Open sjackman opened 2 years ago
I can confirm above, in various forms using conda environment to try to fill holes in library files.
I can get Bandage console text output shown above with just bandage-0.9.0 --help
$ bandage-0.9.0 --help | head
____ _
| _ \ | |
| |_) | __ _ _ __ __| | __ _ __ _ ___
| _ < / _` | '_ \ / _` |/ _` |/ _` |/ _ \
| |_) | (_| | | | | (_| | (_| | (_| | __/
|____/ \__,_|_| |_|\__,_|\__,_|\__, |\___|
__/ |
|___/
Version: 0.9.0
However, when trying to export PNG with text labels it fails with same error shown above:
$ bandage-0.9.0 image contigs.gfa out.png --scope aroundnodes --nodes 1439390 --distance 3
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
It does generate PNG output without text.
However, I can't tell that the --blastrainbow
option is working. The colors look either like categorical colors, or as if the rainbow only had 12 slices. Also, maybe that's my sequence problem. :)
Would really love a non-Ubuntu linux build when you or someone can build one. :) Thanks much in advance. I tried to install dependencies, but it's too big a stretch in our environment. For me anyway.
@jmw86069 brew install brewsci/bio/bandage
on Linux will install Bandage version 0.8.1, but I imagine you're looking for version 0.9.0.
@sjackman Thanks for commenting! Yes I'm hoping for 0.9.0.
It looks like another fork has active development: asl/Bandage, including some new things they're scoping out. That said, they migrated to Qt6, and that looks like an even trickier build environment to set up, at least on systems convenient to me.
Alas, blastrainbow
was not the answer for me, not surprisingly. Different issue altogether.
Ultimately a reasonable workaround for me was to subset the graph, then use desktop Bandage-0.8.1 to review.
I think I can subset the full fastg/gfa to nodes that have BLAST hits, then add +n depth, then save subset GFA to open in this or another tool. (Tbh, I had to look up BLAST syntax again haha. It's been a while.)
I've seen a list of different GFA/GFA2 viewers and tools, but is there another option you use to subset and review an assembly graph? Main thing I wanted from Bandage was to BLAST as a proxy to label specific regions, but I can supply regions in other ways.
The various modes of the Bandage reduce
command line interface is super useful.
@jmw86069 @sjackman We are going to provide appimage for https://github.com/asl/Bandage binaries Note, however, Qt6 requires at least Ubuntu 20.04 LTS, so older systems might be tricky to support. Also, unfortunately it is not possible to include OpenGL libs into appimage as they are quite system-dependent :(
Bandage requires the shared libraries
libGL.so.1
,libfontconfig.so.1
, andlibfreetype.so.6
, which are not included in the AppDir. These libraries can be installed using Homebrew on Linux orapt-get
.Install
mesa
using Homebrew on Linux.Install
libgl1
usingapt-get
.Install
fontconfig
andfreetype
using Homebrew on Linux.Install
fontconfig
andfreetype
usingapt-get
.