From 973f68c6a6d0a5c8202d5acf28090463f2717a0e Mon Sep 17 00:00:00 2001 From: Luan Nguyen <125411678+luan-n-nguyen@users.noreply.github.com> Date: Sun, 13 Oct 2024 15:14:46 +1100 Subject: [PATCH 01/16] Update hmftools-{esvee,purple,linx,redux} (#51294) --- recipes/hmftools-esvee/meta.yaml | 7 ++++--- recipes/hmftools-linx/meta.yaml | 8 +++++--- recipes/hmftools-purple/meta.yaml | 8 +++++--- recipes/hmftools-redux/meta.yaml | 7 ++++--- 4 files changed, 18 insertions(+), 12 deletions(-) diff --git a/recipes/hmftools-esvee/meta.yaml b/recipes/hmftools-esvee/meta.yaml index 96678744d953d..9a11455bde79d 100644 --- a/recipes/hmftools-esvee/meta.yaml +++ b/recipes/hmftools-esvee/meta.yaml @@ -1,17 +1,18 @@ {% set version = "1.0_beta" %} -{% set sha256 = "7ee885d48306e73c0cefacd7d59f2aabd213fc6d78d4ca8489a8d6c25e8ce333" %} +{% set beta_suffix = ".2" %} +{% set sha256 = "75933500cde12741534580d84bdafc6ad7b3290f382973dbcf540580b9453bd9" %} package: name: hmftools-esvee version: '{{ version }}' source: - url: https://github.com/hartwigmedical/hmftools/releases/download/esvee-v{{ version }}/esvee_v{{ version }}.jar + url: https://github.com/hartwigmedical/hmftools/releases/download/esvee-v{{ version }}/esvee_v{{ version }}{{ beta_suffix }}.jar sha256: '{{ sha256 }}' build: noarch: generic - number: 0 + number: 2 run_exports: - {{ pin_subpackage("hmftools-esvee", max_pin="x.x") }} diff --git a/recipes/hmftools-linx/meta.yaml b/recipes/hmftools-linx/meta.yaml index b7d512fde85ad..300175a2287dd 100644 --- a/recipes/hmftools-linx/meta.yaml +++ b/recipes/hmftools-linx/meta.yaml @@ -1,12 +1,13 @@ -{% set version = "1.25" %} -{% set sha256 = "2fa9a91801239ded3e82fcd0ee9987e6181d0e400855420ef7f5000f3b4a96da" %} +{% set version = "2.0_beta" %} +{% set beta_suffix = ".1" %} +{% set sha256 = "34bb84e9563d3847544f5e457211ff9a74473131e5a609ebae960a7a3cfcf8d9" %} package: name: hmftools-linx version: '{{ version }}' source: - url: https://github.com/hartwigmedical/hmftools/releases/download/linx-v{{ version }}/linx_v{{ version }}.jar + url: https://github.com/hartwigmedical/hmftools/releases/download/linx-v{{ version }}/linx_v{{ version }}{{ beta_suffix }}.jar sha256: '{{ sha256 }}' build: @@ -26,6 +27,7 @@ requirements: - r-magick - bioconductor-gviz - circos >=0.69.6 + - perl-gd >=2.76 # Fixes missing GD perl module error (even though circos does install GD) test: commands: diff --git a/recipes/hmftools-purple/meta.yaml b/recipes/hmftools-purple/meta.yaml index ae81543b0e19c..d979ebdf55c18 100644 --- a/recipes/hmftools-purple/meta.yaml +++ b/recipes/hmftools-purple/meta.yaml @@ -1,12 +1,13 @@ -{% set version = "4.0.2" %} -{% set sha256 = "fb534734b4a0833c8d68591e009caea5b654714211a95f23570c1fca9bfa57a9" %} +{% set version = "4.1_beta" %} +{% set beta_suffix = ".1" %} +{% set sha256 = "aa5b1ec3c0e67027750fce6ac71bc31d55c37405c8e00571594d58c837e74a51" %} package: name: hmftools-purple version: '{{ version }}' source: - url: https://github.com/hartwigmedical/hmftools/releases/download/purple-v{{ version }}/purple_v{{ version }}.jar + url: https://github.com/hartwigmedical/hmftools/releases/download/purple-v{{ version }}/purple_v{{ version }}{{ beta_suffix }}.jar sha256: '{{ sha256 }}' build: @@ -21,6 +22,7 @@ requirements: - openjdk >=8 - xorg-libxtst - circos >=0.69.6 + - perl-gd >=2.76 # Fixes missing GD perl module error (even though circos does install GD) - bioconductor-variantannotation - r-cairo - r-cowplot diff --git a/recipes/hmftools-redux/meta.yaml b/recipes/hmftools-redux/meta.yaml index 4cb7214af925a..7abd6496a2637 100644 --- a/recipes/hmftools-redux/meta.yaml +++ b/recipes/hmftools-redux/meta.yaml @@ -1,17 +1,18 @@ {% set version = "1.0_beta" %} -{% set sha256 = "40caa3f1f493a1eb3c0e029f084f3c7d52456dbd9bbc72f118015b525ea9d467" %} +{% set beta_suffix = ".1" %} +{% set sha256 = "0789230f3f7c8fe65c26709fbe4bc95a70e8b7465526dac8c1613d632c43a1e8" %} package: name: hmftools-redux version: '{{ version }}' source: - url: https://github.com/hartwigmedical/hmftools/releases/download/redux-v{{ version }}/redux_v{{ version }}.jar + url: https://github.com/hartwigmedical/hmftools/releases/download/redux-v{{ version }}/redux_v{{ version }}{{ beta_suffix }}.jar sha256: '{{ sha256 }}' build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('hmftools-redux', max_pin="x.x") }} From b8fe8b80524926dd0bed3c8dc0739fc9bba253c4 Mon Sep 17 00:00:00 2001 From: Anthony Fullam Date: Sun, 13 Oct 2024 06:15:56 +0200 Subject: [PATCH 02/16] Add meta_eukaryome_detect (#51328) --- recipes/meta_eukaryome_detect/meta.yml | 47 ++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 recipes/meta_eukaryome_detect/meta.yml diff --git a/recipes/meta_eukaryome_detect/meta.yml b/recipes/meta_eukaryome_detect/meta.yml new file mode 100644 index 0000000000000..e5a65c5575be3 --- /dev/null +++ b/recipes/meta_eukaryome_detect/meta.yml @@ -0,0 +1,47 @@ +{% set name = "meta_eukaryome_detect" %} +{% set version = "0.1.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 0199ad179d36d3683b8122f41b1e5db6c5d7d94324c3fe5187d576fafdfa2cdc + +build: + number: 0 + entry_points: + - meta_eukaryome_detect = meta_eukaryome_detect.meta_eukaryome_detect:main + script: "{{ PYTHON }} -m pip install . -vv --ignore-installed --no-deps" + noarch: python + run_exports: + {{ pin_subpackage(name, max_pin="x") }} + +requirements: + host: + - pip + - python >=3.11 + run: + - ngless + - samtools + - pandas >= 2.0 + - requests +test: + imports: + - meta_eukaryome_detect + commands: + - meta_eukaryome_detect --help + +about: + home: "https://github.com/grp-bork/meta_eukaryome_detect" + license: "MIT License" + license_family: MIT + license_file: LICENSE + summary: "Pathogen, Parasite, Eukaryote and Virus detection in metagenomes." + doc_url: "https://grp-bork.embl-community.io/grp-microbiome-astrology/meta_eukaryome_detect/" + dev_url: "https://github.com/grp-bork/meta_eukaryome_detect" + +extra: + recipe-maintainers: + - fullama From 9213371a73521db7670ad1d3343a89dcc12dca70 Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Sun, 13 Oct 2024 06:31:27 +0200 Subject: [PATCH 03/16] update md5sum and bump eigen version to 3.3.4 (#51331) --- recipes/openms-meta/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/openms-meta/meta.yaml b/recipes/openms-meta/meta.yaml index 32c28922e024f..58917f743b665 100644 --- a/recipes/openms-meta/meta.yaml +++ b/recipes/openms-meta/meta.yaml @@ -12,11 +12,11 @@ source: {% else %} source: url: https://github.com/OpenMS/OpenMS/releases/download/release%2F3.2.0/OpenMS-3.2.tar.gz # since we discarded the trailing 0 during the GHA we have to hard code this, fix it next release - md5: 60ebfe8a45f7e1fb5566d21231b460e8 + md5: e15b34a4ccaf7070d186fd01a6d57f3e {% endif %} build: - number: 4 + number: 5 skip: True # [osx] # Try this when building with GUI @@ -39,7 +39,7 @@ requirements: - libtool - xerces-c - boost-cpp - - eigen >=3.3.2 + - eigen >=3.3.4 - hdf5 >=1.10 - bzip2 - qt-main @@ -71,7 +71,7 @@ outputs: - libtool - xerces-c - boost-cpp - - eigen >=3.3.2 + - eigen >=3.3.4 - hdf5 >=1.10 - bzip2 - qt-main @@ -114,7 +114,7 @@ outputs: - libtool - xerces-c - boost-cpp - - eigen >=3.3.2 + - eigen >=3.3.4 - hdf5 >=1.10 - bzip2 - qt-main From c6c23f39c87fcdd5cb6af90c2e3e1e1421c26ae1 Mon Sep 17 00:00:00 2001 From: Andrea Guarracino <62253982+AndreaGuarracino@users.noreply.github.com> Date: Sat, 12 Oct 2024 23:38:30 -0500 Subject: [PATCH 04/16] Add `cosigt` (#51343) --- recipes/cosigt/build.sh | 7 +++++++ recipes/cosigt/meta.yaml | 38 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 recipes/cosigt/build.sh create mode 100644 recipes/cosigt/meta.yaml diff --git a/recipes/cosigt/build.sh b/recipes/cosigt/build.sh new file mode 100644 index 0000000000000..29bd1a4602122 --- /dev/null +++ b/recipes/cosigt/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin +go mod init cosigt +go mod tidy +go get -d ./... +CGO_ENABLED=0 go build -o $PREFIX/bin/cosigt . diff --git a/recipes/cosigt/meta.yaml b/recipes/cosigt/meta.yaml new file mode 100644 index 0000000000000..c414073e6c5ea --- /dev/null +++ b/recipes/cosigt/meta.yaml @@ -0,0 +1,38 @@ +{% set name = "cosigt" %} +{% set version = "0.1.1" %} + +package: + name: {{ name }} + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + +source: + - url: https://github.com/davidebolo1993/{{ name }}/archive/tags/{{ version }}.tar.gz + sha256: 7db68d7e02424fba7248db4ddd0853f1c634b31e62906037765f1f481e63635d + +requirements: + build: + - {{ compiler('go') }} + +test: + commands: + - cosigt -h + +about: + home: https://github.com/davidebolo1993/{{ name }} + license: 'GNU General Public License v3 (GPLv3)' + license_family: GPL3 + license_file: LICENSE + summary: Cosigt (COsine SImilarity-based GenoTyper) + dev_url: https://github.com/davidebolo1993/{{ name }} + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + recipe-maintainers: + - AndreaGuarracino From acd125a2c9e502e7da511205c1f3a4c361821314 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Sun, 13 Oct 2024 12:58:11 +0200 Subject: [PATCH 05/16] Add phabox (#50753) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * initial commit of phabox * add shebang line * try to finalize phabox builds locally * add sha256 * try to fix linter errir * Update meta.yaml * adapt to 1.0 * fix patch * remove unused file and requirement * that should not change anything * Update recipes/phabox/meta.yaml * add setuptools requirement * wo pyarrow * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * something is really off here * Update meta.yaml * Bump to 2.0.0 --------- Co-authored-by: Björn Grüning --- recipes/phabox/meta.yaml | 55 +++++++++ recipes/phabox/setup.patch | 229 +++++++++++++++++++++++++++++++++++++ 2 files changed, 284 insertions(+) create mode 100644 recipes/phabox/meta.yaml create mode 100644 recipes/phabox/setup.patch diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml new file mode 100644 index 0000000000000..014462e5a79f6 --- /dev/null +++ b/recipes/phabox/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "PhaBOX" %} +{% set version = "2.0.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/KennthShang/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 3e120da4b6c37d1ae9f7291382365012a4efa0c4e704068c1ecd897e5fd8178a + patches: + - setup.patch + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('phabox', max_pin="x.x") }} + +requirements: + host: + - pip + - python + - setuptools + run: + - python + - biopython >=1.84 + - networkx >=3.4 + - numpy >=2 + - pandas >=2 + - pprodigal >=1 + - scipy >=1.14 + - pytorch >=2.4 + - transformers >=4.40 + - datasets >=3 + - pyarrow >=17 + +test: + commands: + - phabox --help + - Cherry_single --help + - PhaGCN_single --help + - PhaMer_single --help + - PhaTYP_single --help + +about: + home: https://github.com/KennthShang/PhaBOX + license: AFL + license_file: LICENSE.md + summary: Phage BOX is a Python library for phage-related tasks + +extra: + recipe-maintainers: + - bernt-matthias diff --git a/recipes/phabox/setup.patch b/recipes/phabox/setup.patch new file mode 100644 index 0000000000000..b5213da9b8f34 --- /dev/null +++ b/recipes/phabox/setup.patch @@ -0,0 +1,229 @@ +diff -ruN PhaBOX-1.0.0-org/Cherry_single.py PhaBOX-1.0.0/Cherry_single.py +--- PhaBOX-1.0.0-org/Cherry_single.py 2024-09-30 10:20:05.496290778 +0200 ++++ PhaBOX-1.0.0/Cherry_single.py 2024-09-30 13:26:23.735605652 +0200 +@@ -16,21 +16,21 @@ + from torch import optim + from torch.nn import functional as F + +-from scripts.ulity import * +-from scripts.preprocessing import * +-from scripts.cnnscript import * ++from phabox.scripts.ulity import * ++from phabox.scripts.preprocessing import * ++from phabox.scripts.cnnscript import * + from shutil import which + from collections import Counter + from Bio import SeqIO + from Bio.SeqRecord import SeqRecord + from Bio.Blast.Applications import NcbiblastnCommandline +-from models.phamer import Transformer +-from models.CAPCNN import WCNN +-from models.PhaGCN import GCN +-from models import Cherry +-from draw import draw_network, drop_network ++from phabox.models.phamer import Transformer ++from phabox.models.CAPCNN import WCNN ++from phabox.models.PhaGCN import GCN ++from phabox.models import Cherry ++from phabox.draw import draw_network, drop_network + from scipy.special import softmax +-from scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask ++from phabox.scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask + + + +diff -ruN PhaBOX-1.0.0-org/draw.py PhaBOX-1.0.0/draw.py +--- PhaBOX-1.0.0-org/draw.py 2024-09-30 10:20:05.500290882 +0200 ++++ PhaBOX-1.0.0/draw.py 2024-09-30 13:27:20.231425936 +0200 +@@ -4,8 +4,8 @@ + import numpy as np + import argparse + import subprocess +-from scripts.ulity import * +-from scripts.preprocessing import * ++from phabox.scripts.ulity import * ++from phabox.scripts.preprocessing import * + import math + import os + import pandas as pd +diff -ruN PhaBOX-1.0.0-org/main.py PhaBOX-1.0.0/main.py +--- PhaBOX-1.0.0-org/main.py 2024-09-30 10:20:05.500290882 +0200 ++++ PhaBOX-1.0.0/main.py 2024-09-30 13:27:33.651385105 +0200 +@@ -16,22 +16,22 @@ + from torch import optim + from torch.nn import functional as F + +-from scripts.ulity import * +-from scripts.preprocessing import * +-from scripts.cnnscript import * ++from phabox.scripts.ulity import * ++from phabox.scripts.preprocessing import * ++from phabox.scripts.cnnscript import * + from shutil import which + from collections import Counter + from Bio import SeqIO + from Bio.SeqRecord import SeqRecord + from Bio.Blast.Applications import NcbiblastnCommandline +-from models.phamer import Transformer +-from models.CAPCNN import WCNN +-from models.PhaGCN import GCN +-from models import Cherry +-from draw import draw_network, drop_network ++from phabox.models.phamer import Transformer ++from phabox.models.CAPCNN import WCNN ++from phabox.models.PhaGCN import GCN ++from phabox.models import Cherry ++from phabox.draw import draw_network, drop_network + from collections import Counter + from scipy.special import softmax +-from scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask ++from phabox.scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask + + + +diff -ruN PhaBOX-1.0.0-org/PhaGCN_single.py PhaBOX-1.0.0/PhaGCN_single.py +--- PhaBOX-1.0.0-org/PhaGCN_single.py 2024-09-30 10:20:05.496290778 +0200 ++++ PhaBOX-1.0.0/PhaGCN_single.py 2024-09-30 13:26:46.099532952 +0200 +@@ -13,21 +13,21 @@ + import scipy.sparse as sparse + + +-from scripts.ulity import * +-from scripts.preprocessing import * +-from scripts.cnnscript import * ++from phabox.scripts.ulity import * ++from phabox.scripts.preprocessing import * ++from phabox.scripts.cnnscript import * + from shutil import which + from collections import Counter + from Bio import SeqIO + from Bio.SeqRecord import SeqRecord + from Bio.Blast.Applications import NcbiblastnCommandline +-from models.phamer import Transformer +-from models.CAPCNN import WCNN +-from models.PhaGCN import GCN +-from models import Cherry +-from draw import draw_network, drop_network ++from phabox.models.phamer import Transformer ++from phabox.models.CAPCNN import WCNN ++from phabox.models.PhaGCN import GCN ++from phabox.models import Cherry ++from phabox.draw import draw_network, drop_network + from scipy.special import softmax +-from scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask ++from phabox.scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask + + from torch import nn + from torch import optim +diff -ruN PhaBOX-1.0.0-org/PhaMer_single.py PhaBOX-1.0.0/PhaMer_single.py +--- PhaBOX-1.0.0-org/PhaMer_single.py 2024-09-30 10:20:05.500290882 +0200 ++++ PhaBOX-1.0.0/PhaMer_single.py 2024-09-30 13:26:53.231510206 +0200 +@@ -16,20 +16,20 @@ + from torch import optim + from torch.nn import functional as F + +-from scripts.ulity import * +-from scripts.preprocessing import * +-from scripts.cnnscript import * ++from phabox.scripts.ulity import * ++from phabox.scripts.preprocessing import * ++from phabox.scripts.cnnscript import * + from shutil import which + from collections import Counter + from Bio import SeqIO + from Bio.SeqRecord import SeqRecord + from Bio.Blast.Applications import NcbiblastnCommandline +-from models.phamer import Transformer +-from models.CAPCNN import WCNN +-from models.PhaGCN import GCN +-from models import Cherry ++from phabox.models.phamer import Transformer ++from phabox.models.CAPCNN import WCNN ++from phabox.models.PhaGCN import GCN ++from phabox.models import Cherry + from scipy.special import softmax +-from scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask ++from phabox.scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask + + + +diff -ruN PhaBOX-1.0.0-org/PhaTYP_single.py PhaBOX-1.0.0/PhaTYP_single.py +--- PhaBOX-1.0.0-org/PhaTYP_single.py 2024-09-30 10:20:05.500290882 +0200 ++++ PhaBOX-1.0.0/PhaTYP_single.py 2024-09-30 13:27:03.755477016 +0200 +@@ -16,20 +16,20 @@ + from torch import optim + from torch.nn import functional as F + +-from scripts.ulity import * +-from scripts.preprocessing import * +-from scripts.cnnscript import * ++from phabox.scripts.ulity import * ++from phabox.scripts.preprocessing import * ++from phabox.scripts.cnnscript import * + from shutil import which + from collections import Counter + from Bio import SeqIO + from Bio.SeqRecord import SeqRecord + from Bio.Blast.Applications import NcbiblastnCommandline +-from models.phamer import Transformer +-from models.CAPCNN import WCNN +-from models.PhaGCN import GCN +-from models import Cherry ++from phabox.models.phamer import Transformer ++from phabox.models.CAPCNN import WCNN ++from phabox.models.PhaGCN import GCN ++from phabox.models import Cherry + from scipy.special import softmax +-from scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask ++from phabox.scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask + + + +diff -ruN PhaBOX-1.0.0-org/scripts/cnnscript.py PhaBOX-1.0.0/scripts/cnnscript.py +--- PhaBOX-1.0.0-org/scripts/cnnscript.py 2024-09-30 10:20:05.608293722 +0200 ++++ PhaBOX-1.0.0/scripts/cnnscript.py 2024-09-30 13:25:46.367731972 +0200 +@@ -3,7 +3,7 @@ + import numpy as np + import torch + import torch.utils.data as Data +-from models.CAPCNN import WCNN ++from phabox.models.CAPCNN import WCNN + from Bio import SeqIO + from Bio.SeqRecord import SeqRecord + from torch import nn +diff -ruN PhaBOX-1.0.0-org/scripts/data.py PhaBOX-1.0.0/scripts/data.py +--- PhaBOX-1.0.0-org/scripts/data.py 2024-09-30 10:20:05.608293722 +0200 ++++ PhaBOX-1.0.0/scripts/data.py 2024-09-30 13:26:08.807655370 +0200 +@@ -2,6 +2,7 @@ + import pickle as pkl + import networkx as nx + import scipy.sparse as sp ++from scipy.sparse.linalg import eigsh + import sys + + +diff -ruN PhaBOX-1.0.0-org/setup.py PhaBOX-1.0.0/setup.py +--- PhaBOX-1.0.0-org/setup.py 2024-09-30 10:20:05.500290882 +0200 ++++ PhaBOX-1.0.0/setup.py 2024-09-30 10:21:12.297733200 +0200 +@@ -3,7 +3,20 @@ + setup( + name='phabox', + version='1.0', +- packages=find_packages(), ++ packages=["phabox"], ++ package_dir={'phabox': '.'}, ++ package_data={ ++ '': ['scripts/*.py', 'models/*.py', 'GTDB/*.py'] ++ }, ++ entry_points={ ++ 'console_scripts': [ ++ 'phabox=phabox.main:main', # Allows running the script with `phabox` command ++ 'Cherry_single=phabox.Cherry_single:main', ++ 'PhaGCN_single=phabox.PhaGCN_single:main', ++ 'PhaMer_single=phabox.PhaMer_single:main', ++ 'PhaTYP_single=phabox.PhaTYP_single:main', ++ ] ++ }, + install_requires=[ + 'numpy==1.21.2', + 'pandas==1.3.4', From c67fb89de53d7fd79d7a08871cdd348088fc4eba Mon Sep 17 00:00:00 2001 From: Xiangyang1984 <58356520+Xiangyang1984@users.noreply.github.com> Date: Mon, 14 Oct 2024 17:16:40 +0800 Subject: [PATCH 06/16] add pneumo-typer recipes (#51358) * add pneumo-typer recipes * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml --- recipes/pneumo-typer/build.sh | 12 +++++++++--- recipes/pneumo-typer/meta.yaml | 9 ++++++--- 2 files changed, 15 insertions(+), 6 deletions(-) diff --git a/recipes/pneumo-typer/build.sh b/recipes/pneumo-typer/build.sh index 6f3abb816792e..e479acb54e013 100644 --- a/recipes/pneumo-typer/build.sh +++ b/recipes/pneumo-typer/build.sh @@ -4,7 +4,8 @@ set -x -e RM_DIR=${PREFIX}/share/pneumo-typer mkdir -p ${RM_DIR} mkdir -p ${PREFIX}/bin -cp -r pneumo-typer-v1.0.1/* ${RM_DIR} +ls -a +cp -r $SRC_DIR/* ${RM_DIR} cp build_env_setup.sh ${RM_DIR} cp conda_build.sh ${RM_DIR} cp metadata_conda_debug.yaml ${RM_DIR} @@ -13,6 +14,11 @@ cat <>${PREFIX}/bin/pneumo-typer #!/bin/bash perl ${RM_DIR}/pneumo-typer.pl \$@ END +# Set a executable file for update_mlstdb_cgmlstdb.pl +cat <>${PREFIX}/bin/update_mlstdb_cgmlstdb +#!/bin/bash +perl ${RM_DIR}/update_mlstdb_cgmlstdb.pl \$@ +END - -chmod a+x ${PREFIX}/bin/pneumo-typer \ No newline at end of file +chmod a+x ${PREFIX}/bin/pneumo-typer +chmod a+x ${PREFIX}/bin/update_mlstdb_cgmlstdb diff --git a/recipes/pneumo-typer/meta.yaml b/recipes/pneumo-typer/meta.yaml index b5265377333d4..676037376f5f9 100644 --- a/recipes/pneumo-typer/meta.yaml +++ b/recipes/pneumo-typer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pneumo-typer" %} -{% set version = "1.0.1" %} -{% set sha256 = "26ff14bc8bd48588e6b2332dfa25fcae2239a89d981a00622b16818a926cf194" %} +{% set version = "1.0.2" %} +{% set sha256 = "5ba1aa25862376d44f612c1f9d25ac9fa9ab76aa10dc88939fb27518bf70e013" %} package: name: "{{ name|lower }}" @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 0 noarch: generic run_exports: - {{ pin_subpackage('pneumo-typer', max_pin="x") }} @@ -36,11 +36,14 @@ test: - makeblastdb -h #- blat - pneumo-typer -h + - update_mlstdb_cgmlstdb -h - prodigal -h about: home: 'https://www.microbialgenomic.cn/Pneumo-Typer.html' summary: 'Pneumo-Typer is a comprehensive prediction and visualization of serotype and sequence type for streptococcus pneumoniae using assembled genomes.' + description: 'Pneumo-Typer is a stand-alone perl application, which requires blat, prodigal, NCBI BLAST+, and several perl Modules (GD, GD::SVG) to be installed before use.' + doc_url: 'https://github.com/Xiangyang1984/Pneumo-Typer' license: GNU General Public License v3.0 or any later version (GPL-3.0-or-later) extra: From c1ac79dcf6450300a907bbc1936f2725fb9cda51 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 14 Oct 2024 05:17:14 -0400 Subject: [PATCH 07/16] Update snakemake to 8.22.0 (#51362) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index b2d9459730c04..f467b3193338e 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,7 +1,7 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg {% set name = "snakemake" %} -{% set version = "8.21.0" %} +{% set version = "8.22.0" %} package: name: {{ name }} @@ -9,7 +9,7 @@ package: source: url: https://pypi.io/packages/source/s/{{ name }}/snakemake-{{ version }}.tar.gz - sha256: dcb30052645ab89facf680ef4ec021143eb5ef862bb2d2de2ec190a616c3c471 + sha256: fe94ee1432ec07af783220bd115ea94b2262072956366a81b6762a9969c11f4a build: number: 0 From 2749972d0e772fba4d23a0e58f8f48041bae2e37 Mon Sep 17 00:00:00 2001 From: Jim Shaw Date: Mon, 14 Oct 2024 02:22:05 -0700 Subject: [PATCH 08/16] Adding the devider recipe (#51365) * Added dbghaplo recipe. * Added dbghaplo recipe v0.02 * space between versioning issue * Changed lofreq command * Update recipes/dbghaplo/meta.yaml Co-authored-by: Michael Hall * Update recipes/dbghaplo/build.sh Co-authored-by: Michael Hall * Update recipes/dbghaplo/meta.yaml Co-authored-by: Michael Hall * Update recipes/dbghaplo/meta.yaml Co-authored-by: Michael Hall * Update recipes/dbghaplo/meta.yaml Co-authored-by: Michael Hall * Added the devider recipe (rename of dbghaplo recipe) --------- Co-authored-by: Michael Hall --- recipes/devider/build.sh | 10 +++++++++ recipes/devider/meta.yaml | 47 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 recipes/devider/build.sh create mode 100644 recipes/devider/meta.yaml diff --git a/recipes/devider/build.sh b/recipes/devider/build.sh new file mode 100644 index 0000000000000..17d5db214e9a0 --- /dev/null +++ b/recipes/devider/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +cargo-bundle-licenses --format yaml --output THIRDPARTY.yml +RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path . +cp scripts/* $PREFIX/bin diff --git a/recipes/devider/meta.yaml b/recipes/devider/meta.yaml new file mode 100644 index 0000000000000..b9ea2b34e8c0d --- /dev/null +++ b/recipes/devider/meta.yaml @@ -0,0 +1,47 @@ +{% set version="0.0.1" %} + +package: + name: devider + version: {{ version }} + +source: + url: https://github.com/bluenote-1577/devider/archive/v{{ version }}.tar.gz + sha256: e2c5e4a2faa51dbfd0ad4cb867d0dc25ea4012e83ec8fea27c1624592fce7dce + +build: + number: 0 + run_exports: + - {{ pin_subpackage('devider', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("cxx") }} + - {{ compiler('rust') }} + - cargo-bundle-licenses + - make + - cmake >=3.12 + run: + - python + - samtools + - minimap2 + - lofreq >=2.1.5 + - tabix + - pysam >=0.16 + +test: + commands: + - devider -h + - run_devider_pipeline -h + - haplotag_bam -h + +about: + home: https://github.com/bluenote-1577/devider + license: MIT + license_file: + - LICENSE + - THIRDPARTY.yml + summary: Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn graphs. + +extra: + recipe-maintainers: + - bluenote-1577 From a8fe9adabdd869c86f5da8803690e835d6304124 Mon Sep 17 00:00:00 2001 From: Anthony Fullam Date: Mon, 14 Oct 2024 11:24:07 +0200 Subject: [PATCH 09/16] Update meta_eukaryome_detect: Rename meta.yml to meta.yaml (#51366) * Rename meta.yml to meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/meta_eukaryome_detect/{meta.yml => meta.yaml} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename recipes/meta_eukaryome_detect/{meta.yml => meta.yaml} (97%) diff --git a/recipes/meta_eukaryome_detect/meta.yml b/recipes/meta_eukaryome_detect/meta.yaml similarity index 97% rename from recipes/meta_eukaryome_detect/meta.yml rename to recipes/meta_eukaryome_detect/meta.yaml index e5a65c5575be3..b7ae05c8ae290 100644 --- a/recipes/meta_eukaryome_detect/meta.yml +++ b/recipes/meta_eukaryome_detect/meta.yaml @@ -22,10 +22,11 @@ requirements: host: - pip - python >=3.11 + - poetry run: - ngless - samtools - - pandas >= 2.0 + - pandas >=2.0 - requests test: imports: From aaef81b3278997d0796753f8a749cc191afee027 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 14 Oct 2024 06:18:03 -0400 Subject: [PATCH 10/16] Update perl-excel-writer-xlsx to 1.13 (#46030) * Update perl-excel-writer-xlsx to 1.12 * Update perl-excel-writer-xlsx to 1.13 * Add run_exports --------- Co-authored-by: Martin Grigorov --- recipes/perl-excel-writer-xlsx/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/perl-excel-writer-xlsx/meta.yaml b/recipes/perl-excel-writer-xlsx/meta.yaml index c66a70eac4338..48eb53c2c4999 100644 --- a/recipes/perl-excel-writer-xlsx/meta.yaml +++ b/recipes/perl-excel-writer-xlsx/meta.yaml @@ -1,16 +1,18 @@ {% set name = "perl-excel-writer-xlsx" %} -{% set version = "1.11" %} -{% set sha256 = "cb3300d23119c698864ef0b73c19a72cba718bfc06ed007359a5313f961cc2a0" %} +{% set version = "1.13" %} +{% set sha256 = "3d60b14e40cd6d93b8e5b40c1bf814122301107fe10e7e6b4120ed3fe87009c9" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/Excel-Writer-XLSX-1.11.tar.gz + url: https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/Excel-Writer-XLSX-1.13.tar.gz sha256: {{ sha256 }} build: + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} number: 0 noarch: generic From fe9fa8e6521b4b1e8829729d2d3a294d2233d857 Mon Sep 17 00:00:00 2001 From: Quentin Blampey <33903498+quentinblampey@users.noreply.github.com> Date: Mon, 14 Oct 2024 12:48:22 +0200 Subject: [PATCH 11/16] adding sopa meta.yaml file (#51367) --- sopa/meta.yaml | 70 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 sopa/meta.yaml diff --git a/sopa/meta.yaml b/sopa/meta.yaml new file mode 100644 index 0000000000000..cbe346742649b --- /dev/null +++ b/sopa/meta.yaml @@ -0,0 +1,70 @@ +{% set name = "sopa" %} +{% set version = "1.1.5" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/sopa-{{ version }}.tar.gz + sha256: f2b7265b5d231bdcca49185e8b2015fea34ea53404336165befb920fb3427fc6 + +build: + entry_points: + - sopa = sopa.main:app + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + +requirements: + host: + - python >=3.9,<3.12 + - poetry-core >=1.0.0 + - pip + run: + - python >=3.9,<3.12 + - spatialdata >=0.2.0 + - spatialdata-io >=0.1.3 + - scanpy >=1.9.8 + - botocore 1.34.19 + - typer >=0.9.0 + - setuptools >=69.2.0 + - flake8 <8.0.0,>=7.0.0 + run_constrained: + - cellpose >=3.0.5 + - opencv >=4.8.0.76 + - pytorch >=2.0.0,!=2.0.1,!=2.1.0 + - toml >=0.10.2 + - loompy >=3.0.7 + - tangram-sc >=1.0.4 + - snakemake >=7.32.4,<8.0.0,<8.1.3 + - pulp >=2.3.1,<3.0.0,<2.8 + - tiffslide >=2.3.1,<3.0.0 + - black >=22.8.0,<23.0.0 + - isort >=5.10.1,<6.0.0 + - pytest >=7.1.3,<8.0.0 + - ipykernel >=6.25.2,<7.0.0 + - mkdocs-material >=9.3.2,<10.0.0 + - mkdocs-jupyter >=0.24.6,<0.25.0 + - mkdocstrings >=0.23.0,<0.24.0 + - mkdocstrings-python >=1.7.3,<2.0.0 + - flake8 >=7.0.0,<8.0.0 + +test: + imports: + - sopa + commands: + - pip check + - sopa --help + requires: + - pip + +about: + home: https://gustaveroussy.github.io/sopa + summary: Spatial-omics pipeline and analysis + license: BSD-3-Clause + license_file: LICENSE + +extra: + recipe-maintainers: + - quentinblampey From 1c1935d58c54bfd0da3c5277ad27f60ba69207f4 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Mon, 14 Oct 2024 11:53:05 +0100 Subject: [PATCH 12/16] thermorawfileparser 1.4.5 (#51368) --- recipes/thermorawfileparser/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/thermorawfileparser/meta.yaml b/recipes/thermorawfileparser/meta.yaml index 13b3928df5f63..79cc2bcc2ed53 100644 --- a/recipes/thermorawfileparser/meta.yaml +++ b/recipes/thermorawfileparser/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ThermoRawFileParser" %} -{% set version = "1.4.4" %} +{% set version = "1.4.5" %} package: name: {{ name|lower }} @@ -21,7 +21,7 @@ build: source: # downloading pre-compiled packages, msbuild is a hell to compile under Linux url: https://github.com/compomics/ThermoRawFileParser/releases/download/v{{ version }}/ThermoRawFileParser{{ version }}.zip - sha256: 5fff9266636422557095b5eea0a18b26f5a9972f49a538d93cb969a6b239a044 + sha256: be1f8fd6f85b20750d5f59c324f031882f911035ff4e93c4e98c9b2d73944b37 requirements: build: From 059406b03a2267330acbfb5436615bddf8f42d73 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 14 Oct 2024 08:09:06 -0400 Subject: [PATCH 13/16] Update resistify to 0.4.0 (#51372) --- recipes/resistify/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/resistify/meta.yaml b/recipes/resistify/meta.yaml index 36d96e8d1b98d..08e802612190e 100644 --- a/recipes/resistify/meta.yaml +++ b/recipes/resistify/meta.yaml @@ -1,5 +1,5 @@ {% set name = "resistify" %} -{% set version = "0.3.0" %} +{% set version = "0.4.0" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 3a8f4ccedf38fb1a7cdb3522ad6497d054bd72164155bcdc03aa23133b030623 + sha256: ba06333873fcb1e07820cb0895755b42a615d289437749846e280bc87d6abf2c build: noarch: python From d073aa992e4d4b9f10089d228e2cae83625ebd0e Mon Sep 17 00:00:00 2001 From: Max Date: Mon, 14 Oct 2024 14:12:41 +0200 Subject: [PATCH 14/16] Add seqspec (#51326) * init o seqspec * add run_exports * add summary * fix: use python-newick * adding setuptools * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Max Schubach --- recipes/seqspec/meta.yaml | 52 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/seqspec/meta.yaml diff --git a/recipes/seqspec/meta.yaml b/recipes/seqspec/meta.yaml new file mode 100644 index 0000000000000..c4a928dfcb61f --- /dev/null +++ b/recipes/seqspec/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "seqspec" %} +{% set version = "0.3.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/seqspec-{{ version }}.tar.gz + sha256: d9e6c283daaca06f58f1090c0c7dcfecf646b9658e62aa873a4e85fef56c56c9 + +build: + run_exports: + - {{ pin_subpackage('seqspec', max_pin="x.x") }} + entry_points: + - seqspec=seqspec.main:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + +requirements: + host: + - python >=3.6 + - pip + - setuptools + run: + - python >=3.6 + - pyyaml >=6.0 + - jsonschema + - python-newick + - requests + - biopython + - packaging + +test: + imports: + - seqspec + commands: + - pip check + - seqspec version -h + requires: + - pip + +about: + home: https://github.com/sbooeshaghi/seqspec + summary: File format that describes data generated from genomics experiments. File format and seqspec tool enable uniform processing of genomics data. + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - visze From e2ea64724efb15554449bb763cd3ce52ed633b95 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 14 Oct 2024 15:34:41 +0300 Subject: [PATCH 15/16] gnparser: add aarch64/arm64 builds (#51376) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/gnparser/build.sh | 2 ++ recipes/gnparser/meta.yaml | 5 ++++- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/recipes/gnparser/build.sh b/recipes/gnparser/build.sh index cac558fdb6ebb..74d98b99db88c 100644 --- a/recipes/gnparser/build.sh +++ b/recipes/gnparser/build.sh @@ -1,5 +1,7 @@ #!/bin/bash +set -xe + cd gnparser CGO_ENABLED=0 go clean diff --git a/recipes/gnparser/meta.yaml b/recipes/gnparser/meta.yaml index c58f527694af0..82ec7ca69faca 100644 --- a/recipes/gnparser/meta.yaml +++ b/recipes/gnparser/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('gnparser', max_pin="x") }} @@ -34,5 +34,8 @@ about: extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 identifiers: - doi:https://doi.org/10.5281/zenodo.5111569 From b9f01abfd2cca0e6fbe89cb7129883bf5b5cc5b6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 14 Oct 2024 09:03:17 -0400 Subject: [PATCH 16/16] Update perl-namespace-autoclean to 0.31 (#51353) * Update perl-namespace-autoclean to 0.31 * perl-namespace-autoclean: add run_exports and arm64 builds Signed-off-by: Martin Tzvetanov Grigorov * Reset the build number * No ARM64 for now. Many missing deps --------- Signed-off-by: Martin Tzvetanov Grigorov Co-authored-by: Martin Tzvetanov Grigorov Co-authored-by: Martin Grigorov --- recipes/perl-namespace-autoclean/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/perl-namespace-autoclean/meta.yaml b/recipes/perl-namespace-autoclean/meta.yaml index 4f562956a35f9..4cc0492a1364e 100644 --- a/recipes/perl-namespace-autoclean/meta.yaml +++ b/recipes/perl-namespace-autoclean/meta.yaml @@ -1,17 +1,19 @@ {% set name = "perl-namespace-autoclean" %} -{% set version = "0.29" %} -{% set sha256 = "45ebd8e64a54a86f88d8e01ae55212967c8aa8fed57e814085def7608ac65804" %} +{% set version = "0.31" %} +{% set sha256 = "d3b32c82e1d2caa9d58b8c8075965240e6cab66ab9350bd6f6bea4ca07e938d6" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/namespace-autoclean-0.29.tar.gz + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/namespace-autoclean-0.31.tar.gz sha256: {{ sha256 }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: