-
Notifications
You must be signed in to change notification settings - Fork 3.3k
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.
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 mumemto recipe #53000
Merged
+72
−0
Merged
Add mumemto recipe #53000
Changes from 2 commits
Commits
Show all changes
7 commits
Select commit
Hold shift + click to select a range
ca03d75
added mumemto v1.1.0 recipe
vikshiv 6e32488
Merge branch 'master' into add_mumemto
vikshiv 484f0b6
Update recipes/mumemto/meta.yaml
vikshiv 18adc49
Update recipes/mumemto/meta.yaml
vikshiv f78869e
moved to build.sh
vikshiv 454af7b
Merge branch 'master' into add_mumemto
vikshiv 0f5203e
changed release hash
vikshiv File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| {% set name = "mumemto" %} | ||
| {% set version = "1.1.0" %} | ||
|
|
||
| package: | ||
| name: {{ name|lower }} | ||
| version: {{ version }} | ||
|
|
||
| source: | ||
| url: https://github.com/vikshiv/mumemto/archive/refs/tags/v{{ version }}.tar.gz | ||
| sha256: e0a42fd5d3afde6366dbc43bb16cc38b5a0c87468a4c6978c4225d361d789f95 | ||
|
|
||
| build: | ||
| number: 0 | ||
| pkg_format: '.conda' | ||
| run_exports: | ||
| - {{ pin_subpackage(name, max_pin='x.x') }} | ||
| script: | ||
| - mkdir build | ||
vikshiv marked this conversation as resolved.
Show resolved
Hide resolved
|
||
| - cd build | ||
| - cmake .. | ||
| - make install | ||
vikshiv marked this conversation as resolved.
Show resolved
Hide resolved
|
||
| - cd .. | ||
| - mkdir -p $PREFIX/bin | ||
| - mkdir -p $SP_DIR/mumemto | ||
| - cp build/mumemto $PREFIX/bin/mumemto_exec | ||
| - cp build/bin/newscanNT.x $PREFIX/bin/ | ||
| - cp mumemto/*.py $SP_DIR/mumemto/ | ||
| - cp mumemto/mumemto $PREFIX/bin/ | ||
vikshiv marked this conversation as resolved.
Show resolved
Hide resolved
|
||
| - mkdir -p $PREFIX/share/licenses/{{ name }} | ||
| - cp LICENSE $PREFIX/share/licenses/{{ name }}/ | ||
| - chmod +x $PREFIX/bin/mumemto | ||
| - touch $SP_DIR/mumemto/__init__.py | ||
|
|
||
| requirements: | ||
| build: | ||
| - {{ compiler('cxx') }} | ||
| - cmake | ||
| - make | ||
| host: | ||
| - python | ||
| run: | ||
| - python | ||
| - matplotlib-base | ||
| - numpy | ||
| - tqdm | ||
| - numba | ||
| - plotly | ||
|
|
||
| test: | ||
| commands: | ||
| - mumemto --help | ||
| - mumemto viz --help | ||
| - mumemto coverage --help | ||
| - mumemto inversions --help | ||
| imports: | ||
| - mumemto.utils | ||
|
|
||
| about: | ||
| home: https://github.com/vikshiv/mumemto | ||
| summary: Finding maximal unique matches across pangenomes | ||
| description: | | ||
| Mumemto is a tool for finding a variety of matches across collections of sequences like a pangenome. | ||
| It includes a visualization tool for visualizing pangenome synteny. | ||
| license: GPL-3.0 | ||
vikshiv marked this conversation as resolved.
Show resolved
Hide resolved
|
||
| license_file: LICENSE | ||
|
|
||
| extra: | ||
| recipe-maintainers: | ||
| - vikshiv | ||
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
As I understand it, changing to
'x'would mean that this package would get pinned to the major version? I anticipate that "minor" (.X.) versions will be substantial and affect usage, so I would rather pin to the second version number. Is this a correct understanding? Thank you.There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I apologize, I re-read the pull request information. My evidence for the minor version breakages is the current update. From v1.0.0 (not on bioconda) to v1.1.0 (first version on bioconda), the usage (flag parameters) and output format are significantly different and not interoperable. However, this is still an initial release so we want to keep the v1 tag. Thus our minor version updates will be substantial and break usage potentially, while our path updates will be for bug fixes.