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.
- Change #!/usr/bin/env python lines in to explicitly call python3
$BIRCH/script$BIRCH/install-scripts
Change shell lines in .blmenus files to call .py scripts, but not explicitly set python interpreter on command line. Looks like all BLAST menus have this.- 3rd party programs
Spades - upgrade to latest versionHisat2
New platforms
Need to add new platforms for BIRCH_PLATFORM.
Choices:
macos-arm64linux-arm64 (do in version 4.0)
In order, these need to be changed in:
1. BioLegato
2. install-scripts
3. getbirch
4. birchdb
5. scripts
BioLegato
- Add citations and links to the BioLegato paper in BMC Bioinformatics.
- Facebook, YouTube
BioLegato About tabtutorials pageBIRCH About pageBioLegato Wiki on GitHub
Get latest BioLegato version onto Git
Phylogeny
uniqid.py - remove the BirchMod and Argument calls so that uniqid.py can act as a standalone script independent from BIRCH.
BLAST+
-
Modify blastdbkit.py with an option to choose among different download protocols. This is because the existing ftp library seems to be unreliable in places with slow or unreliable internet.- urllib.request (Note: wget is not available in earlier versions of Python eg. Python3.10, so wget is not a good choice for now.)
- urllib3 - available as of Python3.6.9, but apparently not in 3.6.8.im
- requests - also not available by default in Python3.10
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