Merge branch 'master' into add_mumemto

bioconda · Dec 31, 2024 · 6e32488 · 6e32488
2 parents ca03d75 + 0dde5ad
commit 6e32488
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diff --git 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
diff --git 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 '
diff --git 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') }}

diff --git 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:

diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "pybiolib" %}
-{% set version = "1.2.261" %}
+{% set version = "1.2.264" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz
-  sha256: 4b53b3189701db8a1dc556634a6e984decd5d2ce87e11bb9a0a3ba2321e7a8ef
+  sha256: 1e9f04d76528848a754b12b1fc93d21f08a65c40347435339858ff850d49a549
 
 build:
   number: 0

diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml
@@ -1,17 +1,17 @@
-{% set version = "0.18.0" %}
+{% set version = "0.18.4" %}
 
 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: 52f39e264e41bf6d405b3bfcf6e6e968d0b8237cac6d0db5f54e02c658792998
 
 requirements:
   build:

diff --git a/recipes/snakemake-storage-plugin-irods/meta.yaml b/recipes/snakemake-storage-plugin-irods/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "snakemake-storage-plugin-irods" %}
-{% set version = "0.1.2" %}
+{% set version = "0.2.0" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_irods-{{ version }}.tar.gz
-  sha256: e5ceac168095bf7a2ef2d82d9d74ddfc6780c1665ecaa75b16041fc2428ead77
+  sha256: 8b8316a4bb024a3a506c918231bda0b101d1c64c1c782fff45968934bf56ec95
 
 build:
   noarch: python

diff --git 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"