BIRCH Version 3.60

New in the current release:

• Python3 compliance - The install process and most scripts should now be completely Python3-compliant.  BIRCH now requires Python3.
  
• First time setup tutorial for MATE desktop
• NCBI BLAST+
• updated to version 2.10.0
• blastdbkit.py  now installs and manages local BLAST v5 databases.
• bldna, blprotein - updated to work with BLAST databases as reorganized in v5.
  
• updated BLAST and FASTA tutorials for v5 databases
  
• FASTA
• updated to v36.3.8h
• output to HTML and blnfetch, blpfetch
• blnfetch, blpfetch can now export to a spreadsheet eg. LibreOffice Calc
• WebLogo updated to v3.7. (Linux x86_64 only. Weblogo 3.7 requires Scipy libraries, which fail to compile on OSX. Therefore, OSX still uses the Python-only Weblogo 3.4.)
• OSX desktop launcher - Replaced older 32-bit launcher with 64-bit launcher
  

• Deleted old libraries in lib-linux-x86_64: jellyfish, fc4libs, gde.fonts, openwin. These were needed by applications that are no longer included in BIRCH.
• tacg
  

• Sequencing read pre-processing and quality control
  
• SeqKit -tasks and statistics on reads
• trim_galore/cutadapt - adapter trimming
• Trimmomatic - adaptor trimming
  
• Pollux - DNA read correction
  
• Rcorrector - RNA read correction
• fastq_pair - eliminate non-paired reads from paired-end files
  
• Genome assembly and annotation
• ABySS - Genome assembly
• SOAPdenovo2 - Genome assembly (Linux only)
  
• SPAdes 3.13.0 - Genome assembly
• Quast - Genome assembly quality report
  
• GFF Utilities (http://ccb.jhu.edu/software/stringtie/gff.shtml#gffcompare)
  
• NCBI tbl2asn updated to version 25.6.
• Transcriptome assembly and gene expression
• rnaspades - RNA transcript assembly
• SOAPdenovo-Trans - RNA transcript assembly (Linux only)
  
• Trinity - RNA transcript assembly (Linux only)
  
• transrate-1.0.3
• Hisat2 v 2.1.0 - map RNA reads to genome (supersedes TopHat)
  
• stringtie (supersedes cufflinks)
• ballgown (supersesdes cuffdiff) (R pkg)
• BioLegato v1.0.4
• overwrite implemented for Table canvas
• Value fields for Text and Number variables allow environment variable substitution.
  
• blnfetch, blpfetch can now retrieve sequences from local BLAST databases or FASTA files
  
• Utilities
• jellyfish
• salmon
• samtools v1.7 (needs documentation, testing)
• makelinks.sh - creates symbolic in current directory to files in a source directory
• pigz - parallel implementation of gzip/gunzip. Speeds up handling of compressed read files
• Other
  
• NCBI sequin  - will be phased out by NCBI. Not updated
  
• Artemis 17.0.1
• REBASE has been updated to release Feb. 26, 2019
  

• Bugzilla #1220 - blnalign, blpalign : Phylip programs fail for some proteins with YF. Fixes a very old bug that would rarely occur.
  
• Bugzilla #1218 - overwrite was not implemented for Table cavas.
• On Mac OSX, the default for BioLegato interfaces using the  table canvas (ie. blnbci, blnfetch, blpfetch, blmarker, bltable) had no borders around cells, which detracted from readability.
  

• Comparative Genomics
• Tutorial: Finding and retrieving complete eukaryotic genomes
• MAUVE - Multiple Genome Alignment viewer
  
• Tutorial: Comparing genomes using Mauve
• Last - programs for comparative genomics, including genomic dotplots
  
• Tutorial: Comparing genomes using dotplots
• Bltable - simple spreadsheet version of BioLegato for generic spreadsheet data.
• Tutorial: Finding and retrieving sequences from NCBI
• Tutorial: in-silico PCR of genes using NCBI Primer-BLAST
• bldna,blprotein - View sequence now defaults to GenBank format.
• blncbi - PROTFETCH now defaults to retrieve sequences to blprotein, rather than text editor.
  
• blastdbkit.py - better recovery when downloading a BLAST database fails.
  

• Bugzilla #1213 - human and mouse genomic_transcript not deleted by birchadmin- These GenBank divisions were not deleted by blastdbkit.py --delete. Another bug was fixed which prevented email notifications from being sent when blastdbkit.py completed.
• Bugzilla #1214 - chooseviewer.py fails to open html files on MacOSX
• Bugzilla #1215 - bldna,blprotein - When launching DXHOM, PXHOM, TESTCODE, NUMSEQ with no data selected, programs would run in an infinite loop.
• Bugzilla #1216 - PXHOM can't work with lowercase amino acids
• Bugzilla #1217 - MacOSX - directory chooser fails to popup

• BLAST+
• upgraded to version 2.5.0
• hits now viewable in HTML, and in a detailed hit summary including in tabular form in blnfetch and blpfetch. The tabular output vastly improves the user's ability to sift through large numbers of hits based on many sorts of output criteria.
  
• BioPython has been upgraded to v 1.68. In particular, this release of BioPython supports the NCBI shift to using HTTPS for web services, rather than HTTP.
  
• FASTQC - Graphical Quality Control Tool for assessing quality of NGS sequencing reads.
  
• Compliance with the phase out of GI numbers from NCBI databases:
• blncbi now retrieves document summaries with Accession numbers, not GI numbers
• Output from BLAST and FASTA now parses only Accession numbers into separate lists. GI numbers are ignored. These programs should still be backward compatible with NCBI old database files that include GI numbers.
  
• delgi.py - Remove GI numbers from GenBank flatfiles, in compliance with the NCBI phase out of GI numbers. The purpose of this script is to create GenBank flatfiles conforming to the new format, as test files for ensuring that software works with these format changes.
• BioLegato 1.0.3
• BioLegato can now run any process in the background. This makes it possible to launch long-running jobs, close BioLegato, logout, and still have the job running until complete. In PCD .blmenus files, the shell command should take the form:
  shell    "(command)&"
  Examples can be found in .blmenu files. Tasks such as database searches and database file installation have been updated to take advantage of this feature. 
• dotter - DNA and protein dotplots. Supports GFF files for genome features. (Linux only).
  
• blsort.py - now supports floating point numbers, in addition to integers and strings.
• birchprops - New tool for managing properties of your BIRCH installation. The current version has only one option, to set URLs that will make the documentation for your local BIRCH documentation readable on the Web. This will only work if your machine is set up as a web server.
• bldna, blprotein - Added Fasta to list of formats saved using Save Selection As
• NCBI Sequin updated to v15.10
  

• Bugzilla #1212 - Getbirch hangs when decompressing archive files during an install/update.
  
• BioLegato - output to GenBank file inserts an extra blank line before ORIGIN line.
• Bugzilla #1209 - Local URLs for documentation not preserved in update.
  

• blastdbkit is a Python script that makes it easy to install and maintain your own copies of NCBI BLAST databases, so that you can search databases using either the BLAST or FASTA programs.
  Features:
  
• can be run at the command line, or in a point and click interface through birchadmin
• functions: Add, Update, Delete
• generates spreadsheets showing disk usage of local databases, and estimates of disk space needed for files databases to be downloaded
  
• email notification when downloads and installs are complete
• for quicker downloads, choose the FTP mirror closest to you
  
• all local databases can be searched using either BLAST or FASTA through the BioLegato interface or the command line
• Standalone BLAST+ updated to version 2.3.0.
• blncbi - New search term to limit searches to a specific molecule type eg. genomic, mRNA, guide RNA, lncRNA etc.
• BIRCH News - This page contains information on the latest features, brief How-To's, short articles on useful BIRCH features, and announcements of new releases. It is linked in the Documentation section on the BIRCH home page.
  

• blncbi - Import from CSV: incorrectly used comma, rather than TAB, as field separator for TSV files.

• Jalview has been upgraded to version 2.9.0b2.
  
• seqfetch.py, blnfetch, blpfetch - now can retrieve sequences from NCBI using ACCESSION numbers or GI numbers. The previous version could only retrieve by GI number. However, NCBI is in the process of phasing out GI numbers, so future development will focus on retrieval by ACCESSION.
  
• bldna,blprotein, blnalign,blpalign - view sequences and annotations in a text editor, using variety of formats. This is especially useful for pasting sequences into web applications.
• MAAFT- Multiple sequence alignment by Fast Fourier Transformations.
  

• The environment variables BLBIRCH_HELP_DIR, BLDNA_HELP_DIR etc. are obsolete, and have been removed from admin/profile.source and admin/cshrc.source.

• Artemis - The Artemis sequence viewer/annotator has been updated to version 16.0.0. It is now  possible to retrieve sequences from NCBI directly to Artemis, and to export sequences from bldna to Artemis. 
• First time setup documentation has been added for the MacOSX desktop.
• Automated customization for settings and Helper Applications. This release introduces a Preferences menu to birchadmin, that lets the user choose Helper Applications for viewing output in different file formats (eg. HTML, PDF, text, graphics). chooseviewer.py determines the type of file and launches the appropriate application.
  
• The BIRCH update/install wizard, getbirch, can now be launched from birchadmin.
• Substantial updating of documentation for BIRCH system administration.
  
• Some BIRCH environment variables that goven how BIRCH behaves can be set in the BIRCH Administration Tool (birchadmin). These variables are no longer set in $BIRCH/local/admin. If you are upgrading from BIRCH 3.0 or earlier, they can be deleted from local.profile.source and local.cshrc.source.
  These include:
  
  •  all GDE variables (eg. GDE_TEXTEDIT, GDE_PDF_VIEWER etc.)
    
  •  BIRCH_TMP
  •  BIRCH_LOGGING
  •  BIRCHJAVACMD
  •  BIRCH_NETSCAPE
  •  BROWSER_OPENURL
  •  lines setting the shell prompt

• Note: Weblogo requires the Python numpy library, which is not distributed with BIRCH. Instructions for installing numpy can be found here.
  
• Bugzilla #1202 - update_local.py fails to copy files to $BIRCH/local
  

• New BioLegato interfaces for NCBI Entrez queries and retrieval
  The middleware for these BioLegato interfaces consists of two Python scripts,  ncbiquery.py and seqfetch.py that can also be used at the command line. These scripts utilize the BioPython Bio::Entrez API.
• blncbi: lets users construct Entrez queries to NCBI and returns results in spreadsheet form, for subsequent retrieval.
• blnfetch: retreives nucleotide sequences from remote BLAST or local FASTA searches.
• blpfetch: retrieves amino acid sequences from remote BLAST or local FASTA searches. 
• BioPython 1.65 is now distributed as part of BIRCH, in the $BIRCH/python directory.
• WebLogo 3.4 - Create sequence logos from multiple DNA or protein alignments
• BioLegato 1.0.2 -
  
  • Export Foreign Format (bldna,blprotein,blnalign,blpalign) - Now has an option to export to a text editor. This is very useful if you want to copy sequences from BioLegato to paste into a web form. All formats supported by READSEQ are available.
  • blnfetch, blpfetch - new BioLegato interfaces that use the NCBI Entrez utilities to retrieve DNA, RNA or amino acid sequences from NCBI.
  • bldna and blprotein will send GI or ACCESSION numbers from BLAST hits directly to blnfetch or blpfetch for easy retrieval of sequences.
  • bldna - GFETCH - retrieve sequences from NCBI using GI or ACCESSION  numbers.
  • PCD has a new type called "textarea" that creates a text box  in a menu. Any text can be pasted into the text box, such as lists of GID numbers or sequences.
  • pcdedit - graphical editor for PCD menus. Still considered an experimental program.
  • BioLego sequence canvas can split horizontally, allowing one to scroll horizontally through two parts of a DNA or protein alignment simultaneously. 
• As a milestone toward making BIRCH completely platform independent the install scripts have been entirely re-written in Python. The shell scripts in install-birch are no longer distributed, and are replaced by Python scripts in install-scripts.
  
• NCBI Sequin - Updated to Version 13.70 on linux-x86_64 and MacOSX. NCBI appears to no longer be supporting Solaris or 32-bit Linux. Consequently, the solaris-sparc, solaris-amd64 and linux-intel binaries have been updated to Version 13.05, the latest version for these platforms.
  

• Bluejay
• Seahawk
• generic_ncbi_data_fetcher.pl

• Bugzilla #1141 - In some installs, the code from htmldoc.py that generated web pages that indexed programs would fail, resulting in blank web pages.
• Linux: added new libXrender.so and libXfixes.so libraries to bin-linux-x86_64 for compatabilty of xace with new linux releases.
• Bugzilla #1182 - BIRCH installer now compares date of currently installed version to prevent installing an older version over a newer version.
• Bugzilla #1183 - Edit --> copy should use FASTA format. Solved by adding Export Foreign Format to send output to a text editor.
• Bugzilla #1184 - GetBirch failed to run update-local.sh. The latter has been replaced with a Python script, update-local.py, which is run by GetBirch.
• Bugzilla #1185 -Need more robust way to recover if BIRCH download fails. Several improvements so that BIRCH only needs a good $BIRCH/local directory for an update to be successful.
• Bugzilla #1186 - Does UNINSTALL-birch.py need to run nobirch.py? 
• Bugzilla #1188 - SaveAs ignores selection and saves all sequences.
• Bugzilla # 1190 - BioLegato failed to read GenBank entries containing the CONTIG keyword. Fixed, so that now BioLegato will create 0-length sequence when reading CONTIG entries. A more sophisticated fix would be to retrieve the complete CONTIG from NCBI, but because these are often in the hundreds of millions of nucleotides, for now we won't go that route.
• Bugzilla #1197 - temp files deleted before chooseviewer.py can open them  
• Bugzilla #1198 - BioLegato can't delete characters unless sequence is in a group 
• Bugzilla #1199 -  Cut and paste in a multiple alignment deletes gaps

• Reorganization of multiple sequence alignment tasks - Tasks for displaying and working with multiple sequence alignments have been moved from bldna  and blprotein into two new BioLegato interfaces: blnalign for aligned DNA or RNA sequences, and blpalign for aligned protein sequences. For example, if you run   TCOFFEE from blprotein to produce a multiple alignment, the output will be sent to blpalign. blpalign can be used to run tasks that only make sense  with aligned sequences, such as phylogenetic analysis or alignment display. By making BioLegato adhere more strictly to object-oriented organization,  it becomes more difficult to accidentally run tasks such as phylogeny using unaligned sequences as input.
  
  As part of this reorganization, mrtrans can now only be run from blpalign. This  makes sense, because it forces the user to already have a protein alignment before trying to run mrtrans.
  
• Local BIRCH web site now displays current release number and timestamp.
• BioLegato.0.7.9
• BioLegato can now Copy and Paste using the system clipboard. This makes it possible to paste seqences from documents, emails etc. into BioLegato, and to paste sequences from BioLegato into web programs.
• numerous bug fixes and performance enhancements including:
• ability to set the text in the BioLegato window header bar
• ability to specify order of items in a PCD menu
• fixes to table canvas selection
• fixes to PCD's platform specificity options
• import column headers from file in table canvas
• better ability to skip improperly constructed PCD menus
• the BIRCH Launcher and birchadmin tool now have a launcher for Release Notes.
• The BLAST+ programs from NCBI replace blastcl3 (netblast). New menus in bldna and blprotein expand the number of search parameters that can be set. 
• SHUFFLE - The option to manually set a random seed when running SHUFFLE has been eliminated from bldna and blprotein. Instead, the script that runs SHUFFLE generates a random seed. Previously if the user didn't set a random seed each time, the same random sequence was generated each time the program was run. There is no obvious advantage to setting a random seed manually, so it is best to just do it automatically to be sure it gets done. 
• Calculation of protein statistics such as molecular weight, pI and amino acid frequencies is done by a new program gstat.py, launched from blprotein.
• Archaeopteryx is a fully-featured program for drawing phylogenetic trees, and overlaying other sorts or data onto trees. Archaeopteryx is the successor to ATV. In future releases, Archaeopteryx will replace ATV. Currently, it can be launched from bltree.  

• NCBI blastcl3 (netblast)
•  prostat and dbstat have been replaced by gstat.py (see above)
  

• On a multi-user BIRCH system on MacOSX, if a user who is not the owner of BIRCH clicks on the BIRCH launcher icon, they get a  permission denied error. (Bugzilla #1178)
• A bug has been fixed in BACHREST, which prevented setting the minimum and maximum length of restriction sequences to search for. (Bugzilla #1174)

• Cytoscape v2.8.3 - Visualize biochemical pathways
• NCBI BLAST+ v2.2.26 - blastp,blastn, blastx, tblastn, tblastx, blast_formatter.

• TM4 MIDAS

• In this version of BIRCH, all BioLegato menus have been translated into a new menu language called BioPCD. BioPCD expands on the functionality of .GDEmenus, and this functionality will expand in future versions. The old .GDE menus are no longer used. During an upgrade from previous versions of BIRCH, your old GDE menus in $BIRCH/local will be translated into BioPCD. All future development of local menus should be done using BioPCD.
• The following environment variables were previously deprecated,and are now removed from $BIRCH/admin/cshrc.source and $BIRCH/admin/profile.source : $DATA, $data, $DB, $db.  In particular, it was discovered that then $DATA was set, it would prevent LibreOffice v3.3 and later from launching.  See bugzilla.redhat.com Bug #834800.
• NEW: birchadmin - This BioLegato tool performs administrative tasks for the BIRCH system. It can be launched from the BIRCH launcher. New  functions include: htmldoc.py, customdoc.py, lbirchdb. birchadmin can only be run when logged in as the BIRCH administrator.
• BIRCH launcher: The DNA, protein, and Multiple alignment menus have been merged into a single menu called "Sequence".
• When launching bldna, blprotein, blmarker or bltree from the BIRCH launcher, the user is prompted to choose a working folder. 
• BioLegato - tool tips and icons have been added to most menus in BioLegato
• BioLegato - it is now possible to set the title to appear at the top of a BioLegato window. 

• fixed a bug in the script that runs mrtrans that prevented mrtrans from running on some OSX systems.
• ribosome - In the previous release, the new version of ribosome was omitted from OSX and linux-intel binaries. The new version is now available on all platforms. (Bugzilla# 1167)
• The Phylip package has been upgraded to version 3.69.
• The BIRCH launcher now prompts for a working folder when started at the command line. This results in all programs launched from the launcher opening in the working directory, rather than the home directory.
• acedb - on some Mac and Linux systems, acedb failed to launch because of missing libraries. These libraries have been added to the current release. (Bugzilla #1156)
• bioLegato.0.7.7a:
• fixed a bug in bioLegatthat prevented canvas from appearing
• fixed a bug that prevented sliders in menus from having negative values (Bugzilla# 1160)
• fixed a bug that prevented bioLegatfrom reading some legacy .gde files. If the sequence contained newline characters, those were included in the sequence (Bugzilla# 1161)
• fixed a bug in which pseudo-GenBank files generated by GDE were not read
• fixed a bug which prevented the Documentation menu from being used. (Bugzilla# 1160)

version 2.8.6

• fixed critical bug in bioLegato 0.7.7 which prevented menus from displaying properly

version 2.8.5

• bioLegato has been upgraded to v0.7.7. This version introduces
    the new table canvas, which is used by blmarker.

• ribosome: new options for formating translated amino acid sequences

• The following programs have been removed do to obsolescence:

  •   GDE (gde, mgde, tgde) - superseded by bioLegato programs bldna, blprotein, blmarker, bltree

  •   clustalw, clustalx - these are superseded by TCOFFEE

  •   Translate - superseded by ribosome

version 2.8

• Getbirch - Getbirch is an automated install updater and installer,  that supersedes these functions in birchconfig. Birchconfig is still used for adding local custom documentation and for uninstalling.

• bioLegato has been reorganized into several new interfaces:

  • birch - launcher for all GUI programs in BIRCH

  • bldna - DNA/RNA sequence tasks

  • blprotein - protein tasks

  • blmarker - molecular markers

  • bltree - phylogenetic trees

• When upgrading from BIRCH 2.7 and earlier, local GDE menus items will be copied to corresponding directories in local/dat. It is important to do a manual check to see if menus have been added to the appropriate bioLegato interface.

• Visualization of data in bioLegato now includes a variety of character color themes for proteins, nucleic acids, markers and phylogenetic trees.

• During a new installation, birchhome.sh failed to change the userid of the BIRCH administrator in passwd.wrm, both for birchdb and lbirchdb. This prevented creation of a local birch database, meaning that documentation for locally-installed programs wouldn't appear in the database. This has been fixed.

• A major reorganization of Python scripts has been done. This addresses future compatibility with Python 3, as well as creating sets of reusable classes that will simplify future development.

• A number of the bioLegato scripts failed to clean up temporary files after execution was completed. These have been fixed.

• The Phylip programs drawgram and drawtree require the libXaw.so.7 library, which is not found in some Linux distributions. This library has been added.

• PostScript files on MacOSX. The utility script PStoPDFviewer.sh automatically runs ps2pdf to convert PostScript files to PDF. However, ps2pdf appears not  to be part of the standard OSX install. PStoPDFviewer has been modified to directly open files using 'open', which knows how to automatically convert PostScript files. This problem prevented viewing of output from drawtree and drawgram.

• Sequin has been upgraded to version 10.0.

• Bluejay has been upgraded to version 1.3.

• ACeDB is now considered a legacy application, and will be replaced with a different lightweight database system in a future release. This is partly because the code was compiled on a 32-bit Linux system in 2003 and is almost impossible to re-compile today. As a temporary fix, the scripts that launch xace or tace (birchdb, lbirchdb, l-gbirchdb and acedemo) have been upgraded to load 32-bit libraries included in lib-linux-intel or lib-linux-x86_64.

• GDE has been frozen as a legacy application, and will no longer undergo development. The program will still work with all GDE menu files as of BIRCH 2.7, but future changes will only affect the biolegato family of programs. IN THE NEXT MAJOR RELEASE, GDE WILL BE DELETED FROM THE BIRCH SYSTEM.