MediaWiki API result
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{
"compare": {
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"torevid": 2,
"*": "<tr><td colspan=\"2\" class=\"diff-lineno\" id=\"mw-diff-left-l1\" >Line 1:</td>\n<td colspan=\"2\" class=\"diff-lineno\">Line 1:</td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div><del class=\"diffchange diffchange-inline\"><strong>MediaWiki has been installed.</strong></del></div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">= BioLib: libraries for the Bio* languages =</ins></div></td></tr>\n<tr><td class='diff-marker'> </td><td class='diff-context'></td><td class='diff-marker'> </td><td class='diff-context'></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div><del class=\"diffchange diffchange-inline\">Consult the [//meta.wikimedia.org/wiki</del>/<del class=\"diffchange diffchange-inline\">Help</del>:<del class=\"diffchange diffchange-inline\">Contents User's Guide] for information on using the wiki software</del>.</div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">''BioLib'' brings together a set of opensource C</ins>/<ins class=\"diffchange diffchange-inline\">C++ libraries and makes them available to all Bio* languages</ins>: <ins class=\"diffchange diffchange-inline\">BioPerl,</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">BioRuby, BioPython, BioJAVA and Bioconductor</ins>.  </div></td></tr>\n<tr><td class='diff-marker'> </td><td class='diff-context'></td><td class='diff-marker'> </td><td class='diff-context'></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div>== <del class=\"diffchange diffchange-inline\">Getting started </del>==</div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">'''Currently supported languages: Perl, Python and Ruby (R and JAVA are planned)'''.</ins></div></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div>* [//www.<del class=\"diffchange diffchange-inline\">mediawiki</del>.org/<del class=\"diffchange diffchange-inline\">wiki</del>/<del class=\"diffchange diffchange-inline\">Special</del>:<del class=\"diffchange diffchange-inline\">MyLanguage</del>/<del class=\"diffchange diffchange-inline\">Manual:Configuration_settings Configuration settings list</del>]</div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div>* [//www.<del class=\"diffchange diffchange-inline\">mediawiki</del>.org/<del class=\"diffchange diffchange-inline\">wiki</del>/<del class=\"diffchange diffchange-inline\">Special</del>:<del class=\"diffchange diffchange-inline\">MyLanguage</del>/<del class=\"diffchange diffchange-inline\">Manual</del>:<del class=\"diffchange diffchange-inline\">FAQ MediaWiki FAQ</del>]</div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div>== <ins class=\"diffchange diffchange-inline\">MODULES </ins>==</div></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div>* [https://<del class=\"diffchange diffchange-inline\">lists</del>.<del class=\"diffchange diffchange-inline\">wikimedia</del>.org/<del class=\"diffchange diffchange-inline\">mailman</del>/<del class=\"diffchange diffchange-inline\">listinfo</del>/<del class=\"diffchange diffchange-inline\">mediawiki-announce MediaWiki release mailing list</del>]</div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div>* [//<del class=\"diffchange diffchange-inline\">www</del>.<del class=\"diffchange diffchange-inline\">mediawiki</del>.<del class=\"diffchange diffchange-inline\">org</del>/<del class=\"diffchange diffchange-inline\">wiki</del>/<del class=\"diffchange diffchange-inline\">Special</del>:<del class=\"diffchange diffchange-inline\">MyLanguage</del>/<del class=\"diffchange diffchange-inline\">Localisation#Translation_resources Localise MediaWiki </del>for <del class=\"diffchange diffchange-inline\">your language</del>]</div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">current BioLib modules:</ins></div></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div>* [//<del class=\"diffchange diffchange-inline\">www</del>.<del class=\"diffchange diffchange-inline\">mediawiki</del>.org/<del class=\"diffchange diffchange-inline\">wiki</del>/<del class=\"diffchange diffchange-inline\">Special</del>:<del class=\"diffchange diffchange-inline\">MyLanguage</del>/<del class=\"diffchange diffchange-inline\">Manual</del>:<del class=\"diffchange diffchange-inline\">Combating_spam Learn how </del>to <del class=\"diffchange diffchange-inline\">combat spam </del>on <del class=\"diffchange diffchange-inline\">your wiki</del>]</div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* [[BioLib Affymetrix]] reads Affymetrix microarray .CEL and .CDF formats</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* [[BioLib Staden io_lib]] reads/writes sequencer trace files, including SFF, ABI, SCF, ALF and PLN formats</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* [[BioLib R/qtl]] support with OO model for Ruby</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">and soon to be included BioLib modules:</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* [[BioliB SAMtools]] libraries for BAM/SAM format, next generation sequencing</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* [[BioliB Emboss]] the European molecular biology open software suite</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* [[BioLib Bio++]] libraries for sequence analysis, phylogenetics, molecular evolution and population genetics</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* [[BioLib libsequence]] library designed to aid writing applications for genomics and evolutionary genetics</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">If you have a requirement not listed here: please use the [[Biolib Poll]]!</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">== NEWS ==</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* Biolib is adding SAMtools [http://thebird.nl/biolib/Adding_BioLib_BAM_SAM_Support.html support] (September 2010)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div>* <ins class=\"diffchange diffchange-inline\">Biolib may get into the Google Summer of Code again with some cool project ideas, see the OBF project idea on accessing JAVA from Perl at </ins>[<ins class=\"diffchange diffchange-inline\">[GSoC2010]] and [https:</ins>//www.<ins class=\"diffchange diffchange-inline\">nescent</ins>.org/<ins class=\"diffchange diffchange-inline\">wg_phyloinformatics</ins>/<ins class=\"diffchange diffchange-inline\">Phyloinformatics_Summer_of_Code_2010#Mapping_the_BEAST_GPU_library_to_Perl_and_R_using_Biolib mapping BEAST at Nescent] (March 2010)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* We are heading for SWIG generated documentation, as described at [[Biolib_Documentation_1.0]] (February 2010)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* First [http</ins>:/<ins class=\"diffchange diffchange-inline\">/emboss.sourceforge.net/ EMBOSS] mappings for Ruby, Perl and Python - a write up on [[mapping EMBOSS]</ins>] <ins class=\"diffchange diffchange-inline\">(November 2009)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div>* <ins class=\"diffchange diffchange-inline\">Xin Shuai and Adam Smith have finalized mapping libsequence and Bio++ libraries to BioLib. See Xin's project [[User:David]] page and [http://gsoc-biolib-libsequence.blogspot.com/ blog], and Adam's project </ins>[<ins class=\"diffchange diffchange-inline\">https:</ins>//www.<ins class=\"diffchange diffchange-inline\">nescent</ins>.org/<ins class=\"diffchange diffchange-inline\">wg_phyloinformatics</ins>/<ins class=\"diffchange diffchange-inline\">PhyloSoC</ins>:<ins class=\"diffchange diffchange-inline\">Mapping_the_Bio%2B%2B_Phylogenetics_toolkit_to_R</ins>/<ins class=\"diffchange diffchange-inline\">BioConductor_and_BioJAVA_using_BioLib page] and [http</ins>:<ins class=\"diffchange diffchange-inline\">//gsoc-biopp.blogspot.com/ blog</ins>]<ins class=\"diffchange diffchange-inline\">.</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">== MILESTONES ==</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div>* <ins class=\"diffchange diffchange-inline\">BOSC Presentation ([http://thebird.nl/download/biolib-bosc2009.pdf slides] July 2009) </ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* Microsoft Windows support added with Cygwin (May 2009)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* BioLib is getting a boost from the Google Summer of Code initiative, thanks to </ins>[https://<ins class=\"diffchange diffchange-inline\">www</ins>.<ins class=\"diffchange diffchange-inline\">nescent</ins>.org/<ins class=\"diffchange diffchange-inline\">wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2009 Nescent] (April 2009)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* GNU Science Library (GSL) support is added to the new [[ASciLib]] (A Science Lib) project (April 2009)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* ''Python'' mappings provided for Affyio and Staden (March 2009)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* BioLib supports OSX; Affyio mapped to ''Perl'' (February 2009)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* ''Perl'' and ''Ruby'' mappings provided for the '''Staden [http://sourceforge.net/projects</ins>/<ins class=\"diffchange diffchange-inline\">staden</ins>/ <ins class=\"diffchange diffchange-inline\">io_lib</ins>] <ins class=\"diffchange diffchange-inline\">library''', for reading of trace files in many formats (January 2009)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div>* <ins class=\"diffchange diffchange-inline\">The source repository has moved to </ins>[<ins class=\"diffchange diffchange-inline\">http:/</ins>/<ins class=\"diffchange diffchange-inline\">github.com</ins>/<ins class=\"diffchange diffchange-inline\">pjotrp/biolib/ github]</ins>. <ins class=\"diffchange diffchange-inline\">The latest changelog is [http://github</ins>.<ins class=\"diffchange diffchange-inline\">com/pjotrp/biolib</ins>/<ins class=\"diffchange diffchange-inline\">commits</ins>/<ins class=\"diffchange diffchange-inline\">master here] (November 2008)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* ''BioRuby'' is the first to benefit from BioLib's Affy support. See the [http</ins>:/<ins class=\"diffchange diffchange-inline\">/github.com/pjotrp/bioruby/tree/master/lib/bio/db/microarray/affymetrix Ruby source code] on Github (September 2008)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* BioLib builds for ''Ruby'' on Linux - both Ruby gem and a [[NIX]] package (August 2008)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* '''Affyio library''' runs for ''Ruby'' reading Affymetrix cel and cdf info correctly - see also [[BioLib Affymetrix]] (June 2008)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* An '''example library''' gets built </ins>for <ins class=\"diffchange diffchange-inline\">''Python'', ''Ruby'' and ''Perl'' using SWIG and cmake 2.6 (June 2008)</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">see also the [[Road map</ins>]<ins class=\"diffchange diffchange-inline\">]. There is potential for other languages like JAVA, R and OCaml.</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">== INTRODUCTION ==</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">BioLib pools resources and provides the mechanisms for having one code</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">base for all important programming languages.</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">The primary mapping mechanism to the Bio</ins>* <ins class=\"diffchange diffchange-inline\">languages is [[SWIG]]. SWIG has</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">come a long way in the last years and maps to all modern high-level</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">languages. See also [[supported data types]] and [[BioLib_best_practises]] .</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">The primary objective of BioLib is compatibility between languages and</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">multi-platform support. The secondary objective of BioLib is</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">efficiency - both of CPU and RAM (why bother to write in C,</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">otherwise).  Think of BioLib as a repository, or kernel, for low-level processing and</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">analysis of biological data. BioLib was incepted at the </ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">Tokyo Biohackathon 2008.</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">For more information see the [[Road map]].</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">== DOCUMENTATION ==</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">The API of included BioLib modules can be found in the [http://thebird.nl/apidoc/biolib/index.html API Documentation]. This documentation is generated straight from the source code. Translating the API to the mapped Perl or Ruby methods is straightforward. One example is [http://thebird.nl/apidoc/biolib/index.html here], others are in the test files (for [http://github.com/pjotrp/biolib/tree/master/src/mappings/swig/perl/test Perl], [http://github.com/pjotrp/biolib/tree/master/src/mappings/swig/ruby/test Ruby] and</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">[http://github.com/pjotrp/biolib/tree/master/src/mappings/swig/python/test Python]).</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">== DOWNLOADING ==</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">For the latest version of ''BioLib'' see the latest </ins>[<ins class=\"diffchange diffchange-inline\">http:</ins>//<ins class=\"diffchange diffchange-inline\">github.com/pjotrp/biolib/tree/master%2Fdoc%2FRELEASE_NOTES.txt?raw=true RELEASE NOTES].</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">BioLib releases (tgz, tar.bz2 and zip) can be downloaded from:</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">http://bio3</ins>.<ins class=\"diffchange diffchange-inline\">biobeat</ins>.org/<ins class=\"diffchange diffchange-inline\">download/nix-biology</ins>/</div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">For the direct access to the latest source tree use</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* [http</ins>:/<ins class=\"diffchange diffchange-inline\">/github.com/pjotrp/biolib/tree/master Biolib on github]</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">* And clone the (master) repository with:</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">  git clone git://github.com/pjotrp/biolib.git</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">== INSTALLATION ==</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">Quick instructions : after downloading the source run</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">  cd biolib</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">  ./configure</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">  make</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">  make test</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">  make install</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">which, by default, creates the ''Perl'' bindings. Configuration parameters are</ins>:</div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">  ./configure --with-ruby</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">or</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">  ./configure --with-python</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div>to <ins class=\"diffchange diffchange-inline\">install a subset, for example Staden-io-lib for ''Ruby'' use</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">  ./configure --with-ruby --with-staden</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">For more information read the [http://github.com/pjotrp/biolib/tree/master/INSTALL INSTALL] file.</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">== REQUESTING MODULES ==</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">If you need a C/C++/FORTRAN/R module or library linked against one of the popular scripting languages, please make that known through the [[Biolib Poll]]. See also [[Interesting_libraries]].</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">== CONTRIBUTING ==</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">All developers writing low-level bioinformatics libraries are</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">encouraged to contribute. A write-up </ins>on <ins class=\"diffchange diffchange-inline\">what it took to map some of the EMBOSS functionality can</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">be found in [[Mapping EMBOSS]]. For a HOWTO read [[Add C Library]]. If you feel you have something that can be</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">shared by other developers sign up to the BioLib mailing list (see below).</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">Unit testing is a critical part of BioLib. Unit tests are conveniently</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">written in high-level languages.</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">The multiplatform build system is based on [[CMake]]. The source trees are</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">maintained with [http://git.or.cz/ git] distributed version control.</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">== MAILING LIST ==</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">Subscribe to the BioLib mailing list [http://lists.open-bio.org/mailman/listinfo/biolib-dev here</ins>]<ins class=\"diffchange diffchange-inline\">.</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">== PACKAGING ==</ins></div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div> </div></td></tr>\n<tr><td colspan=\"2\"> </td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">General support for major platforms is aimed for, including 32-bit and 64-bit Linux, OS X, *BSD, Solaris and Windows.</ins></div></td></tr>\n"
}
}