Merge branch 'master' into discosnp

recipes/alevin-fry/meta.yaml

@@ -1,15 +1,15 @@
-{% set version = "0.8.1" %}
+{% set version = "0.8.2" %}
 
 package:
   name: alevin-fry
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
 
 source:
   url: https://github.com/COMBINE-lab/alevin-fry/archive/v{{ version }}.tar.gz
-  sha256: ecbe927c76a0e084a81ccba4c526a22d3750687d5372625de170b0018de9a5a1
+  sha256: 7feaa5b59c6537eee9d1a2a07797f151ba6a50955a969fa1807dcb7aeb357ab1
 
 requirements:
   build:

recipes/cazy_webscraper/meta.yaml

@@ -1,18 +1,30 @@
 {% set name = "cazy_webscraper" %}
-{% set version = "2.2.8" %}
+{% set version = "2.3.0" %}
+{% set sha256 = "08a12134f124622069d4259c55d0bafc618e4f1d4872992529cd495d782fd21e" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://github.com/HobnobMancer/{{ name|lower }}/archive/v{{ version }}.tar.gz
-  sha256: 6f0272c35d60b2138319ca4a993832c1f35eb880fe21d50e4e39e56c22e2b79b
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cazy_webscraper-{{ version }}.tar.gz
+  sha256: {{ sha256 }}
 
 build:
   number: 0
   noarch: python
-  script: "{{ PYTHON }} -m pip install . --no-deps -vv --ignore-installed ."
+  script: {{ PYTHON }} -m pip install . -vv
+  entry_points:
+    - cazy_webscraper = cazy_webscraper.cazy_scraper:main
+    - cw_get_genbank_seqs = cazy_webscraper.expand.genbank.sequences.get_genbank_sequences:main
+    - cw_get_ncbi_taxs = cazy_webscraper.expand.genbank.taxonomy.get_ncbi_taxs:main
+    - cw_get_genomics = cazy_webscraper.expand.genbank.genomes.get_genome_accs:main
+    - cw_get_gtdb_taxs = cazy_webscraper.expand.gtdb.get_gtdb_tax:main
+    - cw_get_uniprot_data = cazy_webscraper.expand.uniprot.get_uniprot_data:main
+    - cw_extract_db_seqs = cazy_webscraper.expand.extract_seqs.extract_db_seqs:main
+    - cw_get_pdb_structures = cazy_webscraper.expand.pdb.get_pdb_structures:main
+    - cw_query_database = cazy_webscraper.api.cw_query_database:main
+    - cw_get_db_schema = cazy_webscraper.sql.get_schema:main
 
 requirements:
   host:
@@ -22,26 +34,31 @@ requirements:
     - python >=3.8
     - beautifulsoup4
     - biopython
-    - html5lib
+    - bioservices >=1.10.0
     - lxml
     - mechanicalsoup
     - numpy
     - pandas
     - pyyaml
     - requests
-    - sqlalchemy >=1.4.20
+    - saintBioutils >=0.0.25
+    - sqlalchemy ==1.4.20
     - tqdm
-    - saintBioutils >=0.0.23
+    - html5lib
 
 test:
   imports:
     - cazy_webscraper
   commands:
-    - cazy_webscraper -h
+    - cazy_webscraper --help
 
 about:
-  home: https://hobnobmancer.github.io/cazy_webscraper/
+  home: "https://hobnobmancer.github.io/cazy_webscraper/"
+  dev_url: "https://github.com/HobnobMancer/cazy_webscraper"
+  summary: "A tool to automate retrieving data from CAZy, build a local CAZyme SQL database, and throughly interrogating the data. Also, automate retrieving protein data, sequences, EC numbers and structure files for specific datasets in the CAZyme database from UniProt, GenBank and PDB."
   license: MIT
   license_file: LICENSE
-  summary: 'cazy_webscraper automates retrieving of protein, annotation, sequence, structure, genomic and taxonomic data from the CAZy, NCBI, UniProt, RCSB PDB and GTDB databases.'
-  license_family: MIT
+
+extra:
+  identifiers:
+    - doi:10.1101/2022.12.02.518825

recipes/cramino/meta.yaml

@@ -1,16 +1,16 @@
-{% set version = "0.9.7" %}
+{% set version = "0.9.9" %}
 
 package:
   name: cramino
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   skip: true  # [osx]
 
 source:
   url: https://github.com/wdecoster/cramino/archive/v{{ version }}.tar.gz
-  sha256: 7783d703c96a370b0788ae1a04c347117b70c54988cde271c9428a72bbfc92b9
+  sha256: 4892fcee0a5b4b0b7c49ed4f5f54168a15d5c0419e3eacee0d6155a207e194a1
 
 requirements:
   build:

recipes/csvtk/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = "0.25.0" %}
+{% set version = "0.26.0" %}
 
 package:
   name: csvtk
@@ -9,9 +9,9 @@ build:
 
 source:
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_amd64.tar.gz # [osx]
-    md5: 2b2fbdf23e25244ee7063faeb96eda7b # [osx]
+    md5: 8c5c958e0178bd60c1bbc3a553582255 # [osx]
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_amd64.tar.gz # [linux]
-    md5: 4a99213b22a4e94ff85d7e6166dcf7e1 # [linux]
+    md5: 812cdfc09604d4685f2ab5aa39341597 # [linux]
 
 test:
   commands:

recipes/deeplcretrainer/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "DeepLCRetrainer" %}
-{% set version = "0.1.17" %}
-{% set sha256 = "53c99e7d1ee38f5e0a66e406e1976471df5d2716da79fa4d210a5456cef733be" %}
+{% set version = "0.1.19" %}
+{% set sha256 = "48ff2fb813cd1b16ec93b7143549ad0a5ec4a9741b020957e3de33c8532c42c9" %}
 
 package:
   name: {{ name|lower }}

recipes/derna/meta.yaml

@@ -9,9 +9,7 @@ source:
   sha256: 29e6bd6588a3e6d4d48fc2d08ff69a5eddeccbe281c3f802d2052c4c1945230a
 
 build:
-  number: 0
-  # Temporarily skip building on OSX due to mambabuild keyerror: https://github.com/bioconda/bioconda-recipes/issues/41526
-  skip: True  # [osx]
+  number: 1
 
 requirements:
   build:
@@ -31,4 +29,4 @@ about:
   home: https://github.com/elkebir-group/derna
   license: BSD-3-Clause
   license_file: LICENSE
-  summary: "RNA sequence design for a target protein sequence"
+  summary: "RNA sequence design for a target protein sequence"

recipes/emvc-2/meta.yaml

@@ -10,8 +10,7 @@ source:
   sha256: 'edee7e027bb720f625cfc3073798ab39916f1852641cc7f05604ff62b905c7e3'
 
 build:
-  number: 1
-  skip: True  # [osx]
+  number: 2
   # platforms:
   #   - osx-64
 
@@ -35,4 +34,4 @@ about:
   home: https://github.com/guilledufort/EMVC-2
   license: MIT
   license_family: MIT
-  summary: An efficient SNV variant caller based on the expectation maximization algorithm.
+  summary: An efficient SNV variant caller based on the expectation maximization algorithm.

recipes/foldseek/meta.yaml

@@ -1,12 +1,12 @@
-{% set version = "6-29e2557" %}
-{% set sha256 = "04c444de2aab389db5a7790de79350c77bbb0e3f2a3ae2663bb24c9238304368" %}
+{% set version = "7-04e0ec8" %}
+{% set sha256 = "009d722d600248a680b9e1e9dcb3bf799f8be8de41e80a598b7f39a5ced54191" %}
 
 package:
   name: foldseek
   version: {{ version|replace("-", ".")  }}
 
 build:
-  number: 2
+  number: 0
 
 source:
   url: https://github.com/steineggerlab/foldseek/archive/{{ version }}.tar.gz

recipes/gadma/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "gadma" %}
-{% set version = "2.0.0rc25" %}
+{% set version = "2.0.0rc26" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 3eaa2324e5cafad1d40b6a3564f25094654fbc4c9fdbe692a25ef0b98d3d2b76
+  sha256: 35ed38938e26026d3a0f8bb2563320c734713dfc0b201b51ba4d19e08d023953
 
 build:
   number: 0

recipes/gw/meta.yaml

@@ -1,6 +1,6 @@
 
-{% set version = "0.7.0" %}
-{% set sha256 = "92599d100755a5a20dc15ebfb86fdf0818ccc87c6e0a2cc0a7c3061661ed3d25" %}
+{% set version = "0.8.1" %}
+{% set sha256 = "30fc7957aa7ce61e495be798138e2ae7f3ed8022a5d3a1a726103c7f3a8bdc0d" %}
 
 package:
   name: gw
@@ -13,7 +13,7 @@ source:
 
 
 build:
-  number: 2
+  number: 0
 
 requirements:
   build:

recipes/lastz/meta.yaml

@@ -1,16 +1,16 @@
-{% set version = "1.04.15" %}
+{% set version = "1.04.22" %}
 
 
 package:
   name: lastz
   version: "{{ version }}"
 
 build:
-  number: 3
+  number: 0
 
 source:
-  url: http://www.bx.psu.edu/~rsharris/lastz/newer/lastz-{{ version }}.tar.gz
-  sha256: b251080534dd67c25a9d751af464ffff9b2752d6834e75feb3860404174ea40c
+  url: https://github.com/lastz/lastz/archive/refs/tags/{{ version }}.tar.gz
+  sha256: 4c829603ba4aed7ddf64255b528cd88850e4557382fca29580d3576c25c5054a
 
   patches:
     - makefile.patch

recipes/macsyfinder/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "MacSyFinder" %}
-{% set version = "2.1.1" %}
+{% set version = "2.1.2" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: fe27b88a463753000e75d1589b832801852e1702d01a60670b5b0eeaf1a6cbbe
+  sha256: 19369dc15bdf08aac90c8e0bf8dfc51ffa409105738fa9c55131403435fde7c0
 
 build:
   noarch: python

recipes/matchtigs/meta.yaml

@@ -1,19 +1,19 @@
-{% set version = "1.5.5" %}
+{% set version = "2.1.5" %}
 
 package:
   name: matchtigs
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
 
 source:
   url: https://github.com/algbio/matchtigs/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: eb7e74869dee075a16377ca5497dbb08967e34b81ffadae7fa206f9946eb6037
+  sha256: b01f2e3582801eda2f7003a2bf5843c4d4788e71c178eb226e70775aeaf48370
 
 requirements:
   build:
-    - rust >=1.60
+    - rust >=1.65
     - {{ compiler('c') }}
 
 test:

recipes/miniprot/meta.yaml

@@ -1,13 +1,13 @@
-{% set version = "0.11" %}
+{% set version = "0.12" %}
 {% set name = "miniprot" %}
-{% set sha256 = "e76df7b4cbb0bd9d543f4b9ca5a59ae5cf6e6dc342c1784823260c11611e25b7" %}
+{% set sha256 = "869df52d8a3d350e0a5ba6eb0d1685e78bb7087ace9870d196f5fb4761c3a692" %}
 
 package:
   name: "{{ name }}"
   version: "{{ version }}"
 
 build:
-  number: 2
+  number: 0
 
 source:
   url: "https://github.com/lh3/miniprot/archive/refs/tags/v{{ version }}.tar.gz"

recipes/ngsderive/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "ngsderive" %}
-{% set version = "3.1.1" %}
+{% set version = "3.2.1" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: a4979b9d67b3007dbe78324cab40705ab041160416b428a3044a6e5cc046a77d
+  sha256: ca44c1f299e42ad10cff465d24a683a142a93efa82acc0487f58afa367e6ed1f
 
 build:
   number: 0

recipes/niemads/meta.yaml

@@ -1,12 +1,12 @@
-{% set version = "1.0.14" %}
+{% set version = "1.0.15" %}
 
 package:
   name: "niemads"
   version: "{{ version }}"
 
 source:
   url: https://pypi.io/packages/source/n/niemads/niemads-{{ version }}.tar.gz
-  sha256: bf2467714416f3060807790b7d4a722cb72b0f41680e277afccbddbf5009a9d9
+  sha256: c969c8c48ceeae528ecd91d6f41db71d0b19fb680789596d36f65c7c94431bb2
 
 build:
   noarch: python

recipes/phate/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "phate" %}
-{% set version = "1.0.10" %}
-{% set sha256 = "39de6ba19c83713cd5d378c9bcdb4ef9db8f3ca79a0f43c0dddf63a21edff29d" %}
+{% set version = "1.0.11" %}
+{% set sha256 = "10162e9edd09ce5d0e667b0767e96eed6bda5ee877667202ffff0a578ab5076d" %}
 
 package:
   name: "{{ name|lower }}"

recipes/pytrimal/meta.yaml

@@ -1,19 +1,18 @@
 {% set name = "pytrimal" %}
-{% set version = "0.5.5" %}
+{% set version = "0.6.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 1989dac527399f59b3a269e0eb447fc05714a119dbb1a8beb9bcd76c96533858
+  sha256: 4983077f96d665472937cce53979f4ee8514546b51a773e57f919e0fddb5a04b
 
 build:
-  number: 2
+  number: 0
 
-  # Build currently failing for py310 on osx
-  skip: True  #[py2k or (osx and py>39)]
+  skip: True  #[py2k]
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv "
 
 requirements:
@@ -28,6 +27,7 @@ requirements:
   run:
     - python
     - setuptools
+    - archspec
 
 test:
   imports:

recipes/r-ccqtl/meta.yaml

@@ -1,8 +1,8 @@
 {% set name = "ccqtl" %}
-{% set version = "0.0.1-beta.1" %}
-{% set tag = "v0.0.1-beta.1" %}
+{% set version = "0.0.1-beta.2" %}
+{% set tag = "v0.0.1-beta.2" %}
 {% set owner = "cc-qtl" %}
-{% set sha256 = "e70f91398215a556182c7a33d40fc3185153f28b55d1971e517991ab7243bef7" %}
+{% set sha256 = "ba6c7c29eaa78baa5b8a8d909e42cec6c9c1b24860daef077158a60bdd9651fb" %}
 
 package:
   name: r-ccqtl