From a221f7fb2b0075daed1c8ee982c978b617d3e579 Mon Sep 17 00:00:00 2001 From: Nate Olson Date: Tue, 3 May 2022 17:33:43 -0400 Subject: [PATCH] [ci skip] Merge PR 34699 Merge PR #34699, commits were: * Update meta.yaml * adding version information * not including build or ref patch * not updating dipcall * using python build * removing ref patch * changing to AE repo * Merge pull request #1 from bioconda/master updating with bioconda * adding bedtk depdendency to dipcall --- recipes/truvari/build.sh | 10 --------- recipes/truvari/meta.yaml | 39 ++++++++++++++++++++++-------------- recipes/truvari/no_ref.patch | 39 ------------------------------------ 3 files changed, 24 insertions(+), 64 deletions(-) delete mode 100644 recipes/truvari/build.sh delete mode 100644 recipes/truvari/no_ref.patch diff --git a/recipes/truvari/build.sh b/recipes/truvari/build.sh deleted file mode 100644 index 25759a024bf76..0000000000000 --- a/recipes/truvari/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash -set -eu - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp *.py $outdir - -chmod a+x $outdir/truvari.py -ln -s $outdir/truvari.py $PREFIX/bin/truvari diff --git a/recipes/truvari/meta.yaml b/recipes/truvari/meta.yaml index c82234b6c652f..d193abea07142 100644 --- a/recipes/truvari/meta.yaml +++ b/recipes/truvari/meta.yaml @@ -1,35 +1,44 @@ -{% set version = "0.1.2018.08.10" %} -{% set revision = "4b2b314" %} -{% set hash = "3c41f1823f7a54a3c963261f492a012d90e31d94ff72251bfffac3bde886c0f1" %} +{% set version = "3.2.0" %} +{% set hash = "260abcebb202f524340dcae71947938f2b9852a09d8598bd288ff5f69c488ebf" %} package: name: truvari version: {{ version }} build: - noarch: generic - number: 2 + number: 0 + noarch: python + script: python -m pip install --no-deps --ignore-installed . source: - url: https://github.com/spiralgenetics/truvari/archive/{{ revision }}.tar.gz + url: https://files.pythonhosted.org/packages/04/79/5f8ba85e725c31b6a5ec3dcffcf3f5308f6c3de0cf0cf7814185a1edf47f/Truvari-3.2.0.tar.gz sha256: {{ hash }} - patches: - - no_ref.patch requirements: + host: + - python >=3.6 + - pip run: - - python <3 - - pyvcf - - python-levenshtein - - intervaltree - - progressbar2 - - pyfaidx + - python >=3.6 + - pytabix + - bwapy + - pandas + - python-levenshtein ==0.12.2 + - python-edlib >=1.3.8.post2 + - progressbar2 >=3.41.0 + - pysam >=0.15.2 + - intervaltree >=3.0.2 + - joblib >=1.0.1 + - numpy >=1.21.2 + - pytabix >=0.1 + - bwapy >=0.1.4 + - pandas >=1.3.3 test: commands: - truvari --help about: - home: https://github.com/spiralgenetics/truvari + home: https://github.com/ACEnglish/truvari license: MIT summary: 'Structural variant comparison tool for VCFs' diff --git a/recipes/truvari/no_ref.patch b/recipes/truvari/no_ref.patch deleted file mode 100644 index b312c348ce574..0000000000000 --- a/recipes/truvari/no_ref.patch +++ /dev/null @@ -1,39 +0,0 @@ -diff --git a/truvari.py b/truvari.py -index 166bff6..1977177 100755 ---- a/truvari.py -+++ b/truvari.py -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/opt/anaconda1anaconda2anaconda3/bin/python - from __future__ import print_function - import os - import re -@@ -897,6 +897,9 @@ def run(cmdargs): - stats_box["TP-base"] += 1 - if not matched_calls[c_key]: - stats_box["TP-call"] += 1 -+ write_tp_call = True -+ else: -+ write_tp_call = False - # Mark the call for multimatch checking - matched_calls[b_key] = True - matched_calls[c_key] = True -@@ -905,7 +908,8 @@ def run(cmdargs): - annotate_tp(match_entry, *thresh_neighbors[0]) - - tpb_out.write_record(base_entry) -- tpc_out.write_record(match_entry) -+ if write_tp_call: -+ tpc_out.write_record(match_entry) - logging.debug("Matching %s and %s", str(base_entry), str(match_entry)) - else: - stats_box["FN"] += 1 -@@ -938,7 +942,7 @@ def run(cmdargs): - if size < args.sizemin or size > args.sizemax: - c_filt.write_record(entry) - stats_box["call size filtered"] += 1 -- elif args.no_ref and not entry.genotype(sampleB)["GT"].is_variant: -+ elif args.no_ref and not entry.genotype(sampleB).is_variant: - stats_box["call gt filtered"] += 1 - elif regions.include(entry): - fp_out.write_record(entry)