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Upgrade to Java 1.6

BioLegato 1.0.3 In build.xml, compile.version.vm has been changed to 1.6, meaning we now are compliant with Java 1.6. Even 1.6 is getting old. One word of caution - we have to be careful where we compile Java programs. If you compile it on a system that defaults to a newer Java, it won't work on older Java's. It would be good to move to Java 1.7, but we have to determine whether it is reasonable to conclude that the number of older systems still running 1.6 is negligible.

Making BIRCH documentation web-accessible

This can still be done using birchconfig, but for future releases it is best to retire this program. We should be able to incorporate this into Preferences --> Settings, by running a script. It might be possible to create a Java application from the existing birchconfig code.

BioLegato v1.0.3

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.



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

Remaining issues (for further work in a later release):

Remaining ones will be done in BIRCH 3.40.

NUMSEQ, BACHREST and PRIMER3 don't launch the text editor until after the calling Java VM has terminated ie. BioLegato. Why these three programs, and not, for example, TESTCODE or any of the others?


Compliance with NCBI phase-out of GI numbers

NCBI is phasing out sequence GIs - use Accession.Version instead!

GI numbers still need to be handled if they're there, but are not depended upon

Should be able to find BioLegato PCD files using GenBank format by using find command.

BLAST/FASTA scripts need to be able to handle the new format, in which BLAST output will presumably no longer contain GI numbers.

Compliance with NCBI switch from HTTP to HTTPS

See HTTPS at NCBI: Guidance for NCBI web API users

BLAST/FASTA overhall

*Is there an NCBI script of program that gets results back in something like ASN1, and then lets you generate as many different output formats from that report as you want?
-Yes: blast_formatter. See demo scripts and in BIRCHDEV/test/BLASTbenchmark/BIRCHbenchmark. With blast, write -outfmt 11 (XML), and then use blast_formatter to create as many reports as you wish.

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