BIRCHv3.60
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Contents |
Installation
- DONE
May need to add a note to the pre-install instructions that on Fedora/Red Hat we need to install the full JDK using
sudo dnf install java-1.8.0-openjdk
as described in [1].
switch from newuser to newuser.py
Make a symbolic link from newuser to newuser.py. The main issue is getting
newuser.py to find its dependencies, especially createluancher and vncsetup.
Python3 Compliance
Test for Python3 compliance of applications run by BioLegato, using Fedora31 VM as test platform.
fedora31 | peacock | |
---|---|---|
birch | + | + |
birchadmin | + | + |
bldna | + | + |
blncbi | + | + |
blnalign | + | + |
blnfetch | + | + |
blpalign | + | + |
blprotein | + | + |
blpfetch | + | + |
blreads | + | + |
bltable | + | + |
bltree | + | + |
blmarker | + | + |
birch
- Caveat: sequin.py is now Python3 compliant, but Fedora31 is missing one of the libraries needed to run sequin. The last release of Sequin was 15.50 in Jan. 2019. However, NCBI says that Sequin is being phased out. Should we remove Sequin from BIRCH?
BIRCH
- In BioLegato 1.0.4
General solution to setting max. number of CPUs in PCD menus. It is worth looking into whether BioLegato could be modified to do a substitution for environment variables in var items. MATE Tutorial - Mate is such a great environment, we should create a MATE tutorial for setting up your desktop.- How to disable automaximization of windows:
System --> Preferences --> Look and Feel --> Mate Tweak --> Windows --> Window Behavior : Check "Do not auto-maximize new windows."
- How to disable automaximization of windows:
BLAST+
- BLAST version 5 databases:
Updated admin/Settings.default/BLASTDB.list to reflect changes in available databases compared to v4.- Technical documentation for blastdbkit needs to be updated to reflect new databases
- blastdbkit.py needs to be modified for the special cases of human_genome and mouse_genome. These are not supported as of yet.
Adopt BL_CORES_MAX and BL_CORES_DEFAULT to all BLAST and FASTA .blmenus files. These variables need to be set in bldna and blprotein.update to latest version 2.10.0+rewrite Database search tutorial to user BLAST rather than FASTA
FASTA
Upgraded to v36.3.8h</strike
<strike>New wrapper script blfastaout.py,converts tabular output to a form compatible with blnfetch, blpfetch
blncbi
fails to delete small .tmp files created during Entrez searches
blnfetch, blpfetch
add File --> export to spreadsheet
blreads
Reads --> Seqkit sample: wrap in a script that reminds the user to run guesspairs.py so that paired files are grouped before generating sample reads.