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I compiled gingr on qt5 to take advantage of the hidpi scaling support. The menus and most of the dialogs scale as expected, however the fonts of the tree labels and location bar at the top remain tiny on a hidpi display. Is there any way to make the entire UI scale-factor aware on the linux platform?

Hello,

while testing gingr-1.3, built from source code: https://github.com/marbl/gingr/archive/v1.3.tar.gz

when one launch gingr and close the gingr's window without performing any action, gingr segfaut at exit

when on launch gingr, load a file eg: https://harvest.readthedocs.io/en/latest/_downloads/cddfc3923c8a7a6ab1b6df6758ba5a6b/parsnp.ggr, closing the window makes gingr exit normaly.

PS adding an "exit" entry to the menu may be a nice improvement.

regards

Eric

Add a view to display a gene similarity matrix, for viewing patterns of presence/absence and homology, for a set of g genes and G genomes.

Hi,
I've installed the executable version of gingr in an LXDE docker container and instead of menu text I'm getting solid black (or blue squares). Do you have any suggestions to rectify this?
Thanks,
Mark

Tree nodes are currently ordered as they were read from the original Newick file, except when changed by outgrouping or by midpoint rerooting. It would be good to provide options to sort the nodes based on various criteria, for example:

• Number of descendent leaves per child
• Branch length per child
• Deepest leaf distance per child

Nexus files could be parsed for trees, alignments, or pairs of both. Output is also a possibility.

I'm using Gingr (v1.3) to visualize SNPs and I found that certain VCF files are displayed incorrectly. This happens when the ref or alt columns in the VCF files are lowercase instead of uppercase. The VCF spec defines these fields to be case-insensitive.

What's expected:
Gingr should display variant bases below reference bases and emphasize variant positions. Load the attached test.vcf and ref.fa for an example.

What happens:
When the ref and alt VCF columns are lowercase, Gingr does not display variant bases and instead shows the reference base for all genomes. The entire column is emphasized instead of only the variant bases. Load the attached test-lower.vcf and ref.fa for an example.

test.vcf.txt
test-lower.vcf.txt
ref.fa.txt

Tree labels should be customizable, individually or by imported list. Ideally, there should be an interactive bulk labeling dialog that allows stripping of prefixes/suffixes, etc.

Hi,
I would like to run Gingr on Windows 10 platform. Before I try to build it from source codes, I am wondering if this has been done before and is there any build script for windows that you can share. Also, are there any constraints (such as the dependencies) that would prevent a successful build for Windows? Furthermore, if Windows is not a supported platform for Gingr, what's your suggestion to make it available to Windows users?
Thank you in advance!
Tianhong

My core SNP alignment files (aligned FASTA) are usually named with .aln or .afa extension but 'gingr' seems to be a bit controlling with file extensions it will allow with the File::Open dialogue box.

Any change you can add these extensions?

There should be an option to write snapshots as SVG or PDF, and there should be more control over what is displayed (e.g. no row coloring).

Hi.

I'm a microbiologist starting on bioinformatics. So... really, really naive in what concerns Linux.
I'm working with Ubuntu 12.04 and I have just installed harvest (following the instructions for pre-compiled version).
The installation was performed in /usr/local.
Normally, no error was given during install but when i try to run gingr the problems start.
Each time i get an error of this type:

gingr: XXXX : Gtk-CRITICAL: TA_gtk_widget_style_ref : assertion 'GTK_IS_WIDGET (widget)' failed
QNativeImage: Unable to attach to shared memory segment
X error : BadDrawable (invalid Pixmap or Window parameter) 9
Major opcode: 62
Resource_id 0x0

Where you read gingr: XXXX it is a 4 digit number that varies each time i call ./gingr.
And it blocks by computer (graphics) so I have to kill the process.

Has anyone had this problem before? Can you help me? I would really like to test gingr and parsnps as i'm working with a few hundreds of bacterial genomes.

Thank you in advance for your feedback.

best regards,
Patrícia

Hello

while testing gingr-1.3, built from source code: https://github.com/marbl/gingr/archive/v1.3.tar.gz

I have the following warning spitted out by libpng

packbuilder:~ > gingr 
libpng warning: iCCP: known incorrect sRGB profile

fix is quite easy, just use convert to remove the ICC profile for the following .png files

                html/img/logo_med.png \
                html/img/harvest.png \
                html/img/marbl.png

regards

Eric

When I try to import my "snps.mfa" which is my own core-SNP alignment file (no gaps, 20 taxa, ~10000 SNPs) it croaks with this message:

Qt has caught an exception thrown from an event handler. Throwing
exceptions from an event handler is not supported in Qt. You must
reimplement QApplication::notify() and catch all exceptions there.

terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_S_construct null not valid

My colleague suggests it is expecting some particular ID or DESC format?

It is currently difficult or impossible to select clades whose vertical bars are next to or on top of others in while zoomed out, and in some cases while zoomed in.

Possible solutions:

• mouse-over effect (fish-eye or pop-up)
• arbitrary horizontal zooming/scrolling
• explicit clade navigation commands

Input reference is a .gbff file from NCBI and the input sequences are 100 .fna files from NCBI. I do not experience any errors in running parsnp on the command line. Additionally, I checked to make sure that all of the strains were (reasonably) related and they all shared 97-100% identity. Further, I checked the annotated file for the regions missing and they are present in the .gbff file.

./bootstrap.sh
./configure
qmake gingr.pro
make

g++ -c -pipe -std=c++11 -include src/memcpyLink.h -D_GNU_SOURCE -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/mkspecs/default -I. -I/usr/local/include/QtCore -I/usr/local/include/QtGui -I/usr/local/include/QtXml -I/usr/local/include -I. -Isrc -I/usr/local/include -I/usr/local/include -I. -o MainWindow.o src/MainWindow.cpp
src/MainWindow.cpp:20:37: fatal error: QtConcurrent/QtConcurrent: No such file or directory
compilation terminated.
Makefile:769: recipe for target 'MainWindow.o' failed
make: *** [MainWindow.o] Error 1

ubuntu 16.04

qmake -v
QMake version 2.01a
Using Qt version 4.8.5 in /usr/local//lib

where is my error ?
Thank you for your help

It isn't clear to me how to zoom out after selecting a region to zoom. I'm using MacOSX, so maybe swipe_in/swipe_out not effective? Thanks.

i've downloaded Version '1.3' but when selecting it in the Finder and using 'Get Info' it doesn't show any Version-number at all. i guess the CFBundleVersion and CFBundleShortVersionString entries in your Info.plist file are missing.
all apps on macOS are supposed to contain valid version information.