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Update mosdepth recipe #48070

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Update mosdepth recipe #48070

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cde674d
update link
ramprasadn May 24, 2024
663bc7d
Update build.sh
ramprasadn May 24, 2024
b68b048
Update meta.yaml
ramprasadn May 25, 2024
98fed21
Merge branch 'master' into update-mosdepth
mencian Jun 6, 2024
bee617b
Manually add $PREFIX/include to CFLAGS
martin-g Jun 7, 2024
4286307
Try with "--passC:"
martin-g Jun 7, 2024
6125f2d
Also pass `-L$PREFIX/lib` to `--passC:`
martin-g Jun 7, 2024
baffd71
Wrap the C flags in single quotes
martin-g Jun 7, 2024
908eaaa
Pass compiler and linker flags to both `nim install` and `nim build`
martin-g Jun 7, 2024
ed5845f
try adding d4binding to run
mencian Jun 10, 2024
854781a
bump mosdepth to 0.3.9
mencian Oct 22, 2024
80347d9
Merge branch 'master' into update-mosdepth
mencian Oct 22, 2024
2734818
Merge branch 'master' into update-mosdepth
mencian Oct 23, 2024
18ae6cb
Merge branch 'master' into update-mosdepth
ramprasadn Oct 25, 2024
cb2dbb7
Merge branch 'master' into update-mosdepth
ramprasadn Nov 12, 2024
69a9e3c
Update build.sh
ramprasadn Nov 12, 2024
90e48a0
Update build.sh
mencian Nov 25, 2024
d1289e8
Update meta.yaml
mencian Nov 25, 2024
ed033d1
Update build.sh
mencian Nov 25, 2024
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20 changes: 12 additions & 8 deletions recipes/mosdepth/build.sh
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Original file line number Diff line number Diff line change
@@ -1,20 +1,24 @@
#!/bin/sh
#!/bin/bash

if [[ ${target_platform} == osx-64 ]] ; then
curl -SL https://github.com/nim-lang/nightlies/releases/download/latest-version-1-6/macosx_x64.tar.xz -o macosx_x64.tar.xz
if [[ ${target_platform} == "osx-64" ]] ; then
curl -SL https://github.com/nim-lang/nightlies/releases/download/latest-version-2-2/macosx_x64.tar.xz -o macosx_x64.tar.xz
tar -xzf macosx_x64.tar.xz
cd nim-1.6.*
cd nim-2.2.*
export PATH="$PWD/bin:$PATH"
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🛠️ Refactor suggestion

Add error handling for directory changes

Directory changes should handle potential failures.

-    cd nim-2.2.*
+    cd nim-2.2.* || exit 1
     export PATH="$PWD/bin:$PATH"
-    cd ..
+    cd .. || exit 1
     ...
-    cd mosdepth-0.3.9
+    cd mosdepth-0.3.9 || exit 1

Also applies to: 8-8, 16-16

🧰 Tools
🪛 Shellcheck

[warning] 6-6: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.

(SC2164)

cd ..
curl -SL https://github.com/brentp/mosdepth/archive/refs/tags/v${PKG_VERSION}.tar.gz -o mosdepth-latest.tar.gz
tar -xzf mosdepth-latest.tar.gz
cd mosdepth-${PKG_VERSION}
nimble install -y "docopt@0.7.0"
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⚠️ Potential issue

Add error handling for directory changes.

The cd commands should handle potential failures:

-    cd nim-2.2.*
+    cd nim-2.2.* || exit 1
     export PATH="$PWD/bin:$PATH"
-    cd ..
+    cd .. || exit 1
     curl -SL https://github.com/brentp/mosdepth/archive/refs/tags/v${PKG_VERSION}.tar.gz -o mosdepth-latest.tar.gz
     tar -xzf mosdepth-latest.tar.gz
-    cd mosdepth-${PKG_VERSION}
+    cd mosdepth-${PKG_VERSION} || exit 1
📝 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
cd nim-2.2.*
export PATH="$PWD/bin:$PATH"
cd ..
curl -SL https://github.com/brentp/mosdepth/archive/refs/tags/v${PKG_VERSION}.tar.gz -o mosdepth-latest.tar.gz
tar -xzf mosdepth-latest.tar.gz
cd mosdepth-${PKG_VERSION}
cd nim-2.2.* || exit 1
export PATH="$PWD/bin:$PATH"
cd .. || exit 1
curl -SL https://github.com/brentp/mosdepth/archive/refs/tags/v${PKG_VERSION}.tar.gz -o mosdepth-latest.tar.gz
tar -xzf mosdepth-latest.tar.gz
cd mosdepth-${PKG_VERSION} || exit 1
🧰 Tools
🪛 Shellcheck

[warning] 6-6: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.

(SC2164)

[warning] 11-11: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.

(SC2164)

nimble build -y --verbose -d:release
export CFLAGS="$CFLAGS -I$PREFIX/include"
export LDFLAGS="$LDFLAGS -L$PREFIX/lib"
nimble install -y "docopt@0.7.1" --passC:"-I$PREFIX/include" --passL:"-L$PREFIX/lib"
nimble build -y --verbose -d:release -d:d4 --passC:"-I$PREFIX/include" --passL:"-L$PREFIX/lib"
else
curl -SL https://github.com/brentp/mosdepth/releases/download/v$PKG_VERSION/mosdepth -o mosdepth
#Link to mosdepth_d4 is specified below because of https://github.com/brentp/mosdepth/issues/232
curl -SL https://github.com/brentp/mosdepth/releases/download/v$PKG_VERSION/mosdepth_d4 -o mosdepth
chmod +x mosdepth
fi

mkdir -p "${PREFIX}/bin"
cp mosdepth "${PREFIX}/bin/"
chmod 0755 mosdepth
mv mosdepth "${PREFIX}/bin/"
24 changes: 17 additions & 7 deletions recipes/mosdepth/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,9 +1,14 @@
{% set version = "0.3.8" %}
{% set name = "mosdepth" %}
{% set version = "0.3.9" %}

package:
name: mosdepth
name: {{ name }}
version: {{ version }}

source:
url: https://github.com/brentp/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
sha256: 9171ea9a6ddaccd0091db5b85fa9e6cb79516bbe005c47ffc8dcfe49c978eb69

build:
number: 0
run_exports:
Expand All @@ -12,23 +17,28 @@ build:
requirements:
build:
- {{ compiler('c') }}
- curl
host:
- htslib >=1.19.1
- htslib >=1.21
- d4binding
- curl
run:
- d4binding

test:
commands:
- mosdepth -h

about:
home: https://github.com/brentp/mosdepth
dev_url: https://github.com/brentp/mosdepth
doc_url: https://github.com/brentp/mosdepth
home: "https://github.com/brentp/mosdepth"
dev_url: "https://github.com/brentp/mosdepth"
doc_url: "https://github.com/brentp/mosdepth/blob/v{{ version }}/README.md"
license: MIT
license_family: MIT
license_file: LICENSE
summary: 'Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.'

extra:
identifiers:
- doi:10.1093/bioinformatics/btx699
- biotools:mosdepth
- usegalaxy-eu:mosdepth
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