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install_rotate_1.0 #51801

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merged 5 commits into from
Nov 5, 2024
Merged

install_rotate_1.0 #51801

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install_rotate_1.0
Oct 30, 2024
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install_rotate_1.0
Oct 30, 2024
303f045
Update meta.yaml
jayramr Oct 31, 2024
9d15a10
Update recipes/rotate/meta.yaml
jayramr Nov 4, 2024
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Update meta.yaml
jayramr Nov 4, 2024
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7 changes: 7 additions & 0 deletions recipes/rotate/build.sh
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Original file line number Diff line number Diff line change
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#!/bin/bash
set -xe
make CC=$CC INCLUDES="-I$PREFIX/include" CFLAGS+="-g -Wall -O2 -L$PREFIX/lib"
chmod +x rotate
chmod +x composition
mkdir -p ${PREFIX}/bin
cp -f rotate composition ${PREFIX}/bin
37 changes: 37 additions & 0 deletions recipes/rotate/meta.yaml
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{% set name = "rotate" %}
{% set version = "1.0" %}

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

source:
url: "https://github.com/richarddurbin/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz"
sha256: "da8a3c848cc05d59b579c375824008dd2d533c28d8a436a6e4761312d2152906"

build:
number: 0
run_exports:
- {{ pin_subpackage("rotate", max_pin="x") }}
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requirements:
build:
- make
- {{ compiler('c') }}
host:
- zlib
run:
- zlib
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- make
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test:
commands:
- rotate 2>&1 | grep can
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why "grep can" ?

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hi @bgruening for this package, the help menu shows the whole output. To simply the output, i just did a grep. If this is not a recommended practice then , we can keep below as it as. Please advise

rotate
rotate [options] <input fasta filename>
  -x <pos>		position to become new start [0]
  -rc               reverse complement after rotating [false]
  -s <string>       rotate to start of search string
  -m <n_mismatch>   maximum number of mismatches allowed in search [0]
  -o <outfilename>  output file [standard output]
use either -x and optionally -rc, or -s
use filename '-' for standard input
can read .fa.gz files as well as .fa files

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🛠️ Refactor suggestion

Improve test command robustness.

The current test command using grep can is fragile and may not effectively verify the program's functionality. Based on the previous discussion, it would be better to verify the full help output.

Replace the test command with:

  test:
    commands:
-    - rotate 2>&1 | grep can
+    - rotate --help 2>&1  # Verify help menu is accessible
+    - rotate 2>&1  # Verify program runs without arguments and shows usage
📝 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
test:
commands:
- rotate 2>&1 | grep can
test:
commands:
- rotate --help 2>&1 # Verify help menu is accessible
- rotate 2>&1 # Verify program runs without arguments and shows usage


about:
home: "https://github.com/richarddurbin/rotate"
license: MIT
license_family: MIT
license_file: LICENSE
summary: "Simple program to rotate a circular sequence to start at a given position or string."
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