From 1220ede40b877b28d5d5b05be5a00c411f05eaad Mon Sep 17 00:00:00 2001 From: Chris Fields Date: Sat, 17 Dec 2016 13:02:52 -0600 Subject: [PATCH] deversion README, add Changes for updated release --- Changes | 26 +++++++++++++------------- README.md | 14 ++++++-------- 2 files changed, 19 insertions(+), 21 deletions(-) diff --git a/Changes b/Changes index c3b3a64..3906540 100644 --- a/Changes +++ b/Changes @@ -1,8 +1,10 @@ -$Id$ Revision history for bioperl-run modules -Full details of changes between all versions are available online at: -http://www.bioperl.org/wiki/Change_log +1.7.000 + +* Bio::Tools::Run::WrapperBase moved from bioperl core to bioperl-run +* Updaed Samtools wrapper, minimal support for samtools > v.1 added [cjfields] +* Minor updates to sync with BioPerl v. 1.7.x release series 1.6.901 @@ -32,7 +34,7 @@ http://www.bioperl.org/wiki/Change_log * [bug 2798] - patch to fix clustalw premature file unlinking error [Wei Zhou] 1.6.0 Release - + * All Pise and Pise-related modules and scripts have been moved to the new bioperl-pise repository. The Pise service is no longer available and has been replaced by Mobyle. They have been retained as one can still install a Pise @@ -42,7 +44,7 @@ http://www.bioperl.org/wiki/Change_log 1.5.2 Release in sync with bioperl core * Several wrappers updated for newer versions of the programs. - + 1.5.1 Release in sync with bioperl core o First major release in a while, so lots of things in this release @@ -60,7 +62,7 @@ http://www.bioperl.org/wiki/Change_log o Several wrappers updated for newer versions of the programs. TribeMCL, Genewise, RepeatMasker - + 1.2.2 Release update in sync with bioperl core @@ -136,7 +138,7 @@ http://www.bioperl.org/wiki/Change_log o Support for FootPrinter, Genewise, Hmmpfam, Primate, Prints, Profile, Promoterwise, Pseudowise, Seg, Signalp, Tmhmm,TribeMCL, Blat,DBA,Lagan,Sim4,Fasta,ProtML,Vista - + o Added support for PHYLIP apps: Consense, DrawGram, DrawTree, SeqBoot o Added INSTALL.PROGRAMS providing references to download the program binaries. @@ -149,21 +151,19 @@ http://www.bioperl.org/wiki/Change_log runnable wrapper modules. o Support for PAML codeml tested, aaml still waiting - + o Support for Molphy protml, nucml to come o Support for EMBOSS pkg - still need to move component from - bioperl-live Bio::Factory::EMBOSS to this package and + bioperl-live Bio::Factory::EMBOSS to this package and rename it Bio::Tools::Run::EMBOSSFactory or something equivalent. o Support for Clustalw, TCoffee, Local NCBI BLAST. - + o RepeatMasker, Genscan, Pseudowise, TribeMCL, Primate, Eponine. - + o Support for remote analysis through Pise and NCBI Web Blast queue. o Select PHYLIP apps: Neighbor, ProtDist, and ProtPars. - - diff --git a/README.md b/README.md index d1ae1aa..03b8664 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,8 @@ -# Description +# Description -This is bioperl-run version 1.6.x, a developer release. - -*bioperl-run* contain modules that provides a Perl interface to various -bioinformatics applications. This allows various applications to be -used with common BioPerl objects. +This is the home for *bioperl-run*, which contain modules that provides a Perl +interface to various bioinformatics applications. This allows various +applications to be used with common BioPerl objects. See the *Changes* file for more information about what is contained in here. @@ -13,10 +11,10 @@ here. See the accompanying *INSTALL* file for details on installing bioperl-run. - + # Feedback -Write down any problems or praise and send them to +Write down any problems or praise and send them to bioperl-l@bioperl.org. # Bugs -- 2.11.4.GIT