BIRCHv3.50

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Contents

BIRCH

Upgrade to Python 2.7


Upgrade to Java 1.8

BioLegato 1.0.4 - recompiled using Java 1.8

  • Can flamingo and albacore be upgraded to Java 1.7?

other Java programs

birchdb/lbirchdb

The problem is that failure of birchdb to launch Xace or tace has been inconsistent. It works on some days, and not on others. It is as if something keeps getting set or unset.

Although error messages aren't consistent, here's one (on jupiter):

Gtk-WARNING **: Failed to load module "libgail.so": libgail.so: cannot open shared object file: No such file or directory
Gtk-WARNING **: Failed to load module "libatk-bridge.so": libatk-bridge.so: cannot open shared object file: No such file or directory

Other times, this script gives a Segmentation Fault error. Once again, the only place I've had this trouble is on CCL.

BioLegato v1.0.4

Need mechanism for BioLegato to run commands in the background

At present, there is no way for PCD shell commands to run jobs in the background. That is, the Java Virtual Machine cannot terminate until every shell command has terminated. Even if the command ends with an ampersand, it must terminate before the JVM will terminate. That is an annoyance when we want displayed output to persist even after a BioLegato job has terminated, and a potentially major problem if we want to launch long-running or resource-intensive jobs from BioLegato.

It's probably best to write a short demo program to experiment with different approaches.

Hints:

Links:

Solution: In BioLegato 1.0.3, CommandThread.java has been modified so that if a command line ends in '&', it will be run in the background.

Remaining issues:


blsort.py

BLHelper.py

getbirch


These changes can be put into operation without waiting for a new release, since they don't affect the stable release files.
The question is, how?

Test whether jkd is headless

dpkg -l | grep openjdk
ii  openjdk-8-jre-headless:amd64          8u171-b11-0ubuntu0.18.04.1            amd64        OpenJDK Java runtime, using Hotspot JIT (headless)

Solution: Document on GetBirch site that JDK MUST be full JDK, and not headless. If getbirch.jar won't run, install full JDK

Debian/Ubuntu:

sudo apt-get remove openjdk-8-jre-headless
sudo apt-get install openjdk-8-jre

Introducing blreads

bldna,blprotein

bltable

blncbi

BLAST/FASTA overhall

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