From ee29093d9618ac29f8133571d246bab0773a9d26 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Thu, 9 Apr 2026 13:15:14 +0100 Subject: [PATCH 01/10] adding missing dependencies --- recipes/masurca/meta.yaml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml index 0ab8a8219afb3..898995d907297 100644 --- a/recipes/masurca/meta.yaml +++ b/recipes/masurca/meta.yaml @@ -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') }} @@ -21,7 +21,9 @@ requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} + - {{ stdlib("c") }} - make + - cmake - automake - autoconf - libtool @@ -31,11 +33,17 @@ requirements: - bzip2 - libxcrypt - boost-cpp + - xz + - ncurses + - openssl + - gdbm run: - boost-cpp - perl + - python3 - grep - bwa + - file test: commands: From bf2552571a95ca298212e9159e6c2bee6a04ac5a Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Thu, 9 Apr 2026 14:27:01 +0100 Subject: [PATCH 02/10] python --- recipes/masurca/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml index 898995d907297..e2871f92f3619 100644 --- a/recipes/masurca/meta.yaml +++ b/recipes/masurca/meta.yaml @@ -40,7 +40,7 @@ requirements: run: - boost-cpp - perl - - python3 + - python - grep - bwa - file From aa6857c87e55751310a96379df4f73229cb77037 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Thu, 9 Apr 2026 14:59:07 +0100 Subject: [PATCH 03/10] pin c_stdlib and openssl to try resolve hash mismatch --- recipes/masurca/conda_build_config.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/recipes/masurca/conda_build_config.yaml b/recipes/masurca/conda_build_config.yaml index 120557892c2ec..f95bcdc6f2443 100644 --- a/recipes/masurca/conda_build_config.yaml +++ b/recipes/masurca/conda_build_config.yaml @@ -2,3 +2,7 @@ cxx_compiler_version: - 12 # [linux] c_compiler_version: - 12 # [linux] +c_stdlib_version: + - 2.17 # [linux] +openssl: + - 3.5 # [linux] From 4c3b43f08f54e00b04a9d85ebca5af8590c7b8b7 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Thu, 9 Apr 2026 15:21:17 +0100 Subject: [PATCH 04/10] remove conda_build_config.yaml to check if the hash mismatch problem gets resolved --- recipes/masurca/conda_build_config.yaml | 8 -------- 1 file changed, 8 deletions(-) delete mode 100644 recipes/masurca/conda_build_config.yaml diff --git a/recipes/masurca/conda_build_config.yaml b/recipes/masurca/conda_build_config.yaml deleted file mode 100644 index f95bcdc6f2443..0000000000000 --- a/recipes/masurca/conda_build_config.yaml +++ /dev/null @@ -1,8 +0,0 @@ -cxx_compiler_version: - - 12 # [linux] -c_compiler_version: - - 12 # [linux] -c_stdlib_version: - - 2.17 # [linux] -openssl: - - 3.5 # [linux] From 89779174adc1e2271ab4541421368b32f9a98dfb Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Thu, 9 Apr 2026 15:49:39 +0100 Subject: [PATCH 05/10] adding conda_build_config.yaml back --- recipes/masurca/conda_build_config.yaml | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 recipes/masurca/conda_build_config.yaml diff --git a/recipes/masurca/conda_build_config.yaml b/recipes/masurca/conda_build_config.yaml new file mode 100644 index 0000000000000..120557892c2ec --- /dev/null +++ b/recipes/masurca/conda_build_config.yaml @@ -0,0 +1,4 @@ +cxx_compiler_version: + - 12 # [linux] +c_compiler_version: + - 12 # [linux] From 0f313fbb41c1f0fcd07cc89bbcec7aefa74aead1 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Thu, 9 Apr 2026 16:23:53 +0100 Subject: [PATCH 06/10] remove {{ stdlib(c) }} originally added due to linting error --- recipes/masurca/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml index e2871f92f3619..6d5dd346f3cfd 100644 --- a/recipes/masurca/meta.yaml +++ b/recipes/masurca/meta.yaml @@ -21,7 +21,6 @@ requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} - - {{ stdlib("c") }} - make - cmake - automake From 336e89042daf5afbf59992c0059ac5d8776f0fe1 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Thu, 9 Apr 2026 16:29:21 +0100 Subject: [PATCH 07/10] adding skip-lints due to hash problems --- recipes/masurca/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml index 6d5dd346f3cfd..a6207652ead22 100644 --- a/recipes/masurca/meta.yaml +++ b/recipes/masurca/meta.yaml @@ -65,3 +65,5 @@ 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 \ No newline at end of file From b76a58f9059adb0d32fabaf854d861f77125ac2e Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Thu, 9 Apr 2026 19:33:11 +0100 Subject: [PATCH 08/10] fix hardcoded perl shebangs to use env --- recipes/masurca/build.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/masurca/build.sh b/recipes/masurca/build.sh index c727afeb25553..c4739ab2c1fea 100755 --- a/recipes/masurca/build.sh +++ b/recipes/masurca/build.sh @@ -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|' {} + \ No newline at end of file From cbc8edf4d64056709ee81e75128ff610ace4b2ae Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Thu, 9 Apr 2026 21:06:50 +0100 Subject: [PATCH 09/10] adding gzip to run dependencies --- recipes/masurca/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml index a6207652ead22..a1807d34bc214 100644 --- a/recipes/masurca/meta.yaml +++ b/recipes/masurca/meta.yaml @@ -43,6 +43,7 @@ requirements: - grep - bwa - file + - gzip test: commands: From 24c4387d27375cf04e31b4fc8fefb59528938763 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Thu, 9 Apr 2026 21:09:05 +0100 Subject: [PATCH 10/10] adding coreutils to run dependencies --- recipes/masurca/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml index a1807d34bc214..077a4240268db 100644 --- a/recipes/masurca/meta.yaml +++ b/recipes/masurca/meta.yaml @@ -44,6 +44,7 @@ requirements: - bwa - file - gzip + - coreutils test: commands: