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Update masurca: adding missing dependencies #64293

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Merged
mencian merged 12 commits into from
Apr 10, 2026
+14 −1
Merged

Update masurca: adding missing dependencies #64293

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ee29093
adding missing dependencies
LiaOb21 Apr 9, 2026
bf25525
python
LiaOb21 Apr 9, 2026
aa6857c
pin c_stdlib and openssl to try resolve hash mismatch
LiaOb21 Apr 9, 2026
4c3b43f
remove conda_build_config.yaml to check if the hash mismatch problem …
LiaOb21 Apr 9, 2026
8977917
adding conda_build_config.yaml back
LiaOb21 Apr 9, 2026
0f313fb
remove {{ stdlib(c) }} originally added due to linting error
LiaOb21 Apr 9, 2026
336e890
adding skip-lints due to hash problems
LiaOb21 Apr 9, 2026
b76a58f
fix hardcoded perl shebangs to use env
LiaOb21 Apr 9, 2026
c53ac95
Merge branch 'master' into update_masurca
LiaOb21 Apr 9, 2026
cbc8edf
adding gzip to run dependencies
LiaOb21 Apr 9, 2026
24c4387
adding coreutils to run dependencies
LiaOb21 Apr 9, 2026
9ec14c0
Merge branch 'master' into update_masurca
LiaOb21 Apr 9, 2026
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2 changes: 2 additions & 0 deletions recipes/masurca/build.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -47,3 +47,5 @@ ${BINDIR}/masurca -g masurca_config_example.txt
cd ${SRC_DIR}/Flye
make -j"${CPU_COUNT}"
install -v -m 0755 bin/flye* "${PREFIX}/bin"

find "${PREFIX}/bin" -name "*.pl" -exec sed -i '1s|^#!.*perl.*|#!/usr/bin/env perl|' {} +
13 changes: 12 additions & 1 deletion recipes/masurca/meta.yaml
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Expand Up @@ -12,7 +12,7 @@ source:
- 0002-48bit_iterator.patch

build:
number: 0
number: 1
skip: True # [osx]
run_exports:
- {{ pin_subpackage(name, max_pin='x') }}
Expand All @@ -22,6 +22,7 @@ requirements:
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- make
- cmake
- automake
- autoconf
- libtool
Expand All @@ -31,11 +32,19 @@ requirements:
- bzip2
- libxcrypt
- boost-cpp
- xz
- ncurses
- openssl
- gdbm
run:
- boost-cpp
- perl
- python
- grep
- bwa
- file
- gzip
- coreutils

test:
commands:
Expand All @@ -58,3 +67,5 @@ extra:
identifiers:
- biotools:masurca
- doi:10.1093/bioinformatics/btt476
skip-lints:
- compiler_needs_stdlib_c # until https://github.com/bioconda/bioconda-utils/issues/1095 is resolved
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