BIRCHv3.90

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Contents

Installation

  • Fedora seems to come with headless java as default. Oddly, if you type java -version the message gives no indication that it is headless.
    • Java does have a way to set the environment using System.environment to set headless to false.
    • /home/psgendb - Failure to install is often due to stale NSF handles, whose filenames are of the form ".nfs.....". These have to be removed by sysadmins. With v3.70 I tried the tactic of running an uninstall before installing the new version of BIRCH. The uninstall failed because of the stale nfs handles. However, I wasn't able to complete the install because getbirch tries to find the uninstall script through a symbolic link in public_html, which I had already deleted manually. Getbirch should be modified to get all files directly through the FTP site, and not have to go through /home/psgendb.
      IMPORTANT - Are the stale NFS handles coming from BIRCHDEV each and every time I run framework.csh? Better check this.
      Hmmmm... It seems that simply moving the directories containing the stale handles causes the handles to be deleted by the system, after awhile. Still, we may want to check for stale handles before updating BIRCH in /home/psgendb. Maybe makeframework.csh should exclude those as well.
  • We need to test to see if the existing launchers will work in KDE. If not, find out where the launchers go.

BIRCH

Python3 compliance

Need to test on a machine on which python-is-python3 has not been installed. Brassica is currently tasked for this function.

New platforms

Need to add new platforms for BIRCH_PLATFORM.

Choices:

In order, these need to be changed in:
1. BioLegato
2. install-scripts
3. getbirch
4. birchdb
5. scripts

BioLegato


Phylogeny

BLAST+

TESTING

The strategy is to get things working first on CCL, and then test them on other machines. These are done first so that we break things as soon as possible and find out what surprises are in store in various Linux or MacOS releases.

platform linux-x86_64 macos-arm64 osx-x86_64
program/pkg
BLAST+-2.14.0 native binaries not available
using osx-x86_64 binaries
kept back to 2.10.0 due to dyld symbol not found errors
ABySS
SOAPdenovo2 NA NA
Spades 3.15.4 native binaries not available
using osx-x86_64 binaries
Quast 5.2.0
salmon 1.10.1
osx-x86_64 binaries
jellyfish 2.3.0 code non-relocatable
kept back to jellyfish 2.2.10
code non-relocatable
kept back to jellyfish 2.2.10
Rcorrector
v 1.0.6
rnaspades 3.15.4
SOAPdenovo-Trans NA NA
Trinity 2.15.1 Too many Perl Modlue dependency/incompatability issued. Rolling back to 2.14.1 NA NA
Trinity 2.14.1 jellyfish "thread terminated abnormally". Occurred with Trinity's version of jellyfish as well as latest version of jellyfish. It is probably not worth supporting Trinity due to all the dependencies. NA NA
transrate 1.0.3
(no longer supported)
Hisat2

NA - not available on this platform

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