Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add gfaviz #52752

Open
wants to merge 7 commits into
base: master
Choose a base branch
from
Open

Add gfaviz #52752

Show file tree
Hide file tree
Changes from 5 commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
a80fa95
Add gfaviz
pbordron Dec 11, 2024
caaf8f8
fix run_exports
pbordron Dec 11, 2024
c0e6309
fix linter
pbordron Dec 11, 2024
c5adc5c
pin qt-5 exactly
pbordron Dec 11, 2024
456a6bc
fix qmake g++ not found error
pbordron Dec 12, 2024
caaa93d
fix display export for test
pbordron Dec 12, 2024
bbe2ae7
revert test as attaching display fails
pbordron Dec 13, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 18 additions & 0 deletions recipes/gfaviz/build.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
#!/bin/bash

#qmake bugfix: qmake fails if there is no g++ executable available, even if QMAKE_CXX is explicitly set
ln -s $CXX $BUILD_PREFIX/bin/g++
export PATH=$BUILD_PREFIX/bin/:$PATH

qmake
make
mkdir -p "${PREFIX}/bin"

#if [ -z ${MACOSX_DEPLOYMENT_TARGET+x} ]; then

# Install part
if [ "$(uname)" = "Darwin" ]; then
cp "${SRC_DIR}/gfaviz.app/Contents/MacOS/gfaviz" "${PREFIX}/bin/" # [ osx ]
else
cp "${SRC_DIR}/gfaviz" "${PREFIX}/bin/" # [ linux ]
fi
46 changes: 46 additions & 0 deletions recipes/gfaviz/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
{% set name = "gfaviz" %}
{% set version="1.0.0" %}
{% set hash="4bc4327dd182812a9cfd53a39632bf41f461170e142df62ebbd0ba441239a6d4" %}

package:
name: {{ name|lower }}
version: {{ version }}

build:
number: 0
run_exports:
- {{ pin_subpackage(name, max_pin="x") }}

source:
url: https://github.com/ggonnella/gfaviz/archive/refs/tags/v{{ version }}.tar.gz
sha256: {{ hash }}

requirements:
build:
- {{ compiler('cxx') }}
- make
host:
- qt-main =5
- libgl-devel # [ linux ]
martin-g marked this conversation as resolved.
Show resolved Hide resolved
run:
- {{ pin_compatible('qt-main', max_pin='x.x.x') }}

test:
commands:
- which gfaviz
# - gfaviz --help
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
# - gfaviz --help
- DISPLAY=:0.0 gfaviz --help

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

thank for the clue

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Sure!
But now it fails to connect to it ...
I'll try to find other recipes that do something similar.
You can also remove this test and test the produced binary locally.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Yes, must be an headless ci. It was successful on my computer with bioconda-utils build --docker --mulled-test --git-range master.


about:
home: https://github.com/ggonnella/gfaviz
license: ISC
license_file: LICENSE.txt
summary: GfaViz is a graphical interactive tool for the visualization of sequence graphs in GFA format. It supports both the GFA1 and GFA2 formats.

extra:
container:
# needed for libGL
extended-base: true
identifiers:
- doi:10.1093/bioinformatics/bty1046
recipe-maintainers:
- pbordron
Loading