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Add r-saccharis #51468

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cb93e7e
Add recipe for saccharis 2.0 dev18 build 1 to bioconda
AlexSCFraser Jun 13, 2023
f6f773d
updated to use git tag
AlexSCFraser Jun 23, 2023
e647f0b
Merge branch 'master' into saccharis
AlexSCFraser Jun 23, 2023
d37cc1b
updated to use a python package generated from setuptools build, with…
AlexSCFraser Jun 23, 2023
25078ad
Merge remote-tracking branch 'origin/saccharis' into saccharis
AlexSCFraser Jun 23, 2023
ae1285b
lowercased hash, since it's case-sensitive
AlexSCFraser Jun 24, 2023
a7ddfe6
added filename as "fn: saccharis-{{ version }}.tar.gz"
AlexSCFraser Jun 24, 2023
ebbdbc4
removed filename since bioconda considers it an error
AlexSCFraser Jun 24, 2023
3e3a965
update url link
AlexSCFraser Jun 24, 2023
4696ace
update sha256
AlexSCFraser Jun 24, 2023
e68ac62
remove unneeded comments
AlexSCFraser Jun 26, 2023
a5b62b4
remove tests which write files
AlexSCFraser Jun 26, 2023
f2ff867
remove tests which write files, with comment
AlexSCFraser Jun 26, 2023
675e10e
Merge branch 'master' into saccharis
AlexSCFraser Jun 26, 2023
9ce1b21
Merge branch 'saccharis' of https://github.com/saccharis/bioconda-rec…
AlexSCFraser Jun 26, 2023
83b518b
add new release data to bioconda recipe
AlexSCFraser Aug 23, 2023
93dc1ee
Merge branch 'master' into saccharis
AlexSCFraser Aug 23, 2023
7e31b96
change build number to zero to satisfy bioconda linter
AlexSCFraser Aug 24, 2023
a383bb2
Merge remote-tracking branch 'origin/saccharis' into saccharis
AlexSCFraser Aug 24, 2023
68d2dec
Merge branch 'master' into saccharis
AlexSCFraser Aug 24, 2023
9ab5ebd
add blast dependency
AlexSCFraser Aug 29, 2023
12f9814
Merge remote-tracking branch 'origin/saccharis' into saccharis
AlexSCFraser Aug 29, 2023
678ec9e
Merge branch 'master' into saccharis
AlexSCFraser Aug 29, 2023
84a1857
add run_exports breaking change behaviour
AlexSCFraser Aug 29, 2023
e8bbcb9
Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
AlexSCFraser Oct 17, 2024
ccce12d
add r-saccharis package to bioconda-recipes
AlexSCFraser Oct 17, 2024
d5b5f11
add run_exports to r-saccharis
AlexSCFraser Oct 17, 2024
cfc4f4e
Merge branch 'master' into rsaccharis
AlexSCFraser Oct 17, 2024
cebb1b2
fix meta.yaml brackets
AlexSCFraser Oct 17, 2024
ff358fe
Merge remote-tracking branch 'origin/rsaccharis' into rsaccharis
AlexSCFraser Oct 17, 2024
b62d03e
remove numpy spec
AlexSCFraser Oct 18, 2024
c9f6de1
Merge branch 'master' into rsaccharis
AlexSCFraser Oct 18, 2024
07d93d6
update licence identifier
AlexSCFraser Oct 18, 2024
cb3324a
Merge remote-tracking branch 'origin/rsaccharis' into rsaccharis
AlexSCFraser Oct 18, 2024
938cd94
try commenting out magicfor from host because build server doesn't ha…
AlexSCFraser Oct 18, 2024
8d253b5
add pre-link.sh to add r channel
AlexSCFraser Oct 18, 2024
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2 changes: 2 additions & 0 deletions recipes/r-saccharis/build.sh
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@@ -0,0 +1,2 @@
#!/bin/bash
$R CMD INSTALL --build .
2 changes: 2 additions & 0 deletions recipes/r-saccharis/conda_build_config.yaml
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r_base:
- 3.6.3
64 changes: 64 additions & 0 deletions recipes/r-saccharis/meta.yaml
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{% set version = "1.0.4" %}
{% set name = "r-saccharis" %}
{% set build_number = 0%}
{% set filehash = "F02EC69008F688440D7D4230751D1A8C9501F24F2382F399317591C4005DF19F"%}

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

source:
url:
- 'https://github.com/saccharis/rsaccharis/releases/download/{{ version }}/rsaccharis_{{ version }}.tar.gz'
sha256: {{ filehash|lower}}

build:
noarch: generic
number: {{ build_number }}
rpaths:
- lib/R/lib/
- lib/
run_exports:
- {{ pin_subpackage("r-saccharis", max_pin="x.x") }}

requirements:
host:
- r-base
- r-jsonlite
- r-ape
- r-stringr
# - r-magicfor
- r-knitr
- r-dplyr
- r-magrittr
- r-rcolorbrewer
- r-ggnewscale
- r-ggplot2
- bioconductor-ggtree
run:
- r-base
- r-jsonlite
- r-ape
- r-stringr
- r-magicfor
- r-knitr
- r-dplyr
- r-magrittr
- r-rcolorbrewer
- r-ggnewscale
- r-ggplot2
- bioconductor-ggtree

test:
commands:
- 'Rscript -e "library(rsaccharis)"'

about:
home: 'https://github.com/saccharis/rsaccharis'
license: 'GPL-3.0-or-later'
license_family: GPL
summary: 'A rendering package for creating phylogenetic trees from SACCHARIS .json and .tree files, in the R statistical computing language.'
description: 'This package will use metadata .json and .tree files output from SACCHARIS v2 to generate annotated phylogenetic tree PDF files.
Highly customizable, as the formatting of the tree is done using ggplot2. Of course plotting functions can easily be manipulated as desired.
To use, call A_load_data() and B_plots_all() and follow prompts. Our default plots used for publication are domain_ECno_numeric.'
license_file: LICENSE.md
1 change: 1 addition & 0 deletions recipes/r-saccharis/pre-link.sh
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conda config --append channels r
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🛠️ Refactor suggestion

Consider improving error handling and idempotency.

While the current implementation works, it could be improved to handle errors and avoid duplicate entries in the conda config.

Consider refactoring the script as follows:

#!/bin/bash
set -e

if ! conda config --get channels | grep -q '^  - r$'; then
    conda config --append channels r
else
    echo "The 'r' channel is already in the conda configuration."
fi

This refactored version:

  1. Uses set -e to exit on any error.
  2. Checks if the 'r' channel already exists before adding it.
  3. Provides feedback if the channel is already present.
🧰 Tools
🪛 Shellcheck

[error] 1-1: Tips depend on target shell and yours is unknown. Add a shebang or a 'shell' directive.

(SC2148)

⚠️ Potential issue

Add a shebang to improve portability.

The script is missing a shebang, which could lead to inconsistent behavior across different environments.

Add the following shebang at the beginning of the file:

+#!/bin/bash
 conda config --append channels r
📝 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
conda config --append channels r
#!/bin/bash
conda config --append channels r
🧰 Tools
🪛 Shellcheck

[error] 1-1: Tips depend on target shell and yours is unknown. Add a shebang or a 'shell' directive.

(SC2148)

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