
  • dotse/zonemaster - The Zonemaster Project
  • darold/squidanalyzer - Squid Analyzer parses Squid proxy access log and reports general statistics about hits, bytes, users, networks, top URLs, and top second level domains. Statistic reports are oriented toward user and bandwidth control.
  • vti/showmetheshell - HTML5 WebSocket Shell
  • oalders/http-browserdetect - Determine the Web browser, version, and platform from an HTTP user agent string
  • marksteele/collectd-plugins - Collectd Plugins
  • kristofg/rifec - Receive Images From Eye-Fi Cards
  • kirei/fpdns - Net::DNS::Fingerprint
  • gjospin/PhyloSift - Phylogenetic and taxonomic analysis for genomes and metagenomes
  • chrispix/symbolicatecrash-fix - A patch of Apple's symbolicatecrash script, broken in XCode4
  • billkarwin/bk-tools - Scripts I wrote to help using MySQL and Percona products.
  • adelton/docker-freeipa - FreeIPA server and client in Docker containers; see hub.docker.com for the images:
  • OWASP/O-Saft - O-Saft - OWASP SSL audit for testers
  • yllan/moedict-mac - 轉換教育部國語辭典為 Mac 內建字典
  • tokuhirom/cpan-outdated - detect outdated CPAN modules
  • openwebwork/webwork2 - Course management front end for WeBWorK
  • nicolaspanel/libsvm.net - An easy way to use Support Vector Machines in your .NET projects (c# code)
  • jodrell/unbound-block-hosts - a script to convert Dan Pollock's ad blocking hosts file into Unbound local-data.
  • davepacheco/jsstyle - cstyle-based JavaScript style checker
  • cloudflare/lua-resty-cookie - Lua library for HTTP cookie manipulations for OpenResty/ngx_lua
  • c9s/github-taiwan - Taiwan Developers on Github
  • PadreIDE/Padre - Offical repository of the core Padre code
  • rovo89/XposedTools - These tools can be used to compile and package the Xposed framework.
  • openresty/nginx-devel-utils - Utilities for nginx module development
  • openSUSE/obs-build - OBS build script, can be used with OBS or stand alone
  • nichtich/ditaa-markdown - process ditaa diagrams embedded in pandoc markdown
  • bestpractical/prophet - A disconnected, replicated p2p database -- upstream is now http://gitorious.org/prophet
  • aparks517/convert-websters - Convert Webster's Unabridged Dictionary from Project Gutenberg to OSX dictionary
  • ap/titlecase - An attempt to refactor John Gruber’s Title Case program
  • yko/mojo.vim - Vim syntax for mojo epl templates in Mojo projects
  • tseemann/prokka - Rapid prokaryotic genome annotation
  • peterkeen/calorific - Command-line nutrient tracking tool
  • openresty/lua-resty-dns - DNS resolver for the nginx lua module
  • maxmind/MaxMind-DB - Spec and test data for the MaxMind DB file format
  • kazeburo/Kurado - monitor metrics
  • bigpresh/Dancer-Plugin-Database - Dancer::Plugin::Database - easy database support for Dancer applications
  • BaldMansMojo/check_vmware_esx - chech_vmware_esx Fork of check_vmware_api.pl
  • vanstyn/RapidApp - Turnkey ajaxy webapps
  • taylorchu/baker - The bash static site generator with real template engine
  • sujaikumar/assemblage - Tools for working with second gen assemblies, fasta sequences, etc
  • obfuscurity/nagios-scripts - Custom scripts written for Nagios
  • miyagawa/AnyEvent-Twitter-Stream - AnyEvent based Twitter stream consumer
  • miyagawa/AnyEvent-Redis - Asynchronous Redis client
  • drdrang/tp-planner - A set of scripts for printing TaskPaper documents compactly for inserting into a "Junior" sized planner.
  • ccurtsinger/stabilizer - Stabilizer: Rigorous Performance Evaluation
  • zrlram/afterglow - graph visualization tool
  • utcompling/OpenNLP-Models - A project for code to create models from existing corpora and distribute models.
  • theory/dbix-connector - Fast, safe DBI connection management
  • redondos/mutt - mutt configuration
  • p5-app-adventcalendar/p5-app-adventcalendar - let's make advent calendar!
  • motemen/Teto - nicovideo stream player
  • lifeforms/irssi-smartfilter - Irssi JOIN/QUIT smart filter for busy channels
  • genehack/app-gitgot - A tool to make it easier to manage multiple code repositories using different VCSen
  • ytoolshed/multipkg - Automation for package builds
  • willemk/varnish-mobiletranslate - Tool to translate the latest mobile detect script into varnish
  • sashahilton00/spotify-connect-resources - A repository to hold any data/stuff related to reversing the Spotify Connect protocol. Mostly just data dumps at the moment, but if you have something to add to it, be it an implementation, information or just another data dump, make a PR and I will add it asap.
  • kumina/nagios-plugins-kumina - A collection of Nagios plugins that we package.
  • jbergantine/django-template.mode - Django Template Syntax mode for Panic Coda 2
  • jasta/android-dev-tools - Collection of developer tools for working with Android.
  • devel/PowerDNS-API - HTTP API for the PowerDNS Database
  • daniel-nichter/hackmysql.com - Deprecated tools from HackMySQL.com
  • agentzh/cheater - A tool and a language that help generating random complex database instance based on predefined rules
  • GMOD/GBrowse - the Generic Genome Browser
  • yaoweibin/nginx_limit_access_module - support to deny specific variable with HTTP POST interface
  • yanick/git-cpan-patch - System to write patches against CPAN modules via Git
  • synacorinc/dtk - DTK (data toolkit) is a suite of tools for parsing, analyzing, and graphing logs and other datasets.
  • schweikert/postgrey - Postfix Greylisting Policy-Daemon
  • noodba/myawr - awr of MySQL
  • marcusramberg/Mojolicious-Plugin-OAuth2 - OAuth support for Mojolicious
  • lukeredpath/LRMocky - A port of jMock 2.0 for Objective-C
  • linux-test-project/lcov - LCOV
  • gamelinux/echidna - Network Security Monitoring Framework
  • datameet/india-election-data - To map publicly available datasets related to General Assembly (Lok Sabha) elections in India.
  • cmatsuoka/figlet-fonts - A collection of fonts for FIGlet
  • ambs/Books - My repository to book projects... if I eventually have the guts to write more than one...
  • abw/Template-TT3 - A working prototype of the TT3 template language
  • yasuaki/git-doc-ja - Japanese translation of git/Documentation/
  • xdata-skylark/libskylark - Sketching-based Distributed Matrix Computations for Machine Learning
  • typester/nim - minimal command-line based contents generator
  • trapd00r/utils - Small useful utilities for everyday work
  • plack/Plack-Middleware-Session - A very minimalist session library for Plack
  • openxpki/openxpki - OpenXPKI Code
  • onishi/mysqldiff - mysqldiff - mysql scheme diff
  • mikegrb/App-otfile - Serve a single file, once, via HTTP over the local network.
  • mikebrittain/Wesley - Compress and optimize the JPEG, PNG, and GIF files used in your site’s HTML and CSS.
  • kthakore/frozen-bubble - Making frozen bubble cross platform
  • hluk/vimColorsToQtCreator - Convert vim color schemes so they can be used in Qt Creator.
  • cvicente/Netdot - Network Documentation Tool
  • ciembor/TerminalHero - Linux society's response to Guitar Hero. :)
  • carloslima/dhsnapshot - RSnapshot-like backups to DreamHost Backup Service
  • alecchen/doxygen-lua - Make Doxygen support Lua
  • AgileBits/onepassword-utilities - Utilities for 1Password
  • yrmt/dotfiles - a few of yrmt (beastie)'s dotfiles
  • willixix/WL-NagiosPlugins - Clone of naglio-plugins repository for those using old name
  • rafl/moosex-method-signatures - Method declarations with type constraints and no source filter
  • proftpd/proftpd - ProFTPD source code
  • plainblack/Wing - Next generation web services toolkit.
  • msimerson/NicTool - NicTool: a DNS management solution
  • j0hnnMcCock/fuckNSA - fuckNSA
  • dbsrgits/sql-translator - SQL::Translator (SQLFairy)
  • cryptax/dextools - Miscellaenous DEX (Dalvik Executable) tools
  • cosimo/varnish-accept-language - An experimental VCL extension to squash client Accept-Language headers
  • catap/nginx-catap - catap's nginx repository
  • ConSol/omd - OMD - Open Monitoring Distribution Labs Edition
  • 42Lines/cq5tools - Handy CLI tools for working with Adobe's CQ5 CMS product
  • thomasfrivold/SilentBob - SilentBob Firewall
  • starlilyth/Linux-PoolManager - Web based miner manager for CGMiner and clones (SGMiner, Keccak, etc) on Linux (PIMP/BAMT/SMOS, Debian, RedHat/Centos).
  • perl-pod/pod-simple - Framework for Parsing and Formatting POD
  • openresty/opsboy - A rule-based sysadmin tool that helps setting up complex environment for blank machines
  • nekokak/qudo - job queue system
  • moshen/Image-Term256Color - Display images in your 256 color terminal! (kinda) - superseded by https://github.com/moshen/gotermimg
  • kazuho/cppref - man-style access to cppreference.com documents
  • jquelin/dist-zilla-plugin-git - dist::zilla plugin to update your git repository after release
  • jonlives/nagios-jenkins-plugin - A nagios plugin for which lets you check jenkins jobs according to various criteria.
  • ikebe/Pickles - Tiny Web Application Framework.
  • gws/munin-plugin-couchdb - Munin plugins for graphing CouchDB statistics.
  • dyne/gitzone - git-based zone management tool for static and dynamic domains
  • duggan/shlint - A shell linting utility.
  • bloonix/logstash-delete-index - A script to delete Elasticsearch indices of Logstash
  • angavrilov/df-structures - Dwarf Fortress data structure descriptions
  • alibaba/tengine-website - The source code of Tengine's website (tengine.taobao.org)
  • SpiderLabs/thicknet - TCP session interception and injection framework
  • AssetTracker/rt-extension-assettracker - Asset Tracker is an extension for Request Tracker. It integrates asset tracking with your favorite ticketing system.
  • tokuhirom/Daiku - Yet another build tool on Perl5
  • schweikert/mailgraph - Mail plotting script
  • plainblack/Lacuna-Server-Open - The open source Lacuna Server repository.
  • netoptimizer/IPTV-Analyzer - Fast MPEG2 Transport Stream Analyzer, based on Netfilter kernel module
  • kvorg/mojo-handbook - Mojolicious Handbook: a temporary documentation resource for Mojolicious
  • kablamo/VimDebug - Integrate your debugger with Vim. Currently supports Perl, Python, and Ruby. This code is very much in beta.
  • genome/gms - The Genome Modeling System installer (BETA).
  • franckcuny/presque - a simple redis/tatsumaki message queue
  • dgl/cgiirc - CGI:IRC web based IRC client
  • dann/angelos - yet another web application framework
  • Bibzball/Git-Mediawiki - Gate between git and mediawiki
  • trustly/pci-blackbox - PCI-DSS compliant card system built on PostgreSQL and PL/pgSQL
  • tomill/Template-Semantic - Use pure XHTML/XML as a template
  • raboof/realtimeconfigquickscan - Linux configuration checker for systems to be used for real-time audio
  • postcasio/coda2-modes - Syntax modes for Coda 2.
  • norm/homedir - Public home directory files
  • nindwen/config - Arch Linux config-files
  • lvc/pkgdiff - A tool for visualizing changes in Linux software packages
  • jjn1056/DBIx-Class-Migration - Use DBIC::DeploymentHandler and DBIC::Fixtures together for a sane database versioning workflow
  • hpcugent/easybuild-easyconfigs - A collection of easyconfig files that describe which software to build using which build options with EasyBuild.
  • gfx/p5-Data-Validator - Type constraints based data validator for Perl5
  • evalEmpire/method-signatures - Method and function declarations with signatures, no source filter
  • yogan/cope - A colourful wrapper for terminal programs
  • trinityrnaseq/trinityrnaseq - Trinity RNA-Seq de novo transcriptome assembly
  • tokuhirom/p5-router-simple - simple http router
  • thiagorondon/OpenData-BR - OpenData-BR
  • skx/slaughter - The Slaughter system-administration & configuration tool.
  • mizzy/webiblo - Web to ebook project
  • miyagawa/Dist-Milla - Opinionated and Unobtrusive distribution builder
  • meermanr/TVSeriesRenamer - Script for renaming files in a digital video collection. Automatically fetches episode titles from the web.
  • markround/Cacti-iostat-templates - A set of templates to monitor iostat statistics on Unix systems
  • gvalkov/gitolite-sshkey-form - A web app for submitting ssh public keys directly to gitolite
  • ftilmann/latexdiff - Compares two latex files and marks up significant differences between them. Releases on www.ctan.org and mirrors
  • eprints/eprints - EPrints Core
  • eksopl/fuuka - Fuuka Imageboard Archiver
  • aelse/dot-ssh-config - Generate SSH client configurations with support for tunnels
  • Perl5-Alien/Alien-Base - Base classes for Alien:: modules
  • Ovid/example-test-training-material - Sample Code From Ovid's Introductory Testing Course
  • LuRsT/vspark - Like spark, but vertical
  • DjebbZ/Drupal-PHPStorm-Live-Templates - PHPSTorm Live Templates (aka code snippets) for Drupal 7
  • zamiron/ru4sphinx - Creating Russian voice model for cmu-sphinx
  • yappo/p5-Data-Model - Data::Model is Data/Object Mapper and Model Manager.
  • xaicron/p5-www-youtube-download - YouTube video download interface.
  • vti/protocol-websocket - Protocol::WebSocket
  • ukigumo/Ukigumo-Server - This is a ukigumo server application.
  • treasonx/environment - Personal Environment Files (vim, bash, etc)
  • sartak/app-nopaste - easy access to any pastebin
  • rolandwalker/emacs-travis - Travis CI recipe for Emacs libraries.
  • msimerson/sentry - Bruteforce attack blocker (ssh, FTP, SMTP, and more)
  • lookout/ngx_borderpatrol - Edge-authentication
  • ipfire/ipfire-2.x - IPFire 2.x development tree
  • dgl/cpangrep - Search code on CPAN with Regexps
  • bugzilla/bugzilla - Read-only mirror of Bugzilla source from git.mozilla.org/bugzilla/bugzilla.git. Tests at https://travis-ci.org/bugzilla/bugzilla –
  • avar/irssi-bitlbee-facebook-rename - A irssi script to rename chat.facebook.com nicks in bitlbee from e.g. "u1359078110" to "AEvarArnfjord"
  • artm/qtcreator-solarized-syntax - Solarized style for Qt Creator's syntax highlighter
  • SharkHunter/Channel - Channel Browse plugin for PMS
  • OpenElectronicsLab/eeg-mouse - The eeg-mouse is a project to attempt to control a mouse with eeg signals.
  • yusukebe/App-revealup - HTTP Server app for viewing Markdown formatted text as slides
  • yappo/JSTAPd - JSTAPd is Ajax application friendly Javascript Unit Test Server.
  • wayfind/polite - 一个为前端开发者量身打造的Vim配置和插件精选集
  • smallfish/lua-resty-beanstalkd - non-blocking beanstalkd client lib for ngx_lua
  • sixteencolors/sixteencolors - Sixteen Colors ANSI/ASCII Art Archive
  • perigrin/moosex-poe - The illicit love child of Moose and POE
  • ole-tange/tangetools - Ole Tanges personal tools
  • nothingmuch/class-mop - Mirror of Class-MOP.git
  • mjollnir/sf2debpkg - Symfony2 Debian Packaging
  • miyagawa/plack-dispatching-samples - Examples of Plack dispatcher using various CPAN modules
  • miyagawa/Webhook-Growler - Receives Web hooks over Reverse HTTP and notifies via Growl
  • miyagawa/HTTPx-Weblet - the Request/Response objects formerly known as the-old-Plack::Request
  • miyagawa/Corona - Coro based high-performance, asynchronous PSGI web server
  • mengwong/org-asana - Roundtrip synchronization and bidirectional replication between Emacs Org-mode and Asana.com.
  • keydet89/Tools - Tools from WFA 4/e, timeline tools, etc.
  • kan/moxy - Mobile web development proxy
  • goccy/p5-Compiler-Tools-CopyPasteDetector - detect Copy and Paste of Perl5 Codes
  • ctcherry/easy_php_dev - Collection of tools to quickly setup a dynamic PHP dev environment on OSX
  • chromatic/CPAN-Dark - Manage your own DarkPAN
  • chansen/p5-http-tiny - Tiny HTTP Client
  • bobtfish/catalystx-simplelogin - Simple login controller and template bundle for Catalyst
  • bestpractical/git-sync - A tool to synchronize multiple git repositories
  • Gilwyad/mailnesia.com - Anonymous Email in Seconds
  • Ensembl/ensembl-rest - Language agnostic RESTful data access to Ensembl data over HTTP
  • CalculatedContent/tsvm - experiments testing transductive svm for my blog posts
  • zby/WebNano - A really minimalistic web framework.
  • wtsi-hgi/docker-proxify - Allows building and running docker container images from behind a corporate proxy
  • tokuhirom/p5-psgiref - (DEPRECATED)just a prototype!
  • robelix/hard-dj - arduino based DJ MIDI cotroller using Harddisks as jog wheels
  • rjbs/dzil.org - the source for dzil.org
  • perldoc-jp/module-pod-jp - 日本語訳したモジュールをおく場所その2
  • motemen/Plack-Middleware-WebSocket - WebSocket handshake helper middleware
  • kivitendo/kivitendo-erp - Web-based ERP system for the German market
  • hinrik/hailo - A conversation bot using Markov chains
  • g0v/moedict-data-csld - 中華語文知識庫 資料檔
  • freenode/gms - Group Management System
  • doy/reply - read, eval, print, loop, yay!
  • digitalbazaar/json-ld - A Context-based JSON Serialization for Linked Data
  • dcantrell/ldap-for-dhcp - OpenLDAP support for dhcpd in ISC dhcp
  • cjfields/biome - An experimental Moose-based BioPerl implementation
  • brennen/git-feed - git-feed: a script to generate Atom feeds for git commit logs
  • bobthecow/PHP-HTML.mode - A fork of Coda 1.x's PHP-HTML syntax mode. Doesn't work with 2.x :(
  • ant0ine/MongoDB-RDF - Stores RDF-JSON documents in MongoDB
  • adrian-bl/bitflu - Bitflu BitTorrent Client
  • MG-RAST/MG-RAST - metagenomic analysis server site code
  • xaicron/pm-uninstall - Uninstall modules
  • windytan/bitocular - A tool to quickly examine the general structure of a file.
  • toreanderson/clatd - A 464XLAT CLAT implementation for Linux
  • sitaramc/map - Simpler than xargs. More power than xargs.
  • silvansky/macscripts - My Mac OS X scripts for different needs (may need some of my Mac OS X command line utils)
  • nekokak/p5-Kamui - Plack base framework
  • nabokov/mecab-dic-overdrive - create new mecab dic file, with score adjustment in accordance with existing terms.
  • miyagawa/Catalyst-Engine-PSGI - PSGI engine for Catalyst
  • melo/scripts - My personal script stash
  • liedekef/spacewalk_scripts - Several spacewalk scripts
  • kraih/mojolicio.us - Mojolicious Website
  • interconnectapp/discuss - A place to discuss interconnect
  • glidenote/dotfiles - my dotfiles
  • elubow/ec2-consistent-snapshot - EC2 Consistent Snapshot with Mongo Support
  • dalibo/pgshark - Messing with PostgreSQL network traffic to make some usefull things
  • clkao/AnyMQ - Simple message queue based on AnyEvent
  • chrisbra/vim_faq - The Vim FAQ from http://vimdoc.sourceforge.net/
  • PerlDancer/advent-calendar - Articles for the advent calendar
  • Kimtaro/jisho.org - The source for classic.jisho.org
  • shoorick/mojowka - Small wiki based on top of Mojolicious::Lite
  • ]]>     Neel     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/blog/view/42974/list-of-bioinformatics-packages-for-ngs-analysis Sat, 20 Mar 2021 00:28:51 -0500 https://bioinformaticsonline.com/blog/view/42974/list-of-bioinformatics-packages-for-ngs-analysis <![CDATA[List of bioinformatics packages for NGS analysis !]]> Package suites gather software packages and installation tools for specific languages or platforms. We have some for bioinformatics software.

    • Bioconductor – A plethora of tools for analysis and comprehension of high-throughput genomic data, including 1500+ software packages. [ paper-2004 | web ]
    • Biopython – Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the Open Bioinformatics Foundation. Contains the very useful Entrez package for API access to the NCBI databases. [ paper-2009 | web ]
    • Bioconda – A channel for the conda package manager specializing in bioinformatics software. Includes a repository with 3000+ ready-to-install (with conda install) bioinformatics packages. [ paper-2018 | web ]
    • BioJulia – Bioinformatics and computational biology infastructure for the Julia programming language. [ web ]
    • Rust-Bio – Rust implementations of algorithms and data structures useful for bioinformatics. [ paper-2016 ]
    • SeqAn – The modern C++ library for sequence analysis.
    ]]>     Rahul Nayak     https://bioinformaticsonline.com/bookmarks/view/37509/vcftools-perform-common-tasks-with-vcf-files-such-as-file-validation-file-merging-intersecting-complements Tue, 07 Aug 2018 10:01:46 -0500 https://bioinformaticsonline.com/bookmarks/view/37509/vcftools-perform-common-tasks-with-vcf-files-such-as-file-validation-file-merging-intersecting-complements <![CDATA[VCFtools: perform common tasks with VCF files such as file validation, file merging, intersecting, complements]]> VCFtools contains a Perl API (Vcf.pm) and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc. The Perl tools support all versions of the VCF specification (3.2, 3.3, 4.0, 4.1 and 4.2), nevertheless, the users are encouraged to use the latest versions VCFv4.1 or VCFv4.2. The VCFtools in general have been used mainly with diploid data, but the Perl tools aim to support polyploid data as well. Run any of the Perl scripts with the --help switch to obtain more help.

    Many of the Perl scripts require that the VCF files are compressed by bgzip and indexed by tabix (both tools are part of the tabix package, available for download here). The VCF files can be compressed and indexed using the following commands

    bgzip my_file.vcf
    tabix -p vcf my_file.vcf.gz

     

    http://vcftools.sourceforge.net/perl_module.html

    Address of the bookmark: http://vcftools.sourceforge.net/perl_module.html

    ]]>     Rahul Nayak     https://bioinformaticsonline.com/bookmarks/view/43364/ragtag-a-collection-of-software-tools-for-scaffolding-and-improving-modern-genome-assemblies Sat, 11 Sep 2021 00:28:14 -0500 https://bioinformaticsonline.com/bookmarks/view/43364/ragtag-a-collection-of-software-tools-for-scaffolding-and-improving-modern-genome-assemblies <![CDATA[RagTag: a collection of software tools for scaffolding and improving modern genome assemblies]]> RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:

    Address of the bookmark: https://github.com/malonge/RagTag

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/44476/omark-software-for-proteome-protein-coding-gene-repertoire-quality-assessment Wed, 21 Feb 2024 15:01:20 -0600 https://bioinformaticsonline.com/bookmarks/view/44476/omark-software-for-proteome-protein-coding-gene-repertoire-quality-assessment <![CDATA[OMArk: software for proteome (protein-coding gene repertoire) quality assessment]]> OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families.

    Address of the bookmark: https://github.com/DessimozLab/OMArk

    ]]>     LEGE     https://bioinformaticsonline.com/bookmarks/view/41459/jcvipython-utility-libraries-on-genome-assembly-annotation-and-comparative-genomics Tue, 17 Mar 2020 06:19:06 -0500 https://bioinformaticsonline.com/bookmarks/view/41459/jcvipython-utility-libraries-on-genome-assembly-annotation-and-comparative-genomics <![CDATA[JCVI:Python utility libraries on genome assembly, annotation and comparative genomics]]> Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

    https://github.com/tanghaibao/jcvi

    More at https://github.com/tanghaibao/jcvi/wiki

    Address of the bookmark: https://github.com/tanghaibao/jcvi

    ]]>     Jit     https://bioinformaticsonline.com/news/view/396/bioinformatics-introduction-to-perl Thu, 11 Jul 2013 09:49:37 -0500 https://bioinformaticsonline.com/news/view/396/bioinformatics-introduction-to-perl <![CDATA[Bioinformatics: Introduction to PERL]]> This course is aimed at those new to programming and provides an introduction to programming using Perl. By the end of this course, attendees should be able to write simple Perl programs and to understand more complex Perl programs written by others. The course will be taught using the online Learning Perl materials created by Sofia Robb of the University of California Riverside. Further information is available.

    ]]>     Archana Malhotra     https://bioinformaticsonline.com/blog/view/1182/installing-perl-gd-module Mon, 22 Jul 2013 14:02:01 -0500 https://bioinformaticsonline.com/blog/view/1182/installing-perl-gd-module <![CDATA[Installing Perl GD Module]]>

    In comparative genome analysis work, we usually compare more than two genomes and looks for syntenic regions amongst them. In my research I used Evolution Highway (RH) http://eh-demo.ncsa.uiuc.edu/, which is a collaborative project designed to provide a visual means for simultaneously comparing genomes of multiple amniote species. The tool removes the burden of manually aligning these maps and allows cognitive skills to be used toward something more valuable than preparation and transformation of data. In addition to EH, attractive Circos (http://circos.ca/) is also very popular for this kind of analysis.

    The EH is available online, and can be easily access and use, whereas Circos installation is not entirely straightforward. One of the most difficult parts of the installation involves installing the GD library. Since there weren't good instructions for installing this library on the internet I decided to post instructions here in case they are useful to anyone else.

    Following are the steps to install GD modules in Mac OS

    1. Setup

    Create a folder for the files:

    $ mkdir -p /SourceCache
    $ cd /SourceCache

    Get and unpack the required Jpeg-6b and GD libraries:
    Download Jpeg-6b (http://code.google.com/p/google-desktop-for-linux-mirror/downloads/detail?name=jpeg-6b.tar.gz&can=2&q)
    Download GD (http://search.cpan.org/~lds/GD-2.46/)

    Place the "tar.gz" files in "/SourceCache" and double click to unpack.

    2. Install libjpeg

    Copy the "config.sub" and "config.guess" files to "/SourceCache". Note that your "config.sub" and ""config.guess" files may be in a slightly different location. The commands below show where they were on my machine:

    $ cd /SourceCache/jpeg-6b/src
    $ cp /usr/share/libtool/config/config.sub .
    $ cp /usr/share/libtool/config/config.guess .

    Configure libjpeg as follows. Note that this was installed on a 64 bit machine. However, this method may configure it in a 32 bit format. This may not be the best way to configure the installation but it works.

    $ .configure --enable-shared
    $ make

    Check to see if the following directories exist on your machine. Create the missing directories in the following manner:

    $ mkdir -p /usr/local/include
    $ mkdir -p /usr/local/bin
    $ mkdir -p /usr/local/lib
    $ mkdir -p /usr/local/man/man1

    Finish making and installing libjpeg:

    $ make install

    3. Install GD

    $ cd /SourceCache/GD-2.46/GD/
    $ perl Makefile.PL
    $ make
    $ make test (optional)
    $ make html (optional)
    $ make install

    Other way for Mac OS
    The easiest way to get a lot of these is with a program called Fink, which is similar in nature to the CPAN installer, but installs common GNU utilities. Fink is available from <http://sourceforge.net/projects/fink/>.

    Follow the instructions for setting up Fink. Once it's installed, you'll want to run the following as root: fink install gd

    It will prompt you for a number of dependencies, type 'y' and hit enter to install all of the dependencies. Then watch it work.

    To prevent creating conflicts with the software that Apple installs by default, Fink creates its own directory tree at /sw where it installs most of the software that it installs. This means your libraries and headers for libgd will be at /sw/lib and /sw/include instead of /usr/lib and /usr/local/include. Because of these changed locations for the libraries, the Perl GD module will not install directly via CPAN, because it looks for the specific paths instead of getting them from your environment. But there's a way around that :-)

    Instead of typing "install GD" at the cpan> prompt, type look GD. This should go through the motions of downloading the latest version of the GD module, then it will open a shell and drop you into the build directory. Apply below patch to the Makefile.PL file (save the patch into a file and use the command patch < patchfile.)

    Then, run these commands to finish the installation of the GD module:

    perl Makefile.PL
    make
    make test
    make install
    And don't forget to run exit to get back to CPAN.

     

    Install on MS Window, using PPM

    C:\Documents and Settings\Owner>ppm
    PPM interactive shell (2.2.0) - type 'help' for available commands.
    PPM> install GD
    Install package 'GD?' (y/N): y
    Installing package 'GD'...
    Downloading http://ppm.ActiveState.com/PPMPackages/5.6plus/MSW. ...
    Installing C:\Perl\site\lib\auto\GD\GD.bs
    Installing C:\Perl\site\lib\auto\GD\GD.dll
    Installing C:\Perl\site\lib\auto\GD\GD.exp
    Installing C:\Perl\site\lib\auto\GD\GD.lib
    Installing C:\Perl\html\site\lib\GD.html
    Installing C:\Perl\site\lib\GD.pm
    Installing C:\Perl\site\lib\qd.pl
    Installing C:\Perl\site\lib\auto\GD\autosplit.ix
    PPM>


    If you can't install it from ppm. You can download it:
    http://ppm.ActiveState.com/PPMPackages/5.6plus/MSW.


    BTW,All Perl 5.6.1 Modules are located at:

    http://ppm.ActiveState.com/PPMPackages/5.6plus/MSW.

     

    Install the Perl GD Module on Linux

    $ sudo perl -MCPAN -e shell

    Since it was the first time I had run this command on this particular machine I had to answer a lot of questions but simply selected the defaults for everything as this usually works for me. Once in the CPAN shell I entered

    $ install Bundle::CPAN

    and selected all of the defaults again. Once the CPAN bundle had finished installing I tried to install GD::Graph by typing

    $ install GD::Graph

    but it failed with hundreds of errors – the first of which was

    GD.xs:7:16: error: gd.h: No such file or directory

    This was fixed with the following apt-get command (in the bash shell)

    $ sudo apt-get install libgd2-xpm-dev

    back in the CPAN shell I still couldn’t get GD::Graph to build and I guessed this was because of some left over files from the failed build. I don’t know the command to clean things up inside the CPAN shell and am too lazy to read the docs so I simply went into the .cpan/build directory in my home directory and deleted anything that started with GD – eg

    $ rm -rf GD-2.35-HC_vkB

    $ rm -rf GDGraph-1.44-Evfibe

    and so on. Those strings at the end (VkB and so on) look random so they might be different on your machine. Then I went back into the CPAN shell and ran

    $ install GD::Graph

    There were a few dependencies which the script fetched and installed for me but everything worked smoothly.

    Manual and other Perl Module instalation are mentioned in my previous blog @ http://bioinformaticsonline.com/blog/view/710/how-to-install-perl-modules-manually-using-cpan-command-and-other-quick-ways

    ]]>     Jit