From af6debdbe2933a6eb64925e82a5c2d74f8d42a5b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 28 Dec 2024 13:46:46 -0500 Subject: [PATCH 01/10] Update perl-term-table to 0.024 (#52986) --- recipes/perl-term-table/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-term-table/meta.yaml b/recipes/perl-term-table/meta.yaml index c2c092b1d7bdd..9b8663954557c 100644 --- a/recipes/perl-term-table/meta.yaml +++ b/recipes/perl-term-table/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-term-table" %} -{% set version = "0.023" %} -{% set sha256 = "e45042face1801d99c0bead6ca5f363a34e0e055f4fe6b0ccb208de481072bd3" %} +{% set version = "0.024" %} +{% set sha256 = "52288538c3b0514bcd2b61f645686c256619e56a421ae992e2b76d31927c4ece" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Term-Table-0.023.tar.gz + url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Term-Table-0.024.tar.gz sha256: {{ sha256 }} build: From 04d4c6370f9658bd22935518cf985519dfed87cd Mon Sep 17 00:00:00 2001 From: dslarm <38504854+dslarm@users.noreply.github.com> Date: Sat, 28 Dec 2024 18:48:44 +0000 Subject: [PATCH 02/10] Bump the build. (#52763) --- recipes/ngscheckmate/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/ngscheckmate/meta.yaml b/recipes/ngscheckmate/meta.yaml index 6d394d70d7dbe..7a2dd1af0b353 100644 --- a/recipes/ngscheckmate/meta.yaml +++ b/recipes/ngscheckmate/meta.yaml @@ -9,7 +9,7 @@ source: md5: 42d4578e02a81e4e55857f126ae719af build: - number: 1 + number: 2 noarch: generic run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} From 0bd92662e3ba251f180b4022bd3693328625a1c4 Mon Sep 17 00:00:00 2001 From: "Charles E. Grant" Date: Sat, 28 Dec 2024 10:54:22 -0800 Subject: [PATCH 03/10] Update crux-toolkit to 4.2 (#51986) --- recipes/crux-toolkit/meta.yaml | 85 ++++++++++++++++++++-------------- 1 file changed, 49 insertions(+), 36 deletions(-) diff --git a/recipes/crux-toolkit/meta.yaml b/recipes/crux-toolkit/meta.yaml index 04ea9d0b8ce6a..cf96b461e5ece 100644 --- a/recipes/crux-toolkit/meta.yaml +++ b/recipes/crux-toolkit/meta.yaml @@ -1,36 +1,49 @@ -{% set version = "4.1" %} - -package: - name: crux-toolkit - version: {{ version }} - -source: - - url: https://noble.gs.washington.edu/crux-downloads/crux-{{ version }}/crux-{{ version }}.Linux.x86_64.zip # [linux] - sha256: c056f1e632dfaf8d0c6f6769fbdaf78eef6fd586a6b732d88ad0c01fe2da077d # [linux] - - url: https://noble.gs.washington.edu/crux-downloads/crux-{{ version }}/crux-{{ version }}.Darwin.x86_64.zip # [osx] - sha256: 9f7b060e67ec250e4c2a10b783eb1777497ec0d1151e5bc9630f67f411b595ac # [osx] - -build: - number: 2 - script: "mkdir -p $PREFIX/bin; chmod a+x bin/*; cp bin/* $PREFIX/bin" - -requirements: - build: - # both needed as run-time dependencies - - {{ compiler('c') }} - - {{ compiler('cxx') }} - -test: - commands: - - crux version 2> /dev/null | grep -q 'Crux version' - -about: - home: http://crux.ms - summary: A cross-platform suite of analysis tools for interpreting protein mass spectrometry data - license: Apache-2.0 - license_family: Apache - dev_url: https://github.com/crux-toolkit/crux-toolkit - -extra: - skip-lints: - - should_not_be_noarch_source +{% set version = "4.2" %} + +package: + name: crux-toolkit + version: {{ version }} + +source: + - url: https://noble.gs.washington.edu/crux-downloads/crux-{{ version }}/crux-{{ version }}.Linux.x86_64.zip # [linux] + sha256: b5c1a02416f0220beb6106e12a7b330932dec396291ae364af8f2153a1e1655d # [linux] + - url: https://noble.gs.washington.edu/crux-downloads/crux-{{ version }}/crux-{{ version }}.Darwin.x86_64.zip # [osx] + sha256: 5f1fb9124391cec30608740fdce3aea7fcb3f19330531ea90f6ecf81b8583d00 # [osx] + +build: + number: 0 + script: "mkdir -p $PREFIX/bin; chmod a+x bin/*; cp bin/* $PREFIX/bin" + run_exports: + - {{ pin_subpackage('crux-toolkit', max_pin="x")}} + + binary_relocation: False + detect_binary_files_with_prefix: False + missing_dso_whitelist: + - /lib64/libpthread.so.0 + - /lib64/libgomp.so.6 + - /lib64/libstdc.so.6 + - /lib64/libm.so.6 + - /lib64/libgcc_s.so.1 + - /lib64/libc.so.6 + +requirements: + run: +test: + commands: + - export LD_LIBRARY_PATH=/opt/conda/lib64 crux version + + +about: + home: http://crux.ms + summary: A cross-platform suite of analysis tools for interpreting protein mass spectrometry data + license: Apache-2.0 + license_family: Apache + dev_url: https://github.com/crux-toolkit/crux-toolkit + +extra: + recipe-maintainers: + - CharlesEGrant + - wsnoble + - acquayefrank + skip-lints: + - should_be_noarch_generic From 1cb591f6c82a0783a5989b75c60db435835e6d79 Mon Sep 17 00:00:00 2001 From: Jeffrey Barrick Date: Sat, 28 Dec 2024 17:49:33 -0600 Subject: [PATCH 04/10] Update isescan to use fraggenescan >= 1.32 dependency so it is compatible with MacOSX (#52987) * Updated isescan recipe to use fraggenescan >= 1.32 to work on MacOSX * Bump version number * Added run_exports * Fix run_exports * Fix run_exports * Add additional platforms * Remove additional platforms --- recipes/isescan/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/isescan/meta.yaml b/recipes/isescan/meta.yaml index a9b6e0ced397f..48fc50933b499 100755 --- a/recipes/isescan/meta.yaml +++ b/recipes/isescan/meta.yaml @@ -9,18 +9,20 @@ source: sha256: 90ef6bc660e471347f65864bd3563f769ed4b79b1a932195f353c5e86351ab05 build: - number: 2 - skip: True # [osx] + number: 4 + run_exports: + - {{ pin_subpackage('isescan', max_pin="x.x") }} requirements: build: - {{ compiler('c') }} + run: - python >=3 - numpy >=1.8 - scipy >=0.13.1 - fastcluster - - fraggenescan <=1.30 + - fraggenescan >=1.32 - hmmer >=3.1b2 - blast >=2.2.31 - biopython >=1.62 @@ -32,4 +34,4 @@ test: about: home: https://github.com/xiezhq/ISEScan license: GNU General Public License - summary: 'A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome ' + summary: 'A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome ' \ No newline at end of file From dc0bb5b28d78e075b921986d4619367c09aad5c8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 29 Dec 2024 08:50:06 -0500 Subject: [PATCH 05/10] Update simpleaf to 0.18.1 (#52989) --- recipes/simpleaf/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml index e8c26f34f97b7..0981ffc1ccea1 100644 --- a/recipes/simpleaf/meta.yaml +++ b/recipes/simpleaf/meta.yaml @@ -1,17 +1,17 @@ -{% set version = "0.18.0" %} +{% set version = "0.18.1" %} package: name: simpleaf version: {{ version }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage("simpleaf", max_pin="x.x") }} source: url: https://github.com/COMBINE-lab/simpleaf/archive/v{{ version }}.tar.gz - sha256: f83a792677d7e83c16ec68143b6b6be8537d72560626a5ef2d5e26a0276a4244 + sha256: b043d39a602e55b7dc52ddfec4e12f3d33d7407d7a8961f30a08ef9efeacf1cf requirements: build: From b9536ec4e63b3bb412d8a34ebc9a29b2ab037e38 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 29 Dec 2024 14:37:48 -0500 Subject: [PATCH 06/10] Update simpleaf to 0.18.2 (#52990) --- recipes/simpleaf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml index 0981ffc1ccea1..422dfd17dc42c 100644 --- a/recipes/simpleaf/meta.yaml +++ b/recipes/simpleaf/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.18.1" %} +{% set version = "0.18.2" %} package: name: simpleaf @@ -11,7 +11,7 @@ build: source: url: https://github.com/COMBINE-lab/simpleaf/archive/v{{ version }}.tar.gz - sha256: b043d39a602e55b7dc52ddfec4e12f3d33d7407d7a8961f30a08ef9efeacf1cf + sha256: 4273ce031cbe89995b7f0fed0a6d5dbfe24e42a6749c7a50b52dc20e5104c1f7 requirements: build: From 0178bb668b4e10e8ff2d5aa9e01a7044a7beaf93 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Dec 2024 03:25:31 -0500 Subject: [PATCH 07/10] Update teloscope to 0.0.6 (#52991) * Update teloscope to 0.0.6 * Add openssl as a host dependency --------- Co-authored-by: Martin Grigorov --- recipes/teloscope/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/teloscope/meta.yaml b/recipes/teloscope/meta.yaml index 6181216b96c73..caffb2191f6f6 100644 --- a/recipes/teloscope/meta.yaml +++ b/recipes/teloscope/meta.yaml @@ -1,11 +1,11 @@ {% set name = "teloscope" %} -{% set version = "0.0.5" %} +{% set version = "0.0.6" %} package: name: {{ name }} version: {{ version }} source: url: https://github.com/vgl-hub/teloscope/releases/download/v{{version}}/teloscope.v{{version}}-with_submodules.zip - sha256: 750625065aa433a266dc7bb09433c9d79797024b23eb4171b675d2dc13bf8db5 + sha256: 1f300bd42c408791bdb7463a37530da2ebe72f64d90e8087cf895a9abc88c8b3 build: number: 0 run_exports: @@ -16,6 +16,7 @@ requirements: - {{ compiler('cxx') }} host: - zlib + - openssl test: commands: - teloscope -h | grep "teloscope" From 972e4cbebd539e70ea0189404788373471352927 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Dec 2024 12:32:03 -0500 Subject: [PATCH 08/10] Update simpleaf to 0.18.4 (#52996) --- recipes/simpleaf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml index 422dfd17dc42c..be2283fe7e300 100644 --- a/recipes/simpleaf/meta.yaml +++ b/recipes/simpleaf/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.18.2" %} +{% set version = "0.18.4" %} package: name: simpleaf @@ -11,7 +11,7 @@ build: source: url: https://github.com/COMBINE-lab/simpleaf/archive/v{{ version }}.tar.gz - sha256: 4273ce031cbe89995b7f0fed0a6d5dbfe24e42a6749c7a50b52dc20e5104c1f7 + sha256: 52f39e264e41bf6d405b3bfcf6e6e968d0b8237cac6d0db5f54e02c658792998 requirements: build: From 5c8caebf41a11e7ffd37b1ecea6a8e2d64c465dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Dec 2024 18:09:55 -0500 Subject: [PATCH 09/10] Update pybiolib to 1.2.264 (#52998) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index bbf6764fa3ce9..d639d1e9aa78f 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.2.261" %} +{% set version = "1.2.264" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 4b53b3189701db8a1dc556634a6e984decd5d2ce87e11bb9a0a3ba2321e7a8ef + sha256: 1e9f04d76528848a754b12b1fc93d21f08a65c40347435339858ff850d49a549 build: number: 0 From 0dde5ada81869d752669d512d5d6a8d2220d659c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Dec 2024 18:10:07 -0500 Subject: [PATCH 10/10] Update snakemake-storage-plugin-irods to 0.2.0 (#52997) --- recipes/snakemake-storage-plugin-irods/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-storage-plugin-irods/meta.yaml b/recipes/snakemake-storage-plugin-irods/meta.yaml index 698ed88bc3071..b4bdafd8f6119 100644 --- a/recipes/snakemake-storage-plugin-irods/meta.yaml +++ b/recipes/snakemake-storage-plugin-irods/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-irods" %} -{% set version = "0.1.2" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_irods-{{ version }}.tar.gz - sha256: e5ceac168095bf7a2ef2d82d9d74ddfc6780c1665ecaa75b16041fc2428ead77 + sha256: 8b8316a4bb024a3a506c918231bda0b101d1c64c1c782fff45968934bf56ec95 build: noarch: python