BIRCHv3.87
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Contents |
BioLegato 1.1.0
Include directive
DONE. see PCD_Include
Java 11
See if BioLegato can compile with Java 11, or Java 17. Are there any deprecated API calls that need to be changes?
blastdbkit.py
replace optparse with argparse
DONE.
create list files to be used with Include
DONE.
MAFFT
On BIRCH, MAFFT is v7.470. Need to upgrade MAFFT. DONE
The latest version is 7.490, 2021/Oct/30.
BUG!! Versions 7.463 – 7.486 had a serious bug in the FFT-NS-i option; unnecessarily much memory was requested and the calculation sometimes failed. This bug also affected the --auto option. Please use 7.487 or higher. (2021/Jul/25)
TESTING
The strategy is to get things working first on CCL, and then test them on cutting edge Linux distributions in virtual machines. These are done first so that we break things as soon as possible and find out what surprises are in store in new Linux releases.
| host | system | status |
| CCL - BIRCHDEV | RHEL7 | OK |
| brassica - Fedora35 VM | fedora35 | OK |
| brassica - Ubuntu22 VM | Ubuntu 22.0.4 LTS | nd |
| brassica | MATE Ubuntu 18.0.4 LTS | OK |
| peacock | MacOSX | OK |
| maui | Ubuntu MATE 20.0.4 LTS | OK |
| wotan | Scientific Linux 7 | OK |
| flamingo | Ubuntu MATE 18.0.4 LTS | OK |
| canola (rm 335) | Ubuntu MATE 20.04.2 LTS | OK |
| triticum | Ubuntu MATE 22.04 LTS | OK |
| CCL - psgendb | RHEL7 | OK |
