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

Jump to bottom

Add ntsm recipe https://github.com/JustinChu/ntsm #52262

Merged
merged 12 commits into from
Nov 25, 2024
Merged

Add ntsm recipe https://github.com/JustinChu/ntsm #52262

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
12 commits
Select commit Hold shift + click to select a range
8b85cfa
Add ntsm recipe https://github.com/JustinChu/ntsm
JustinChu Nov 20, 2024
d8e5d8e
Fix linter issues with ntsm yaml recipe.
JustinChu Nov 22, 2024
10b3e5b
Merge branch 'master' into master
JustinChu Nov 22, 2024
c494b18
fix url
JustinChu Nov 22, 2024
5cf23a2
Merge branch 'master' of https://github.com/JustinChu/bioconda-recipes
JustinChu Nov 22, 2024
45071da
bump version to fix make portability issue
JustinChu Nov 23, 2024
b79f74d
update ntsm-1.2.0 sha256
JustinChu Nov 23, 2024
55b1168
Update build.sh
mencian Nov 25, 2024
cf0934b
Update meta.yaml
mencian Nov 25, 2024
6730092
Update meta.yaml
mencian Nov 25, 2024
090bb82
Update build.sh
mencian Nov 25, 2024
da1e7e0
add make back to run reqs
mencian Nov 25, 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
21 changes: 21 additions & 0 deletions recipes/ntsm/LICENSE
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
MIT License

Copyright (c) 2021 Justin Chu

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
18 changes: 18 additions & 0 deletions recipes/ntsm/build.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
#!/bin/bash -euo

set -xe

export CFLAGS="-I$PREFIX/include -O3"
export LDFLAGS="-L$PREFIX/lib"
export CPATH="${PREFIX}/include"
export CXXFLAGS="-I${PREFIX}/include -O3 -std=c++17"
export CPPFLAGS="-isystem/${PREFIX}/include"

./configure --prefix=${PREFIX} --disable-dependency-tracking --disable-silent-rules

make -j ${CPU_COUNT}
make install

mkdir -p ${PREFIX}/bin
cp -rf ntsm-scripts ntsmSiteGen ${PREFIX}/bin

50 changes: 50 additions & 0 deletions recipes/ntsm/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,50 @@
{% set version = "1.1.0" %}

package:
name: ntsm
version: {{ version }}

source:
url: https://github.com/JustinChu/ntsm/releases/download/{{ version }}/ntsm-{{ version }}.tar.gz
sha256: 85dc064249edc2836edf55c91f626d11bcb045e57bbdebff02fc4ff2bd9a7b53

build:
skip: true # [osx or win]
number: 0

requirements:
build:
- {{ compiler('cxx') }}
- llvm-openmp # [osx]
- make
host:
- zlib
- libgomp
run:
- llvm-openmp # [osx]
- zlib
- libgomp
- make
Copy link
Contributor

Choose a reason for hiding this comment

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

Do you need 'make' to run the app ?

Copy link
Contributor Author

Choose a reason for hiding this comment

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

Not for most parts of the program but for a pipeline generating a sites file from a vcf & genome fasta: https://github.com/JustinChu/ntsm/blob/main/ntsmSiteGen

- samtools
- bwa
- perl
Copy link
Contributor

Choose a reason for hiding this comment

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

🛠️ Refactor suggestion

Add version constraints for runtime dependencies.

Consider adding version constraints for critical dependencies like samtools, bwa, and perl to ensure reproducibility and prevent potential compatibility issues.

Additionally, there might be a conflict between libgomp and llvm-openmp if OSX builds are enabled in the future.

  run:
    - llvm-openmp  # [osx]
    - zlib
    - libgomp
    - make
-   - samtools
-   - bwa
-   - perl
+   - samtools >=1.15
+   - bwa >=0.7.17
+   - perl >=5.26
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
requirements:
build:
- {{ compiler('cxx') }}
- llvm-openmp # [osx]
- make
host:
- zlib
- libgomp
run:
- llvm-openmp # [osx]
- zlib
- libgomp
- make
- samtools
- bwa
- perl
requirements:
build:
- {{ compiler('cxx') }}
- llvm-openmp # [osx]
- make
host:
- zlib
- libgomp
run:
- llvm-openmp # [osx]
- zlib
- libgomp
- make
- samtools >=1.15
- bwa >=0.7.17
- perl >=5.26


test:
commands:
- ntsmCount --help
- ntsmVCF --help
- ntsmEval --help
- ntsmSiteGen -h

about:
home: "https://github.com/JustinChu/ntsm"
summary: "ntsm - Nucleotide Sequence/Sample Matcher"
license: "MIT"
license_family: MIT
license_file: LICENSE
dev_url: "https://github.com/JustinChu/ntsm"
doc_url: "https://github.com/JustinChu/ntsm/blob/{{ version }}/README.md"

extra:
additional-platforms:
- linux-aarch64
Loading