Skip to content

add panmap#64193

Open
amkram wants to merge 3 commits intobioconda:masterfrom
amkram:add-panmap
Open

add panmap#64193
amkram wants to merge 3 commits intobioconda:masterfrom
amkram:add-panmap

Conversation

@amkram
Copy link
Copy Markdown

@amkram amkram commented Apr 6, 2026

Pangenome-based sequence placement, alignment, and genotyping.

Preprint: https://www.biorxiv.org/content/10.64898/2026.03.29.711974v1


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

General instructions

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
  • New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
  • PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
  • Please post questions on Gitter or ping @bioconda/core in a comment.

Instructions for avoiding API, ABI, and CLI breakage issues

Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation).
Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case run_exports statement
semantic versioning {{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x) {{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions {{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions {{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning {{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

Bot commands for PR management

Please use the following BiocondaBot commands:

Everyone has access to the following BiocondaBot commands, which can be given in a comment:

@BiocondaBot please add label Add the please review & merge label.
@BiocondaBot please fetch artifacts Post links to CI-built packages/containers.
You can use this to test packages locally.

Note that the @BiocondaBot please merge command is now depreciated. Please just squash and merge instead.

Also, the bot watches for comments from non-members that include @bioconda/<team> and will automatically re-post them to notify the addressed <team>.

@amkram amkram force-pushed the add-panmap branch 10 times, most recently from 7d0afa5 to 273f972 Compare April 7, 2026 00:58
@@ -0,0 +1,60 @@
#!/bin/bash
set -ex
Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

Please use -u also.

@@ -0,0 +1,60 @@
#!/bin/bash
Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

Use #!/usr/bin/env bash


test:
commands:
- panmap --help
Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

does panman need testing too?

- panmap --help

about:
home: "https://github.com/amkram/panmap"
Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

use {{ name }} ?

license_family: MIT
license_file: "panmap/LICENSE"
summary: "Pangenome-based sequence placement, alignment, and genotyping"
dev_url: "https://github.com/amkram/panmap"
Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

Use {{ name }}

- autoconf
- automake
- libtool
host:
Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

In the Cmakefile there was mention of htslib, minimap2 etc
Are those deps?

@tseemann tseemann added the new recipe Brand new recipe label Apr 7, 2026
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

new recipe Brand new recipe

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants