<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/35543?offset=460 https://bioinformaticsonline.com/opportunity/view/42165/bioinformatics-scientistresearch-software-engineer-at-university-of-dundee-dundee-united-kingdom Wed, 26 Aug 2020 10:31:25 -0500 <![CDATA[Bioinformatics Scientist/Research Software Engineer at University of Dundee Dundee, United Kingdom]]> We are recruiting for an exceptional individual to join us as a computational scientist, bioinformatician, or (research) software engineer with an interest in interactive data analysis platforms for biology and medicine within our Jalview (www.jalview.org) research software engineering team.

More at https://www.jobs.dundee.ac.uk/fe/tpl_uod01.asp?s=4A515F4E5A565B1A&jobid=104342,2382988671&key=147934117&c=99413415238921&pagestamp=sesxbbuyifokdsfygf

Last date: 30th August 2020

Informal enquiries about this position may be made to Prof. Geoff Barton (gjbarton@dundee.ac.uk) or Dr Jim Procter (jprocter@dundee.ac.uk). To find out more about Jalview research software engineering team please visit www.jalview.org and www.compbio.dundee.ac.uk

]]> https://bioinformaticsonline.com/pages/view/33839/awesome-perl-frameworks-libraries-and-software-part-2 Fri, 07 Jul 2017 04:09:04 -0500 https://bioinformaticsonline.com/pages/view/33839/awesome-perl-frameworks-libraries-and-software-part-2 <![CDATA[Awesome perl frameworks, libraries and software - PART 2]]>
  • licheng/gccfilter - gccfilter is a perl filter to colorize and simplify (or expand) gcc diagnostic messages. gccfilter is particularly aimed at g++ (i.e. dealinging with C++) messages which can contain lot of template-related errors or warnings difficult to sort out.
  • klenin/cats-main - Programming contest control system
  • kazuho/p5-Net-DNS-Lite - pure-perl DNS resolver with support for timeout
  • japhb/perl6-bench - Benchmark and compare Perl 6 implementations against perl5
  • ingydotnet/pquery-pm - Perl Port of jQuery
  • grondilu/libbitcoin-perl - bitcoin perl library
  • fayland/perl-git-store - Git as versioned data store in Perl
  • dpavlin/perl-Mifare-MAD - pretty print Mifare Classic MAD - Mifare Application Directory from dump files
  • cpan-testers/CPAN-Reporter - (Perl) Adds CPAN Testers reporting to CPAN.pm
  • cog/perlbaldoc - Perlbal documentation
  • clbecker/perl-wiktionary-parser - Client and parser of documents pulled from the wiktionary api
  • btrott/Crypt-OpenPGP - Pure-Perl OpenPGP implementation
  • briandfoy/git-github-creator - (Perl) Create a Github repository for your Perl module
  • bradchoate/text-textile - Text::Textile -- Perl module for handling Textile format
  • apache/mod_perl - Mirror of Apache mod_perl
  • adrianh/test-class - Test::Class - an xUnit testing framework for Perl 5.x
  • yannk/perl-avro - Perl implementation Avro Data Serializer. See new official repo
  • xme/known_hosts_bruteforcer - Perl script to bruteforce SSH known_hosts files.
  • Util/Blue_Tiger - Perl 5 to Perl 6 Translator
  • typester/anyevent-jsonrpc-lite-perl - AnyEvent::JSONRPC::Lite
  • tokuhirom/http-session - http session management library for perl
  • test-class-moose/test-class-moose - Serious testing for serious Perl
  • schwern/Perl-Signatures-Common - A common definition and test suite for Perl function signatures.
  • pjcj/Gedcom.pm - Gedcom - a Perl module to manipulate Gedcom genealogy files
  • mj41/auto-unrar - Smart Perl scripts (for Linux) to auto unrar / extract a directory structure containing RAR archives.
  • lukeross/MuttrcBuilder - A web-based builder for Mutt's .muttrc files.
  • lstein/LibVM-EC2-Perl - Simple version of Perl Amazon EC2 modules that supports the tag API
  • kappa/perl-httpd-benchmarks - Searching for fastest small Perl httpd
  • jmlynesjr/wxPerl-wxBook-Examples - wxPerl examples ported from "Cross-Platform GUI Programming with wxWidgets" - "The wxBook"
  • jmcnamara/spreadsheet-parseexcel - Perl module to read Excel binary files
  • Geo-omics/scripts - General scripts used in the lab. Almost all of them are in core perl, i.e require no modules that don't already come with a perl installation. These script are currently in use by the Lab, so expect full support. This material is based upon work supported by the National Science Foundation under Grant Number EAR-1035955. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
  • garu/POD2-PT_BR - Brazilian portuguese translation of Perl core documentation
  • DrHyde/perl-modules-Number-Phone - Number::Phone and friends
  • daoswald/retester - Perl and Mojolicious based web application for testing and debugging regular expressions.
  • boumenot/p5-Net-Amazon - Perl framework for accessing amazon.com using REST.
  • book/HTTP-Proxy - A pure Perl HTTP proxy
  • bingos/devel-patchperl - (perl) Patch perl source a la Devel::PPort's buildperl.pl
  • zenogantner/PDL-ML - machine learning example code in PDL (Perl Data Language)
  • zakame/perl-google-plus - Simple Perl interface for Google+
  • zag/ru-perl6-book - Russian perl6 book
  • typester/github-ircbot-perl - ircbot to broadcast github post-receive message to irc
  • trinitum/RedisDB - Perl extension to access Redis
  • trapd00r/pimpd2 - Perl Interface for the Music Player Daemon 2 | http://search.cpan.org/dist/App-Pimpd/
  • tokuhirom/Tiffany - Template-For-All, Generic interface for perl template engines.
  • toddr/perl-net-jabber-bot - Net::Jabber::Bot module for Perl
  • splitbrain/irclogger - A Perl/PHP tool to log an IRC channel and make it searchable on the Web
  • SoylentNews/rehash - Forked from Slashcode, rehash is the codebase that powers SoylentNews.org, powered by mod_perl 2
  • skaji/relocatable-perl - self-contained, portable perl binaries
  • simonwistow/Module-Pluggable - Automatically give your Perl module the ability to have plugins
  • robinsmidsrod/unnamed-perl-cms-project - Creating a newbie-deployable CMS framework for Perl
  • rmayorga/fooberto - perl-ugly-home-made-bot
  • RexOps/rex-apache-deploy - Manage Website deployments (for PHP, Perl, Tomcat, ...)
  • polocky/p5-Polocky - Web Application Framework with Perl
  • perkinsms/Perl-GTFS - Perl modules for handling GTFS (transit) data
  • perigrin/xml-toolkit - Framework for Marshaling XML to Perl (moose) Classes and back.
  • nothingmuch/search-gin - Generalized indexing for Perl
  • msimerson/mail-dmarc - Mail::DMARC, a complete DMARC implementation in Perl
  • mndrix/net-couchdb - Perl interface for CouchDB
  • melo/perl-anyevent-nsq - A AnyEvent-based client for NSQ.io
  • mbarbon/language-p - An experimental Perl 5 parser/compiler written in Perl 5
  • masak/yarn - A proof-of-concept blogging application using Perl 6's Web.pm
  • mariuz/perl-dbd-firebird - Perl DBI driver for Firebird
  • marioroy/mce-perl - Many-Core Engine for Perl - Module
  • lyokato/p5-oauth-lite - Perl OAuth Library
  • lstein/Perl-GD - Perl GD module for bitmap graphics
  • keiya/KeiSpade-CMS - The contents management system that uses SQLite3. Written in Perl, HTML5.
  • jquelin/games-pandemic - a cooperative pandemic board game written in perl
  • johntdyer/ftptail - Perl application written by Will Moffat which allows you to tail log files over FTP
  • jjl/Spark-Form - The Spark::Form Perl module for effortlessly handling forms.
  • HackerOrientado/BypassCF - Script in Perl for Bypass CloudFlare
  • gugod/railsish - A perl webapp framework with rails-like convention-based coding style.
  • Farow/hexchat-scripts - Perl scripts for HexChat
  • exercism/xperl5 - Exercism Exercises in Perl 5
  • Ensembl/ensembl-variation - The Ensembl Variation Perl API and SQL schema
  • eiro/p5-perlude - Shell and Powershell pipes, haskell keywords mixed with the awesomeness of perl. forget shell scrpting now!
  • edsu/www-wikipedia - Simple Perl client for grabbing content out of Wikipedia
  • domm/Game-PerlInvaders - simple space invaders game implemented using Perl & SDL
  • davorg/xml-feed - The CPAN module XML::Feed
  • daoswald/Inline-CPP - Perl Module: Inline::CPP: Include C++ code inline within Perl code.
  • cpan-testers/Test-Reporter - (Perl) Sends perl module test results to CPAN Testers
  • CpanelInc/Custom-cPanel-Module - Example Perl module for extending the cPanel API
  • cosimo/perl5-net-statsd - Net::Statsd is a Perl client for Etsy's statsd metric collection daemon
  • chromatic/Modern-Perl - The Modern::Perl CPAN Distribution
  • cho45/Text-Xatena - Perl module for parsing Xatena syntax (like Hatena syntax)
  • chicks-net/megamap - MegaRAID® Linux drive map
  • c9s/perldoc-zhtw-translation - Perldoc Translation in zh-tw
  • aanoaa/p5-hubot - hubot perl port
  • yanick/Perl-Achievements - Write some perl, gather some badges of merit.
  • vti/text-caml - A mustache-like template engine for Perl
  • vti/perlresume.org - perlresume.org
  • vmaselli/PerlTools - Perl scripts for several purpose
  • vlet/iec104 - Perl implementation of IEC 60870-5-104 standard (server and client)
  • theory/semver - Semantic version object for Perl
  • spencertipping/ni - A Perl script that says "ni" to data
  • silnrsi/font-ttf - Font::TTF Perl Module
  • SFR-ZABBIX/Zabbix-API - Perl distribution to access the JSON-RPC API of a Zabbix server
  • sendgrid/sendgrid-perl - Perl module for SendGrid's API
  • rvosa/bio-phylo - Bio::Phylo - Phyloinformatic analysis using Perl
  • rafl/tpf-soc - Documents for organising a Google Summer of Code for The Perl Foundation
  • pkrumins/youtube-uploader - A Perl program that uploads videos to YouTube without any APIs.
  • pjf/ipc-system-simple - Perl module to make running system commands and capturing errors as simple as possible.
  • PerlGameDev/Box2D-perl - Box2D for perl
  • Ovid/Corinna - Generate Perl classes from XML schemas
  • osfameron/Foose - Functional Perl
  • mpeters/html-template - Perl HTML::Template module
  • modernistik/Nmap-Parser - Parse nmap scan data with Perl (official repo)
  • mjdominus/Linogram - Declarative constraint-based structured drawing system in Perl (as per chapter 9 of "Higher-Order Perl")
  • mickeyn/PONAPI - a Perl client/server implementation of {json:api} v1.0
  • markusb/pdf-create - Perl module to create PDF files
  • libraryhackers/library-callnumber-lc - Perl and Python modules for normalizing Library of Congress call numbers
  • kingpong/perl-PDF-WebKit - Convert HTML to PDF using WebKit (wkhtmltopdf)
  • kensanata/hex-mapping - Tools to work with hex maps for roleplaying games. Usually web applications written in Perl and producing SVG output.
  • jzawodn/perl-Redis - Improved version of the Perl Redis client that's available on CPAN
  • jirutka/apcupsd-snmp - Apcupsd module for Net-SNMP
  • ingydotnet/inline-pm - Write Perl subroutines in other programming languages
  • Htbaa/WebService-Rackspace-CloudFiles - Perl Interface to Rackspace Cloud Files service
  • gugod/markapl - (Perl) Markup as Perl
  • gbarr/perl-beanstalk-client - Perl client library for beanstalkd
  • frodwith/Amazon-MWS - Perl API bindings to Amazon Marketplace Web Services
  • ess/citadel - Citadel is a replacement for dos-deflate (ddos.sh) implemented in Perl.
  • damog/www-tumblr - Perl interface for the Tumblr API
  • cosimo/perl5-device-gsm - a Perl5 class to handle communication with a gsm modem or gsm cell phone, send sms, etc...
  • clip9/adbren - adbren - Rename and organize anime using this AniDB API client written in perl
  • zostay/P6W - The Web API for Perl 6 (P6W)
  • zigorou/yokohama-pm-10 - Presentation of Yokohama Perl Monger #10
  • xaicron/p5-win32-unicode - perl unicode-friendly wrapper for win32api.
  • VerbalExpressions/PerlVerbalExpressions - Perl Regular expressions made easy
  • trizen/perl-scripts - A collection of day-to-day Perl scripts which prove some ideas or implement some useful practicability.
  • swannman/pdf2gerb - Perl script converts PDF files to Gerber format
  • substack/dnode-perl - Asynchronous remote method calls with transparently wrapped callbacks... in perl!
  • silnrsi/font-ttf-scripts - Font::TTF::Scripts perl module
  • sanko/net-bittorrent - Perl based BitTorrent module available on CPAN
  • sanko/Finance-Robinhood - Trade stocks and ETFs with free brokerage Robinhood and Perl
  • rurban/illguts - Perl illustrated guts
  • rjbs/MIME-Lite - the perl library MIME::Lite
  • rjbs/CPAN-Uploader - perl library (and program) to upload dists to the cpan
  • rizen/Ouch - Perl exceptions that don't hurt.
  • rafl/twigils - Twigils for Perl 5
  • pullingshots/Shipment - perl interface into various shipping web service API's - FedEx, UPS, Purolator, Temando
  • portcullislabs/ssl-cipher-suite-enum - PERL script to enumerate supported SSL cipher suites supported by network services (principally HTTPS).
  • PerlChina/advent.perlchina.org - CN Perl Advent
  • perl-catalyst/Catalyst-Components-Concepts-Cases - A Perl Catalyst documentation project
  • naoya/perl-hadoop - A frontend framework of Hadoop-Streaming for perl without Moose
  • mrihtar/Garmin-FIT - Perl code for reading and conversion of Garmin FIT binary files
  • mbarbon/extutils-xspp - Perl XS for C++
  • masak/tardis - Time traveling debugger in Perl 6
  • kthakore/TetrisPL - Tetris in MVC SDL Modern Perl Style
  • kjetilk/RDF-LinkedData - RDF::LinkedData is a Perl module for setting up Linked Data server
  • keeth/Net-OAuth - OAuth 1.0 for Perl
  • kberov/PerlProgrammingCourse - A relatively full beginner-to-intermediate Perl trainig course
  • kazuho/p5-test-httpd-apache2 - Apache2 starter for testing perl modules
  • kazuho/p5-Cache-LRU - a simple, fast implementation of an LRU cache in pure perl
  • juster/perl-cpanplus-dist-arch - CPANPLUS backend for building Archlinux pacman packages
  • Juniper/netconf-perl - Perl library for Netconf
  • jrockway/eventful - application framework for Perl
  • jrockway/devel-repl - pluggable REPL for Perl that doesn't suck
  • jquelin/games-risk - classical 'risk' board game in perl
  • ingydotnet/test-base-pm - Extendable Perl Testing
  • gisle/data-dump - A Perl module for pretty printing of data structures
  • Getty/p5-facebook - Facebook SDL in Perl
  • GeneDesign/GeneDesign - Synthetic biology library in Perl
  • FelipeSt4rk/FindSubDomain - Find sub domains with Perl
  • fayland/perl-javascript-beautifier - Perl: Beautify Javascript (beautifier for javascript)
  • ding-lab/hotspot3d - 3D hotspot mutation proximity analysis tool
  • dermesser/fastcgi-wrappers - This repository contains two FastCGI wrappers written in Perl. The first may execute any executable file in the same way CGI does, the second one does inline-eval of Perl scripts to avoid any forking.
  • degtyarev-dm/mojolicious-lite-openshift - Mojolicious::Lite Perl framework quickstart repo
  • dave-theunsub/gtk3-perl-demos - This repository is intended to give perl-Gtk3 users some example programs. It's not rocket surgery, you know.
  • CowboyTim/python-storable - python module that will be able to read/write perl storable
  • cosimo/perl5-net-statsd-server - A Perl port of Etsy's statsd server - Simple daemon for easy stats aggregation
  • cooper/juno - a seriously modern IRC daemon written from scratch in Perl. designed to be ridiculously extensible, painlessly reloadable, and excessively configurable
  • colinnewell/Jenkins-API - Jenkins API Wrapper for Perl
  • clintongormley/Elastic-Model - Use ElasticSearch as a NoSQL database in Perl
  • claesjac/javascript - The JavaScript module for Perl
  • canada/PerlDocJp - This Web application let perldoc.jp Japanized pod document browsable and searchable just like search.cpan.org
  • calid/zmq-ffi - version agnostic Perl bindings for zeromq
  • avar/sendmail-pmilter - Perl binding of Sendmail Milter protocol
  • aquaron/Business-Stripe - Perl bindings for Stripe payment system
  • apparentlymart/libdanga-socket-anyevent-perl - Danga::Socket reimplementation in terms of AnyEvent
  • agentzh/makefile-graphviz-pm - Perl CPAN module Makefile::GraphViz - Draw building flowcharts from Makefiles using GraphViz
  • xoma/Russian-translate-of-Mojolicious-guides - Перевод документации и рецептов для Perl-фреймворка Mojolicious
  • xaicron/p5-JSON-WebToken - JSON Web Token (JWT) implementation for Perl
  • wickline/whack - find the perl sub most in need of refactoring
  • vti/turnaround - DEPRECATED: A Perl TIMTOWTDI web framework
  • uzulla/pyazo - Gyazo And Gifzo compatible server by perl
  • ukautz/Net-Amazon-DynamoDB - Simple perl interface for Amazon DynamoDB
  • thedarkwinter/Net-DRI - Perl EPP Client: Net-DRI-0.X_tdw based on Net-DRI-0.96_05
  • tadzik/neutro - Simple module installer for Perl 6
  • stockholmuniversity/nagios-nrpe - A pure perl implementation of the Nagios NRPE daemon and client
  • skx/chronicle2 - Chronicle is a simple blog compiler, written in Perl with minimal dependencies.
  • sjdy521/Mojo-StrawberryPerl - 基于StrawberryPerl打包而成的包含Perl-5.24+cpanm+Mojo-Webqq+Mojo-Weixin的完整Windows运行环境
  • scrottie/WWW-Workflowy - Faked up Workflowy API for Perl using Workflowy's JSON protocol
  • run4flat/C-TinyCompiler - Perl bindings for the Tiny C Compiler
  • robkinyon/dbm-deep - DBM::Deep Perl module
  • rjbs/Email-ARF - Email::ARF perl module for parsing ARF
  • rjbs/Config-INI - Config::INI perl module
  • ranguard/svg-tt-graph - Perl module for creating SVG graphs
  • plainblack/JSON-RPC-Dispatcher - A JSON-RPC 2.0 server for Perl.
  • pjf/perl589delta - The perl589delta.pod file for the 5.8.9 release of Perl
  • perigrin/adam-bot-framework - An IRC bot framework in Perl based on Moose & POE
  • ollyg/Net-Appliance-Session - Development of Net::Appliance::Session Perl distribution
  • ollyg/Catalyst-Plugin-AutoCRUD - Development of Catalyst::Plugin::AutoCRUD Perl distribution
  • nlewis/Net-ILO - Perl interface to HP Integrated Lights-Out
  • NET-A-PORTER/NAP-policy - Policy / pragma for Perl code written at NAP
  • neevek/minerl - A blog-aware static site generator written in perl.
  • miyagawa/Perlbal-Plugin-PSGI - Perlbal plugin to run PSGI applications
  • metacpan/metacpan-client - Home of the official MetaCPAN Perl API client.
  • mattn/p5-Growl-GNTP - Perl implementation of GNTP Protocol (Client Part)
  • marcschwartz/WriteXLS - CRAN Package WriteXLS: Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX) files from one or more data frames. Each data frame will be written to a separate named worksheet in the Excel spreadsheet. The worksheet name will be the name of the data frame it contains or can be specified by the user.
  • Leont/file-map - Memory mapping for Perl
  • kuzuha/WWW-Pixiv - Perl interface for www.pixiv.net
  • jozef/Debian-Apt-PM - locate Perl Modules in Debian repositories
  • jjn1056/Perl-Catalyst-AsyncExample - maybe some sort of async with catalyst
  • hprose/hprose-perl - Hprose for Perl
  • hoytech/Session-Token - Secure, efficient, simple random session token generation
  • gunnarbeutner/linux-kstat - Sun::Solaris::Kstat perl module for linux-zfs
  • gshank/ravlog - Perl Catalyst blog
  • fmgoncalves/p5-cassandra-simple - Cassandra::Simple Perl Module - Easy to use, Perl oriented client interface to Apache Cassandra.
  • fayland/perl-app-github - App::GitHub CPAN module
  • eserte/cpan-testers-matrix - the code behind matrix.cpantesters.org
  • dnmfarrell/Stasis - an encrypting archive tool using tar, gpg and perl
  • dk/Net-Eboks - perl API for eboks.dk
  • dagolden/extutils-parsexs - converts Perl XS code into C code
  • chrisa/perl-Net-SAML2 - Perl Net::SAML2 module
  • chorny/smart-comments - Perl programming module for easier debugging
  • chetanganatra/Excel-2-Elasticsearch - Small and quick Perl script to inject records from MS Excel (.xlsx as well as .xls) directly into Elasticsearch.
  • cbowns/fitbit-oauth-perl - A couple of perl scripts to get a Fitbit OAuth token and to use that token to upload Weightbot CSV data to Fitbit
  • bricas/statistics-r - Controls the R (R-project) interpreter through Perl
  • brianwrf/myPadBuster - It is a Python+Perl script to exploit ASP.net Padding Oracle vulnerability.
  • briandfoy/mycpan-indexer - (Perl) Index a Perl distribution
  • briandfoy/module-release - (Perl) Automate software releases
  • Brasil-Perl-Mongers/perl-pro - Site de divulgação de vagas de emprego para programadores Perl no Brasil.
  • bostonaholic/test-more-behaviour - Rspec-style tests in Perl
  • borisdaeppen/EBook--MOBI - Ebook in MOBI format with Perl
  • book/Test-Database - Perl extension to provide database handles in a test environment
  • beppu/pod-server - a web server for locally installed perl documentation -- think gem_server for perl
  • awwaiid/continuity - Stateful Web Apps in Perl
  • apparentlymart/libnet-openid-perl - OpenID libraries for Perl
  • ambs/Quiki - Quick Wiki in Perl
  • alambike/eixo-docker - Suite of Perl modules to interact with Docker
  • abw/Badger - Perl application programming toolkit
  • abh/colobus - Perl NNTP server
  • Zverik/gpxplanet-tools - Perl scripts for processing OpenStreetMap's GPX planet
  • zipf/perldoc-es - Documentación de Perl en Español / Spanish translation of Perl core docs
  • yusukebe/Shiori - Yet another Perl implementation of Shiori web-app.
  • yoshiki/perl-app-waffy - Twitter proxy for iPhone, Mobile(jp) and IRC
  • yoe/sreview - sreview review system
  • yappo/p5-Groonga - Perl Module of Groonga
  • yannk/perl-anyevent-xmpp - my patches to AnyEvent::XMPP
  • woodpeck/osm-revert-scripts - A collection of Perl scripts to handle reverts on OpenStreetMap
  • wertarbyte/hetzner-robot-perl - Perl module and command line tool for control over the Hetzner robot
  • tokuhirom/cgi-extlib-perl - General extlib/ for Perl CGI applications.
  • tlily/tigerlily - perl client for the lily chat server
  • tima/perl-amazon-s3 - A portable client library for working with and managing Amazon S3 buckets and keys.
  • subogero/rename - Perl rename as a separate package
  • sstrigler/chatbot - a jabber channel bot written in perl
  • softlayer/softlayer-api-perl-client - A set of Perl libraries that assist in calling the SoftLayer API.
  • singingfish/Citeproc-Markdown - Perl module for integrating with CSL processor inside Zotero for plain text / markdown citation support
  • scottp/extjs-direct-perl - A minimal perl implementation of ExtJS 3.0 Ext.Direct serverside stack
  • s-aska/markdown-binder - Ajax Markdown Viewer written in Perl, to run under Plack.
  • ruoso/games-perl - Series of blog posts on how to write games in Perl
  • Potatohead/local-lib-profiles - management scripts for perl's local lib
  • petdance/html-lint - HTML::Lint, the Perl module for HTML checking
  • patschbo/BaNG - Backup Next Generation for Linux & Mac (using rsync and btrfs snapshots, Web-Frontend, Statistics, History-Merger)
  • NoodlesNZ/statsd-perl-mysql - MySQL stats logging for Statsd/Graphite
  • naoya/hadoop-streaming-frontend - A frontend framework of Hadoop-Streaming for perl
  • nagios-plugins/nagios-plugin-perl - Perl module Nagios::Monitoring::Plugin
  • masak/psyde - A static webpage manager (written in Perl 6)
  • masak/p6cc2012 - The Perl 6 coding contest, 2012 edition
  • MarkGannon/XBRL - Perl Module for Reading XBRL
  • makamaka/JSON-PP - JSON::PP for perl core module
  • MadsAlbertsen/miscperlscripts - Small collection of random useful perl scripts
  • lestrrat/Data-Localize - Object Oriented Localization Tool For Perl
  • kasei/attean - A Perl Semantic Web Framework
  • kablamo/git-ribbon - A Perl script that helps you read through the latest changes on a project.
  • ingydotnet/yaml-pm6 - YAML Implementation for Perl 6
  • ingydotnet/testml-pm6 - TestML for Perl 6
  • ikruglov/HADaemon-Control - Create init scripts for Perl high-available (HA) daemons
  • ido50/Tenjin - Fast templating engine with support for embedded Perl
  • ICGC-TCGA-PanCancer/PCAP-core - NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project
  • hiratara/p5-Data-Monad - A implementation of monads in Perl 5.
  • hinrik/grok - Perl 6 documentation reader
  • hatena/perl5-test-apache-rewriterules - Test::Apache::RewriteRules - Testing Apache's Rewrite Rules
  • gonzoua/book-tools - perl modules to work with ePUB and FB2 ebook formats
  • fayland/dist-zilla-plugin-perltidy - Dist::Zilla with Perl::Tidy
  • ErinsMatthew/Import-IMDb-Ratings-Into-trakt.tv - A Perl script that will load your IMDb ratings into trakt.tv
  • dscho/dsstore - A remote-hg mirror of the Perl project to generate .DS_Store files (even on non-MacOSX), based on https://wiki.mozilla.org/DS_Store_File_Format
  • dpavlin/Biblio-SIP2 - Simple 3M SIP2 Standard Interchange Protocol implementation in perl
  • dinomite/Mac-iTunes-Library - Mac::iTunes::Library Perl module
  • diegok/Gardel - Gardel is a very simple perl web framework that also has a hat. ( Inspired on sinatra.rb )
  • demianriccardi/p5-HackaMol - Object-Oriented Perl 5, Moose Library for Molecular Hacking
  • daoswald/JSON-Tiny - Perl module for encoding and decoding JSON in a minimalistic way, based on Mojo::JSON, adapted to stand alone.
  • cryptostorm/cstorm_widget - The Perl source code to the Cryptostorm widget
  • briandfoy/test-file - (Perl) Check file attributes
  • bingos/poe-component-irc - A fully event-driven perl IRC client module
  • bingos/gumbybrain - (perl) < GumbyBRAIN> when the kids had killed the man, i had the source now.
  • beanz/anyevent-mqtt-perl - Perl modules for MQTT protocol (http://mqtt.org/) using AnyEvent
  • Akron/Sojolicious - OStatus for Perl - A social toolbox for Mojolicious
  • achillean/shodan-perl - Perl library for SHODAN
  • zzengineer/crawlpl - compact crawling tools written in perl
  • zigorou/perl-json-pointer - A JSON Pointer implementation for Perl
  • zakame/hashids.pm - Hashids, ported for Perl
  • ysasaki/Text-Sass-XS - Perl Binding for libsass
  • yapceurope/perl-events - Information about all Perl conferences and workshops
  • xing/perl-beetle - High availability AMQP messaging with redundant queues
  • wbuntine/text-bags - Perl scripts for massaging document collections in various ways to prepare them for topic modelling.
  • victori/perlbal-plugin-mogilefs - Perlbal Plugin to serve data from MogileFS
  • UUPharmacometrics/PsN - Perl-Speaks-NONMEM
  • urandom/p2js - IWL Perl To Javascript converter
  • urandom/iwl - IWL - perl web widget library
  • unbit/unbit-bars - A Perl Curses::UI interface for uWSGI metrics subsystem
  • typester/text-microtemplate-extended-perl - Template engine extended from Text::MicroTemplate
  • troywill/foscam-zoneminder - Zoneminder Perl control module for the Foscam FI8910W wireless IP Camera
  • tominsam/bot-basicbot-pluggable - Pluggable perl IRC bot
  • tokuhirom/p5-fcgi-client - FCGI client library in pure perl
  • tokuhirom/http-mobileattribute - HTTP::MobileAttribute is a perl module for handle japanese mobile phones
  • timbunce/Dist-Surveyor - Survey installed perl modules and determine the specific distribution versions they came from
  • thoukydides/heatmiser-wifi - Web interface, SiriProxy plugin and Perl libraries for Heatmiser Wi-Fi Thermostats
  • tadzik/perl6-File-Tools - File::Tools – common shell commands replacements
  • szabgab/PDE - Perl Development Environment
  • sparky/perl-Net-Curl - Object-oriented wrapper for libcurl
  • sludin/http2-perl - Perl implementation of the HTTP/2.0 protocol
  • slimakuj/perl - :dromedary_camel: Materiały do warsztatów z Perla
  • reyjrar/Parse-Syslog-Line - Flexible library for parsing syslog messages in Perl
  • revmischa/av-streamer - Perl bindings for libav/ffmpeg
  • pstuifzand/docker-perl - Perl library for Docker http://docker.io/
  • potyl/perl-Gtk3-WebKit - Perl bindings for the gtk3 port of WebKit
  • petdance/perl-critic-bangs - Perl::Critic::Bangs -- Extra policies for Perl::Critic
  • Perl-Toolchain-Gang/local-lib - local::lib - create and use a local lib/ for perl modules with PERL5LIB
  • Perl-Toolchain-Gang/File-chdir - (Perl) a more sensible way to change directories
  • PerlDancer/perldancer-book - a book about the Perl Dancer micro framework
  • pedros/WWW-Wordnik-API - Wordnik API perl implementation
  • PagerDuty/pagerduty-nagios-pl - Nagios Integration for PagerDuty via Perl Wrapper
  • osfameron/acme--monads - Monads in pure Perl, using Devel::Declare
  • odyniec/Dancer-Plugin-DebugToolbar - Debugging toolbar for Perl Dancer web applications
  • obuk/Cv-Olive - Cv module is perl interface to OpenCV library.
  • norm/p5-css-prepare - Perl module to preprocess CSS files
  • norbu09/Giovanni - a Perl based deployment system
  • nigelm/html-scrubber - Perl extension for scrubbing/sanitizing html
  • neilb/WebService-HackerNews - An interface to the official Hacker News API (for Perl 5)
  • naoya/perl-thrift-server - Thrift server implementation for perl
  • mtve/bitcoin-pl - BitCoin perl implementation
  • moritz/tufte - SVG plotting library for Perl 6
  • mndrix/Finance-MtGox - MtGox API bindings for Perl
  • masartz/p5-webservice-hatena-bookmark-lite - A Perl Interface for Hatena::Bookmark AtomPub API
  • masak/farm - Little Animal Farm, a WWII polish family game, implemented in Perl 6
  • LiosK/Finance--Quote--YahooJapan - Finance::Quote::YahooJapan - A Perl module that enables GnuCash to get quotes of Japanese stocks and mutual funds from Yahoo! Finance JAPAN.
  • Leont/threads-lite - An Erlang style threading library for perl
  • khenn/Lacuna - Perl API for accessing Lacuna webservices
  • kevinbosak/Minecraft-Perl - Perl libs to manipulate Minecraft data files
  • kentaro/perl-dbix-rico - Yet, yet, ... yet another ORM for Perl
  • kentaro/perl-app-socialskk - SKK Goes Social
  • jkahn/twitter-bot - Perl library for writing simple bots for twitter
  • jimbomorrison/git.generate-changelog - Small perl script for generating a pretty changelog from git commits
  • jhthorsen/mojo-redis2 - Pure-Perl non-blocking I/O Redis driver
  • ironcamel/Net-OpenStack-Compute - Perl bindings for the OpenStack compute api.
  • ingydotnet/testml-pm - TestML for Perl
  • infobyte/isr-sqlget - ISR-sqlget It's a blind SQL injection tool developed in Perl.
  • HariSekhon/lib - Perl Utility Library for my other repos
  • gugod/acme-cpanauthors-taiwanese - (Perl) We are Taiwanese CPAN Authors!
  • gphat/io-storm - Perl support for Twitter's Storm distributed computational system.
  • goccy/p5-Test-AutoGenerator - automatically generate perl test code.
  • gisle/mozilla-ca - Perl module that provides Mozilla's CA cert bundle in PEM format
  • ghedo/p5-LLVM - Perl bindings to the Low Level Virtual Machine
  • gfx/Perl-Module-Install-XSUtil - Support XS-based modules in the term of Module::Install
  • gfx/Acme-Perl-VM - A Perl5 Virtual Machine in Pure Perl
  • getsentry/perl-raven - A perl sentry client
  • gbarr/AnyEvent-MongoDB - perl AnyEvent MongoDB client driver
  • gaal/app-csv - App::CSV Perl module, csv command line tool
  • fukawi2/boxcutter - Perl parser for converting iTunes playlists to a more useful format (eg, m3u)
  • exodist/Child - (perl) Object oriented simple interface to fork()
  • dwimperl/dwimperl-linux - Batteries included Perl distribution for Linux
  • dwery/hue-perl - A Perl module for the Philips Hue light system
  • dpirotte/perl-mail-chimp - MailChimp API wrapper for Perl
  • dnorman/perl-DBR - A different approach to ORM for perl
  • dnmfarrell/perltricks-static - PerlTricks.com is a website dedicated to Perl programming code and community news.
  • dluxhu/perl-parallel-forkmanager - Parallel::ForkManager
  • dams/riak-client - Perl Riak Client
  • damil/DBIx-DataModel - UML-based Object-Relational Mapping (ORM) framework for Perl
  • cowholio4/log4perl_gelf - Log::Log4perl::Layout::GELF
  • cowens/perlopref - A quick reference guide for Perl 5 operators
  • bunk3r/perlbackdoor - advanced Perl Backdoor
  • bokkypoobah/TheDAOVoter - Perl script to list and vote on The DAO proposals
  • alexei/silverstripe-unidecode - Unidecode is a PHP version of the perl module Text::Unicode. It takes UTF-8 data and tries to represent it in US-ASCII characters.
  • aleimba/bac-genomics-scripts - Collection of scripts for bacterial genomics
  • aichaos/rivescript-perl - A RiveScript interpreter for Perl. RiveScript is a scripting language for chatterbots.
  • adamziaja/perl - my simple :dromedary_camel: perl5 scripts
  • aallan/perl-modules-for-astronomy - Astronomy related Perl Modules.
  • yannk/perl-anyevent-superfeedr - Perl5 Interface to superfeedr.com - RT notifications of feed updates
  • vti/perltuts.com-tutorials - Tutorials for perltuts.com
  • typepad/perl-typepad-api - WWW::TypePad
  • tune-it/jplbot - Simple jabber and telegram bot written in perl
  • tociyuki/libtext-tepl-runtime-perl - Text::Tepl::Runtime - Basic runtime filters for Text::Tepl
  • theory/pod-site - Build browsable HTML documentation for your Perl app
  • syndicut/virt-backup - Perl script to backup qemu machines by Daniel Berteaud daniel@firewall-services.com
  • Starlink/ORAC-DR - The ORAC-DR astronomy data reduction pipeline
  • soh335/p5-Data-Wheren - wheren module for perl
  • skx/predis - A redis-server written in Perl.
  • shadowcat-mst/pumpkin-perl-staging - Staging repostiory for the Pumpkin Perl patchset
  • sekia/Algorithm-LibLinear - A Perl binding for LIBLINEAR, a library for classification/regression using linear SVM and logistic regression.
  • sebthebert/WWW-PushBullet - PushBullet Perl module
  • russoz/DataFlow - Data-flow framework for Perl
  • run4flat/perl_nvcc - A CUDA compiler and linker wrapper for Perl's toolchain.
  • run4flat/Alien-Cairo - Perl Alien package for libCairo
  • rs/net-server-mail - Extensible Perl implementation of the STMP protocol and its different evolutions (ie: ESMTP, LMTP)
  • rramsden/TCP-IP-Stack - computer science 460 group project written in perl
  • rjbs/Sub-Exporter - a sophisticated, customizable code exporter for Perl
  • rjbs/Email-MIME-Kit - (Perl) build messages from templates
  • rjbs/Data-Section - perl library read data from parts of the DATA section
  • riusksk/StrutScan - Struts2 Vuls Scanner base perl script
  • renormalist/data-dpath - A perl lib to provide access to data structures inspired by XPath
  • rafl/nanomsg-raw - nanomsg bindings for Perl
  • pkrumins/youtube-video-downloader-in-perl - Wrote this real quick as I needed to get some vids
  • pjlsergeant/perl6status - Perl 6 Status document
  • perlbot/perlbuut - new version of perlbot, based on buubot
  • p5-shorten/www-shorten - Perl interface to various URL-shortening sites
  • Ovid/test--most - Test::Most -- The most commonly needed testing functionality in Perl
  • openerserver/openerserver_perl - Http Container for run any code with http server.
  • nwellnhof/Net-Google-Analytics - Perl interface to the Google Analytics Core Reporting API
  • nferraz/Perl-Data-Warehouse-Toolkit - Make simple ETL and Data Warehouse tasks easy, and complex tasks possible.
  • mpdehaan/Elevator - A pluggable object-oriented data layer for Perl and Moose
  • moznion/Perl-PrereqScanner-Lite - Lightweight Prereqs Scanner for Perl
  • miki/Hoppy - Flash XMLSocket Server ( perl implementation )
  • melo/amqp-tools - An AMQP stack for Perl
  • maio/perl-Koans - Perl Koans
  • lestrrat/Orochi - A DI Container For Perl
  • lestrrat/Algorithm-ConsistentHash-Ketama - Ketama Consistent Hashing for Perl (XS)
  • klenin/cats-judge - Automated judging system for programming contests
  • kazeburo/Apache-LogFormat-Compiler - Compile LogFormat to perl-code
  • jmcnamara/pod-simple-wiki - A Perl Module for creating Pod to Wiki filters.
  • jimdigriz/freeradius-oauth2-perl - FreeRADIUS OAuth2 (OpenID Connect) using rlm_perl
  • jhthorsen/net-isc-dhcpd - Perl module that interacts with ISC DHCPd
  • jatimon/ThumbScanner - WDTV Perl based movie sheet generator
  • ikegami/perl-LWP-Protocol-AnyEvent-http - Event loop friendly HTTP and HTTPS backend for Perl's LWP
  • ihh/gfftools - Perl scripts for working with the GFF format
  • iamcal/perl-Flickr-API - Perl interface to the Flickr API
  • hoytech/Thrust - Perl language bindings for Thrust https://github.com/breach/thrust
  • hotwolf/HSW12 - Assembler and IDE for NXP/Freescale/Motorola's HC11, HC12, S12, S12X, and XGATE CPUs
  • hakobe/pig - Perl IRC Gateway
  • gugod/rubyish-perl - For writting perl code with some ruby feeling.
  • gisle/tkx - A Tk interface for Perl
  • gisle/digest-md5 - The Digest::MD5 Perl module
  • gbarr/perl-TimeDate - time & date parsing and formatting perl library
  • gbarr/perl-IO - Perl IO modules -- THESE MODULES ARE NO LONGER MAINTAINED OUTSIDE THE perl5 DISTRIBUTION. Send all patched to 
    • ]]>     Neel     https://bioinformaticsonline.com/bookmarks/view/34618/mashmap-a-fast-and-approximate-software-for-mapping-long-reads-pacbioont-or-assembly-to-reference-genomes Tue, 12 Dec 2017 17:23:31 -0600 https://bioinformaticsonline.com/bookmarks/view/34618/mashmap-a-fast-and-approximate-software-for-mapping-long-reads-pacbioont-or-assembly-to-reference-genomes <![CDATA[MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s)]]> MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It does not compute the alignments explicitly, but rather estimates a k-mer based Jaccard similarity using a combination of Winnowing and MinHash. This is then converted to an estimate of sequence identity using the Mash distance. An appropriate k-mer sampling rate is automatically determined given minimum local alignment length and identity thresholds. The efficiency of the algorithm improves as both of these thresholds are increased.

    Address of the bookmark: https://github.com/marbl/MashMap

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/38445/orthoani-an-improved-algorithm-and-software-for-calculating-average-nucleotide-identity Wed, 12 Dec 2018 08:36:08 -0600 https://bioinformaticsonline.com/bookmarks/view/38445/orthoani-an-improved-algorithm-and-software-for-calculating-average-nucleotide-identity <![CDATA[OrthoANI: An improved algorithm and software for calculating average nucleotide identity]]> OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95~96% and large comparison studies have demonstrated both algorithms to produce near identical reciprocal similarities. Details of the OrthoANI algorithm is given in (Lee et al. 2015). OAT employs an easy-to-follow Graphical User Interface that allow researchers to calculate OrthoANI values between genomes of interest without unfamiliar Command Line Environments. Moreover, the OAT_cmd command-line software can be integrated into preexisting bioinformatics pipelines. 

    Address of the bookmark: https://www.ezbiocloud.net/tools/orthoani

    ]]>     Abhimanyu Singh     https://bioinformaticsonline.com/bookmarks/view/39019/iq-tree-efficient-software-for-phylogenomic-inference Mon, 18 Feb 2019 04:25:11 -0600 https://bioinformaticsonline.com/bookmarks/view/39019/iq-tree-efficient-software-for-phylogenomic-inference <![CDATA[IQ-TREE: Efficient software for phylogenomic inference]]> A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time

    IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE is freely available at http://www.cibiv.at/software/iqtree

    Address of the bookmark: http://www.iqtree.org/

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/43683/genview-a-phylogeny-based-comparative-genomics-software-to-analyze-the-genetic-environment-of-genes Tue, 28 Dec 2021 01:49:03 -0600 https://bioinformaticsonline.com/bookmarks/view/43683/genview-a-phylogeny-based-comparative-genomics-software-to-analyze-the-genetic-environment-of-genes <![CDATA[GEnView: A phylogeny based comparative genomics software to analyze the genetic environment of genes]]> A phylogeny based comparative genomics software to analyze the genetic environment of genes. The user can select one or several taxa and provide one or several reference protein(s). Genomes and plasmids (based on user choice) will be downloaded from the NCBI Assembly/NR database and searched for the respective gene. Alternatively, custom genomes can be provided. User selected stretches (20kbp by default) of the genes genetic environment are extracted, annotated and aligned between all genomes. The sequences are then visualized, enabling comparison of synteny and gene content.

    More at https://pubmed.ncbi.nlm.nih.gov/34951622/

    Address of the bookmark: https://github.com/EbmeyerSt/GEnView

    ]]>     Abhi     https://bioinformaticsonline.com/blog/view/37000/install-imagemagick-from-unix-source Wed, 20 Jun 2018 11:22:43 -0500 https://bioinformaticsonline.com/blog/view/37000/install-imagemagick-from-unix-source <![CDATA[Install ImageMagick from Unix Source]]> ImageMagick builds on a variety of Unix and Unix-like operating systems including Linux, Solaris, FreeBSD, Mac OS X, and others. A compiler is required and fortunately almost all modern Unix systems have one. Download ImageMagick.tar.gzfrom www.imagemagick.org or a mirrors and verify its message digest.

    Unpack the distribution with this command:

    tar xvzf ImageMagick.tar.gz

    Next configure and compile ImageMagick. Note the pkg-config script is required so that ImageMagick can find certain optional delegate libraries on your system. To configure, type:

    $ cd ImageMagick-7.0.8
    $ ./configure
    $ make

    If ImageMagick configured and compiled without complaint, you are ready to install it on your system. Administrator privileges are required to install. To install, type

    sudo make install

    You may need to configure the dynamic linker run-time bindings:

    sudo ldconfig /usr/local/lib

    Finally, verify the ImageMagick install worked properly, type

    /usr/local/bin/convert logo: logo.gif

    For a more comprehensive test, run the ImageMagick validation suite. Ghostscript is a prerequisite, otherwise the EPS, PS, and PDF tests will fail.

    make check

    Congratulations, you have a working ImageMagick distribution and you are ready to use ImageMagick to convert, compose, or edit your images or perhaps you'll want to use one of the Application Program Interfaces for C, C++, Perl, and others.

    The above instructions will satisfy a great number of ImageMagick users, but we suspect a few will have additional questions or problems to consider. For example, what does one do if ImageMagick fails to configure or compile? Or what if you don't have administrator privileges and what if you don't want to install ImageMagick in the default /../usr/local folder? You will find the answer to these questions, and more, in Advanced Unix Source Installation.

    jitendra@jitendra-UNLOCK-INSTALL[Downloads] git clone https://github.com/ImageMagick/ImageMagick.git []
    Cloning into 'ImageMagick'...
    remote: Counting objects: 124593, done.
    remote: Compressing objects: 100% (77/77), done.
    remote: Total 124593 (delta 94), reused 94 (delta 64), pack-reused 124452
    Receiving objects: 100% (124593/124593), 76.94 MiB | 24.07 MiB/s, done.
    Resolving deltas: 100% (106498/106498), done.
    Checking connectivity... done.
    jitendra@jitendra-UNLOCK-INSTALL[Downloads] cd ImageMagick []
    jitendra@jitendra-UNLOCK-INSTALL[ImageMagick] make []
    make: *** No targets specified and no makefile found. Stop.
    jitendra@jitendra-UNLOCK-INSTALL[ImageMagick] ./configure []
    checking build system type... x86_64-pc-linux-gnu
    checking host system type... x86_64-pc-linux-gnu
    checking target system type... x86_64-pc-linux-gnu
    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... yes
    checking for a thread-safe mkdir -p... /bin/mkdir -p
    checking for gawk... gawk
    checking whether make sets $(MAKE)... yes
    checking whether make supports nested variables... yes
    checking whether UID '1000' is supported by ustar format... yes
    checking whether GID '1000' is supported by ustar format... yes
    checking how to create a ustar tar archive... gnutar
    checking whether make supports nested variables... (cached) yes
    configuring ImageMagick 7.0.8-3
    checking whether build environment is sane... yes
    checking for style of include used by make... GNU
    checking for gcc... gcc
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables...
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking whether gcc understands -c and -o together... yes
    checking dependency style of gcc... gcc3
    checking how to run the C preprocessor... gcc -E
    checking for grep that handles long lines and -e... /bin/grep
    checking for egrep... /bin/grep -E
    checking for ANSI C header files... yes
    checking for sys/types.h... yes
    checking for sys/stat.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for memory.h... yes
    checking for strings.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for unistd.h... yes
    checking minix/config.h usability... no
    checking minix/config.h presence... no
    checking for minix/config.h... no
    checking whether it is safe to define __EXTENSIONS__... yes
    checking for ar... ar
    checking the archiver (ar) interface... ar
    checking for gcc... (cached) gcc
    checking whether we are using the GNU C compiler... (cached) yes
    checking whether gcc accepts -g... (cached) yes
    checking for gcc option to accept ISO C89... (cached) none needed
    checking whether gcc understands -c and -o together... (cached) yes
    checking dependency style of gcc... (cached) gcc3
    checking for g++... g++
    checking whether we are using the GNU C++ compiler... yes
    checking whether g++ accepts -g... yes
    checking dependency style of g++... gcc3
    checking for gcc option to accept ISO C99... none needed
    checking for gcc option to accept ISO Standard C... (cached) none needed
    checking how to run the C preprocessor... gcc -E
    checking for a sed that does not truncate output... /bin/sed
    checking for fgrep... /bin/grep -F
    checking how to print strings... printf
    checking for ld used by gcc... /usr/bin/ld
    checking if the linker (/usr/bin/ld) is GNU ld... yes
    checking for gcc option to accept ISO C99... (cached) none needed
    checking CFLAGS for maximum warnings... -Wall
    checking whether make sets $(MAKE)... (cached) yes
    checking whether ln -s works... yes
    checking for a sed that does not truncate output... (cached) /bin/sed
    checking for gawk... (cached) gawk
    checking if malloc debugging is wanted... no
    checking for __attribute__... yes
    checking for C compiler vendor... gnu
    checking for gcc architecture flag...
    checking for x86 cpuid 0 output... d:756e6547:6c65746e:49656e69
    checking for x86 cpuid 1 output... 306a9:3100800:7fbae3ff:bfebfbff
    checking whether C compiler accepts -mtune=ivybridge... yes
    checking for gcc architecture flag... -mtune=ivybridge
    checking for pkg-config... /usr/bin/pkg-config
    checking pkg-config is at least version 0.20... yes
    checking size of size_t... 8
    checking for C compiler vendor... (cached) gnu
    ./configure: line 9486: AX_COMPILER_FLAGS: command not found
    checking CFLAGS for maximum warnings... (cached) -Wall
    checking if LD -Wl,--version-script works... yes
    checking for linker lazyload option... none
    checking whether gcc is Clang... no
    checking whether pthreads work with -pthread... yes
    checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
    checking whether more special flags are required for pthreads... no
    checking for PTHREAD_PRIO_INHERIT... yes
    checking for gcc option to support OpenMP... -fopenmp
    checking for pthread_join using gcc -pthread ... yes
    checking whether gcc is Clang... (cached) no
    checking for joinable pthread attribute... (cached) PTHREAD_CREATE_JOINABLE
    checking whether more special flags are required for pthreads... (cached) no
    checking for PTHREAD_PRIO_INHERIT... (cached) yes
    checking whether we are using the Microsoft C compiler... no
    checking CL/cl.h usability... no
    checking CL/cl.h presence... no
    checking for CL/cl.h... no
    checking OpenCL/cl.h usability... no
    checking OpenCL/cl.h presence... no
    checking for OpenCL/cl.h... no
    checking windows.h usability... no
    checking windows.h presence... no
    checking for windows.h... no
    checking for OpenCL library... no
    checking for special C compiler options needed for large files... no
    checking for _FILE_OFFSET_BITS value needed for large files... no
    checking for _LARGEFILE_SOURCE value needed for large files... no
    checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
    checking the name lister (/usr/bin/nm -B) interface... BSD nm
    checking the maximum length of command line arguments... 1572864
    checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
    checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
    checking for /usr/bin/ld option to reload object files... -r
    checking for objdump... objdump
    checking how to recognize dependent libraries... pass_all
    checking for dlltool... no
    checking how to associate runtime and link libraries... printf %s\n
    checking for archiver @FILE support... @
    checking for strip... strip
    checking for ranlib... ranlib
    checking command to parse /usr/bin/nm -B output from gcc object... ok
    checking for sysroot... no
    checking for a working dd... /bin/dd
    checking how to truncate binary pipes... /bin/dd bs=4096 count=1
    checking for mt... mt
    checking if mt is a manifest tool... no
    checking for dlfcn.h... yes
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    checking if gcc PIC flag -fPIC -DPIC works... yes
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    checking for ld used by g++... /usr/bin/ld -m elf_x86_64
    checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
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    checking if g++ PIC flag -fPIC -DPIC works... yes
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    checking how to hardcode library paths into programs... immediate
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    checking size of float_t... 4
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    checking size of ssize_t... 8
    checking size of unsigned int*... 8
    checking for signed 8-bit type... signed char
    checking for unsigned 8-bit type... unsigned char
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    checking for unsigned maximum type... unsigned long
    checking for pointer difference type... unsigned long
    checking whether our compiler supports __func__... yes
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    checking types of arguments for select... int,fd_set *,struct timeval *
    checking return type of signal handlers... void
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    checking whether clock_gettime supports CLOCK_REALTIME... yes
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    checking whether g++ accepts -g... (cached) yes
    checking dependency style of g++... (cached) gcc3
    checking whether the compiler recognizes bool as a built-in type... yes
    checking whether the compiler implements namespaces... yes
    checking if g++ supports namespace std... yes
    checking whether the compiler supports ISO C++ standard library... yes
    checking for g++ option to support OpenMP... -fopenmp
    checking whether C++ compiler is sufficient for Magick++... yes
    checking for X11 configure files...
    checking for GOMP_parallel_start in -lgomp... yes
    -------------------------------------------------------------
    checking for BZLIB...
    checking bzlib.h usability... no
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    checking for X... libraries , headers
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    checking for IceConnectionNumber in -lICE... yes
    -------------------------------------------------------------
    checking for X11...
    checking for shmctl... yes
    checking for XShmAttach in -lXext... yes
    checking for XShapeCombineMask in -lXext... yes
    checking for XtSetEventDispatcher in -lXt... yes
    -------------------------------------------------------------
    checking for ZLIB... yes

    -------------------------------------------------------------
    checking for DPS...
    checking DPS/dpsXclient.h usability... no
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    checking if DPS package is complete... no
    -------------------------------------------------------------
    checking for fftw3... no

    -------------------------------------------------------------
    checking for FLIF...
    checking flif.h usability... no
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    -------------------------------------------------------------
    checking for FlashPIX...
    checking fpxlib.h usability... no
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    checking for FPX_OpenImageByFilename in -lfpx... no
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    -------------------------------------------------------------
    checking for ddjvuapi... no

    -------------------------------------------------------------
    checking for FONTCONFIG... yes

    -------------------------------------------------------------
    checking for FREETYPE... yes

    -------------------------------------------------------------
    checking for RAQM... no

    -------------------------------------------------------------
    checking for GVC... no

    -------------------------------------------------------------
    checking for HEIF... no

    -------------------------------------------------------------
    checking for JBIG...
    checking jbig.h usability... yes
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    checking if JBIG package is complete... yes
    -------------------------------------------------------------
    checking for JPEG...
    checking jconfig.h usability... yes
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    checking jerror.h usability... yes
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    checking jmorecfg.h usability... yes
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    checking for jpeg_read_header in -ljpeg... yes
    checking for JPEG library is version 6b or later... yes
    checking if JPEG package is complete... yes
    -------------------------------------------------------------
    checking for LCMS2... no

    -------------------------------------------------------------
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    -------------------------------------------------------------
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    -------------------------------------------------------------
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    -------------------------------------------------------------
    checking for OPENEXR... no

    -------------------------------------------------------------
    checking for PANGO... yes

    checking for PANGO... yes

    -------------------------------------------------------------
    checking for PNG... yes

    -------------------------------------------------------------
    checking for RAW_R... no

    -------------------------------------------------------------
    checking for TIFF...
    checking tiff.h usability... yes
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    checking tiffio.h usability... yes
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    checking for TIFFSwabArrayOfTriples... yes
    -------------------------------------------------------------
    checking for WEBP... no
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    checking for WMF support ...
    checking for libwmf/ipa.h... no
    checking if WMF package is complete ... no
    -------------------------------------------------------------
    checking for XML... yes

    -------------------------------------------------------------
    checking for ImageMagick delegate programs...
    checking for bpgdec... bpgdec
    checking for bpgenc... bpgenc
    checking for blender... blender
    checking for xdg-open... /usr/bin/xdg-open
    checking for ufraw-batch... ufraw-batch
    checking for soffice... /usr/bin/soffice
    checking for dvips... /usr/bin/dvips
    checking for magick... magick
    checking for magick... magick
    checking for xterm... /usr/bin/xterm
    checking for dot... /usr/bin/dot
    checking for hp2xx... hp2xx
    checking for html2ps... html2ps
    checking for ilbmtoppm... /usr/bin/ilbmtoppm
    checking for ppmtoilbm... /usr/bin/ppmtoilbm
    checking for JxrDecApp... JxrDecApp
    checking for JxrEncApp... JxrEncApp
    checking for lepton... lepton
    checking for lp... /usr/bin/lp
    checking for lpr... /usr/bin/lpr
    checking for gimp... /usr/bin/gimp
    checking for magick... magick
    checking for avconv... avconv
    checking for ffmpeg... (cached) avconv
    checking for avconv... avconv
    checking for ffmpeg... (cached) avconv
    checking for mrsidgeodecode... mrsidgeodecode
    checking for mv... /bin/mv
    checking for pcl6... pcl6
    checking for gsx... no
    checking for gsc... no
    checking for gs... /usr/bin/gs
    checking for rm... /bin/rm
    checking for rsvg-convert... rsvg-convert
    checking for inkscape... inkscape
    checking for uniconvertor... uniconvertor
    checking for dwebp... dwebp
    checking for cwebp... cwebp
    checking for curl... /usr/bin/curl
    checking for gxps... gxps
    checking for Apple fonts directory... not found!
    checking for Dejavu fonts directory... not found!
    checking for Ghostscript fonts directory... /usr/share/fonts/type1/gsfonts/
    checking for URW-base35 fonts directory... not found!
    checking for Windows fonts directory... not found!
    checking for gnutar... no
    checking for gtar... no
    checking for tar... tar
    checking for perl... perl
    checking for rpmbuild... no
    checking for rpm... no
    checking for 7za... 7za
    checking for zip... zip
    -------------------------------------------------------------
    checking for Ghostscript...
    checking for Ghostscript version... 9.18
    checking for gs color device... pnmraw
    checking for gs alpha device... pngalpha
    checking for gs CMYK device... pamcmyk32
    checking for gs mono device... pbmraw
    checking for gs PDF writing device... pdfwrite
    checking for gs PS writing device... ps2write
    checking for gs EPS writing device... eps2write
    -------------------------------------------------------------
    Update ImageMagick configuration
    checking that generated files are newer than configure... done
    checking that generated files are newer than configure... done
    configure: creating ./config.status
    config.status: creating common.shi
    config.status: creating config/configure.xml
    config.status: creating config/delegates.xml
    config.status: creating config/ImageMagick.rdf
    config.status: creating config/MagickCore.dox
    config.status: creating config/MagickWand.dox
    config.status: creating config/Magick++.dox
    config.status: creating config/type-apple.xml
    config.status: creating config/type-dejavu.xml
    config.status: creating config/type-ghostscript.xml
    config.status: creating config/type-urw-base35.xml
    config.status: creating config/type-windows.xml
    config.status: creating config/type.xml
    config.status: creating ImageMagick.spec
    config.status: creating Magick++/bin/Magick++-config
    config.status: creating MagickCore/ImageMagick.pc
    config.status: creating Magick++/lib/Magick++.pc
    config.status: creating MagickCore/MagickCore-config
    config.status: creating MagickCore/MagickCore.pc
    config.status: creating MagickCore/version.h
    config.status: creating Makefile
    config.status: creating magick.sh
    config.status: creating PerlMagick/check.sh
    config.status: creating PerlMagick/default/Magick.pm
    config.status: creating PerlMagick/Makefile.PL
    config.status: creating PerlMagick/default/Makefile.PL
    config.status: creating PerlMagick/quantum/Makefile.PL
    config.status: creating PerlMagick/quantum/quantum.pm
    config.status: creating PerlMagick/quantum/quantum.xs
    config.status: creating PerlMagick/quantum/typemap
    config.status: creating utilities/animate.1
    config.status: creating utilities/compare.1
    config.status: creating utilities/composite.1
    config.status: creating utilities/conjure.1
    config.status: creating utilities/convert.1
    config.status: creating utilities/display.1
    config.status: creating utilities/identify.1
    config.status: creating utilities/ImageMagick.1
    config.status: creating utilities/import.1
    config.status: creating utilities/magick.1
    config.status: creating utilities/magick-script.1
    config.status: creating utilities/mogrify.1
    config.status: creating utilities/montage.1
    config.status: creating utilities/stream.1
    config.status: creating MagickWand/MagickWand-config
    config.status: creating MagickWand/MagickWand.pc
    config.status: creating config/config.h
    config.status: executing MagickCore/magick-baseconfig.h commands
    config.status: creating MagickCore/magick-baseconfig.h - prefix MAGICKCORE for config/config.h defines
    config.status: executing depfiles commands
    config.status: executing libtool commands
    config.status: executing default commands
    config.status: executing magick.sh.in commands
    config.status: executing MagickCore-config.in commands
    config.status: executing MagickWand-config.in commands
    config.status: executing Magick++-config.in commands
    config.status: executing PerlMagick/check.sh.in commands
    configure:
    ==============================================================================
    ImageMagick is configured as follows. Please verify that this configuration
    matches your expectations.

    Host system type: x86_64-pc-linux-gnu
    Build system type: x86_64-pc-linux-gnu

    Option Value
    ------------------------------------------------------------------------------
    Shared libraries --enable-shared=yes yes
    Static libraries --enable-static=yes yes
    Build utilities --with-utilities=yes yes

     

    /usr/bin/install -c -m 644 ./www/api/MagickCore/tab_l.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/tab_r.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/tabs.css /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/threshold_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/threshold_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/threshold_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/timer_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/timer_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/timer_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/token_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/token_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/token_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/transform_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/transform_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
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    /usr/bin/install -c -m 644 ./www/api/MagickCore/tree.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
    /usr/bin/install -c -m 644 ./www/api/MagickCore/type_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
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    /usr/bin/install -c -m 644 ./www/api/MagickCore/utility_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
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    /usr/bin/install -c -m 644 ./www/api/MagickCore/version_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
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    /usr/bin/install -c -m 644 ./www/api/MagickCore/vms_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
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    /usr/bin/install -c -m 644 ./www/api/MagickCore/widget_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
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    /usr/bin/install -c -m 644 ./www/api/MagickCore/xml-tree_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
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    mkdir -p -- /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
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    /usr/bin/install -c -m 644 ./www/api/MagickWand/convert_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
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    /usr/bin/install -c -m 644 ./www/api/MagickWand/dirs.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
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    /usr/bin/install -c -m 644 ./www/api/MagickWand/identify_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
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    /usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand-private_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand-private_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/stream_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/stream_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/stream_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/struct__CompositeOptions.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/struct__DrawingWand.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/struct__DrawVTable.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/struct__MagickWand.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/struct__PixelIterator.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/struct__PixelWand.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/studio_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/studio_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/tab_b.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/tab_l.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/tab_r.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/tabs.css /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/tree.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/wand_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /usr/bin/install -c -m 644 ./www/api/MagickWand/wandtest_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
    /bin/mkdir -p '/usr/local/share/doc/ImageMagick-7'
    /usr/bin/install -c -m 644 LICENSE ChangeLog NEWS.txt '/usr/local/share/doc/ImageMagick-7'
    /bin/mkdir -p '/usr/local/include/ImageMagick-7/Magick++'
    /usr/bin/install -c -m 644 Magick++/lib/Magick++/Blob.h Magick++/lib/Magick++/CoderInfo.h Magick++/lib/Magick++/Color.h Magick++/lib/Magick++/Drawable.h Magick++/lib/Magick++/Exception.h Magick++/lib/Magick++/Functions.h Magick++/lib/Magick++/Geometry.h Magick++/lib/Magick++/Image.h Magick++/lib/Magick++/Include.h Magick++/lib/Magick++/Montage.h Magick++/lib/Magick++/Pixels.h Magick++/lib/Magick++/ResourceLimits.h Magick++/lib/Magick++/SecurityPolicy.h Magick++/lib/Magick++/Statistic.h Magick++/lib/Magick++/STL.h Magick++/lib/Magick++/TypeMetric.h '/usr/local/include/ImageMagick-7/Magick++'
    /bin/mkdir -p '/usr/local/include/ImageMagick-7'
    /usr/bin/install -c -m 644 Magick++/lib/Magick++.h '/usr/local/include/ImageMagick-7'
    /bin/mkdir -p '/usr/local/share/man/man1'
    /usr/bin/install -c -m 644 MagickCore/MagickCore-config.1 MagickWand/MagickWand-config.1 Magick++/bin/Magick++-config.1 utilities/ImageMagick.1 utilities/animate.1 utilities/compare.1 utilities/composite.1 utilities/conjure.1 utilities/convert.1 utilities/display.1 utilities/identify.1 utilities/import.1 utilities/magick.1 utilities/magick-script.1 utilities/mogrify.1 utilities/montage.1 utilities/stream.1 '/usr/local/share/man/man1'
    /bin/mkdir -p '/usr/local/lib/pkgconfig'
    /usr/bin/install -c -m 644 MagickCore/ImageMagick.pc MagickCore/MagickCore.pc MagickCore/ImageMagick-7.Q16HDRI.pc MagickCore/MagickCore-7.Q16HDRI.pc MagickWand/MagickWand.pc MagickWand/MagickWand-7.Q16HDRI.pc Magick++/lib/Magick++.pc Magick++/lib/Magick++-7.Q16HDRI.pc '/usr/local/lib/pkgconfig'
    make[2]: Leaving directory '/home/jitendra/Downloads/ImageMagick'
    make[1]: Leaving directory '/home/jitendra/Downloads/ImageMagick'
    jitendra@jitendra-UNLOCK-INSTALL[ImageMagick] []

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/39726/jackalope-a-swift-versatile-phylogenomic-and-high-throughput-sequencing-simulator Fri, 26 Jul 2019 00:58:12 -0500 https://bioinformaticsonline.com/bookmarks/view/39726/jackalope-a-swift-versatile-phylogenomic-and-high-throughput-sequencing-simulator <![CDATA[jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator]]> jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. All outputs can be written to standard file formats.

    A swift, versatile phylogenomic and high-throughput sequencing simulator https://jackalope.lucasnell.com

    Address of the bookmark: https://github.com/lucasnell/jackalope

    ]]>     Abhimanyu Singh     https://bioinformaticsonline.com/bookmarks/view/26380/hicdat Fri, 12 Feb 2016 05:23:44 -0600 https://bioinformaticsonline.com/bookmarks/view/26380/hicdat <![CDATA[HiCdat]]> HiCdat: a fast and easy-to-use Hi-C data analysis tool

    HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic features, and on comparative studies. It uses simple input and output formats and can therefore easily be integrated into existing workflows or combined with alternative tools.

    More at http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0678-x

    Address of the bookmark: https://github.com/MWSchmid/HiCdat

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/28200/machine-learning Fri, 01 Jul 2016 12:57:12 -0500 https://bioinformaticsonline.com/bookmarks/view/28200/machine-learning <![CDATA[Machine Learning !!!]]> In machine learning, computers apply statistical learning techniques to automatically identify patterns in data. These techniques can be used to make highly accurate predictions.

    Keep scrolling. Using a data set about homes, we will create a machine learning model to distinguish homes in New York from homes in San Francisco.

    Address of the bookmark: http://www.r2d3.us/visual-intro-to-machine-learning-part-1/

    ]]>     Gudiya Pal