BIRCH
3.90 Released
NEW
and Updated
Software
applications
and features:
- BioLegato version 1.1.2
- PCD files now support include directive
- About - Citation for BioLegato paper in BMC
Bioinformatics
- New Platform: macos-arm64
- Export to CSV/TSV no longer encloses cells in double
quotes
- NEW - MacOS-ARM64
(phase I) - This is the first release to support
macos-arm64, also known as Apple Silicon, M1, M2 or M3.
- arm64 native binaries are now included for the
following packages/programs
- cd-hit
- FASTA
- FSAP
- LAST
- MAFFT
- Phylip
- pollux
- primer3
- Rcorrector
- samtools
- seqkit
- Weighbor
- XYLEM
- All remaining x86_64 binaries currently run by
hardware emulation by rosetta2
- NCBI BLAST - updated to version 2.14.0+. Default for
protein searches is now blastp-fast, blastx-fast and
tblastx-fast. With this option, finding amino acid
sequences with >=50% identity is much faster.
- BLAST - substantial revision and updating of BLAST
tutorial
- FASTA - updated to version fasta36-36.3.8 (May 2023)
- LAST - updated to version 1512
- primer3 - updated to 2.4.0
- Seqkit - updated to version 2.4.0
- NEW - MaxAlign
- removes sequences from a multiple alignment that
result in excessive gaps
- jellyfish updated to version 2.3.0 (linux only)
- Quast updated to version 5.2.0
- Rcorrector updated to version 1.0.6
- SPAdes updated to version 3.15.4
- samtools updated to version 1.179
- salmon updated to version 1.10.1; transrate modified
to use salmon 1.10.1
DELETED
applications:
- FSAP (obsolete) - intrest
- XYLEM (obsolete) - findkey, xylem_identify, phyl2flat,
flat2phyl
End of Life Platforms
RHEL 7 - Red Hat Enterprise Linux and related
distributions will no longer be supported in future
releases of BIRCH. Subsequent releases will be developed
and tested on RHEL 8 or later.
Ubuntu 18 - Ubuntu LTS 18.0.4 LTS and related
distributions will no longer be supported in future
releases of BIRCH. Subsequent releases will be developed
and tested on Ubuntu 20.0.4 LTS or later.
Python2 - BIRCH no longer requires python2. All python
scripts now use python3.
Bug
Fixes
(See BIRCH
Bugzilla at
Bioinformatics.org:
http://www.bioinformatics.org/bugs/?group_id=543)
- getbirch.jar - For BIRCH installs over long distances,
downloads would sometimes time out. This has been fixed
by changing the download buffer size to 8192.
- On some systems, Python scripts must be called by
explicitly specifying 'python3', rather than 'python'.
Although this can be fixed by installing
python-is-python3, we are hardcoding 'python3' into
python calls as an ongoing process. This release fixes
some scripts, but others may still be present.
- For systems on which python 2 is not installed, the
'python' command will not be available. While installing
python-is-python3 can fix that, we have eliminated most
of these calls in the current release. The goal is that
it will not be necessary to install python-is-python3 in
a future release.
- Weblogo - on some systems EPS output contained
terminal messages, preventing files from being converted
to PDF for viewing. Fixed.
- Bugzilla
#1211 - BioLegato table canvas exported fields in
double quotes. This feature was originally for
compatability with earlier versions of Excell, but
caused problems when importing TSV files into BioLegato.
Modern spreadsheets can read CSV and TSV files, so
quoting is no longer used when exporting.
- pal2nal.py - pal2nal.py is a wrapper script for
running pal2nal.pl. If an amino acid sequence ended with
an 'X', pal2nal.pl would fail, complaining that the
protein didn't match the DNA sequence. pal2nal.py now
changes 'X' to gap ('-') to avoid this problem.
|
December 31, 2023
|
BIRCH 3.87 Released
- BioLegato PCD files now support include directive
- MAFFT - Updated to v 7.505
- Minor documentation updates
|
August 4, 2022
|
Version 3.86 (May 20,
2022)
NEW
and Updated
Software
applications
and features:
- In OSX, the desktop app to launch the BIRCH BioLegato
application is in $BIRCH/admin/launchers/birch.app.
Although BioLegato is a 64-bit Java application, the
launcher was an old one generated when apps were 32-bit.
Beginning with OSX Catalina, 32-bit apps will no longer
run. The BIRCH application was still able to
launch from the command line. This app has been
regenerated as a 64-bit launcher using Platypus on a
High Sierra Mac.
- Updated User Settings documentation with information
on NCBI transition to 3rd party authentication.
- NCBI database list has been updated to include the
following databases newly available for FTP download:
(env_nr, mito, pat_aa, refseq_select_prot)
- FASTA has been updated to version 36.3.8i.
- Jalview - updated to version 2.11.2.0.
- FastQC - updated to version 0.11.9
- Cytoscape - updated to version 3.9.0
- Mesquite - updated to version 3.70.
- trim_galore - updated to version 0.68
- cutadapt - updated to version 3.7.
- Trinity - updated to version 2.14.0
DELETED
applications:
- ArrayNorm - gives errors with most recent JavaVMs;
package is no longer supported.
Bug
Fixes
(See BIRCH
Bugzilla at
Bioinformatics.org:
http://www.bioinformatics.org/bugs/?group_id=543) |
May 20, 2022
|
Log4j2 vulnerability status
At present, it does not appear that any of the Java
programs distributed with BIRCH presents vulnerabilities
due to the log4j2
exploit. We have confidence in this assertion for
several reasons:
- Log4j2
applies only to Java applications
- A scan of
all Java applications, including source code and .jar
files was done to identify potentially vulnerable
applications.
- Some older
applications use versions of log4j that are not
susceptible to this exploit.
- None of
these applications acts as a web or peer-to-peer
server
- All BIRCH
applications run with user permissions only. None uses
admin permissions.
Out of an
abundance of caution, further investigation into this
potential problem are ongoing.This message will be updated
accordingly.
We will take this
opportunity to remind all BIRCH users that your best
defenses against potential security threats are to
- run system updates on a routine
basis
- back up your files offsite (eg.
to the cloud or network-attached storage)
- change your passwords frequently.
|
December 21, 2021
|
BIRCH 3.85 Released
- Web
documentation reorganized for easier navigation and
local customization at each BIRCH site.
|
Sept. 6, 2021
|
BIRCH 3.80 Released
- improvements
to BLAST search results
- improvements
and updates for multiple alignment and phylogeny
- numerous
updated software packages
- extensive
improvements to pre-processing and QC of sequencing
reads
https://youtu.be/8RqR1va-hYU"> |
July 5, 2021
|
BIRCH
3.70 Released
- improvements
and updates for multiple alignment and phylogeny
- personalized
user settings for BIRCH environment, including NCBI
Entrez API keys
- NCBI Entrez
keyword searches now support Neighbor and LinkOut
searches
|
July 22, 2020
|
BIRCH 3.60 Released
- First time setup tutorial for MATE desktop
- Python3 compliance
- Updates to BLAST, FASTA database searches
|
April 26, 2020
|
BIRCH 3.50 Released |
June 20, 2019
|
BIRCH 3.40 Released
|
May 2, 2017
|
Installing and
Searching Local BLAST Databases
|
May 19, 2016
|
BIRCH 3.20 Released |
May 19, 2016
|
BIRCH 3.15 Released
|
Jan. 6, 2016
|