Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
47 lines (40 sloc) 2.22 KB
{% set name = "gmap-fusion" %}
{% set version = "0.4.0" %}
{% set build = "0" %}
package:
name: {{ name }}
version: {{ version }}
source:
url: https://github.com/GMAP-fusion/GMAP-fusion/releases/download/v{{ version }}/GMAP-fusion-v{{ version }}.FULL.tar.gz
md5: af49da9f8b1849224e0a8c1ede16cfe5
build:
number: {{ build }}
requirements:
build:
run:
- perl
- perl-set-intervaltree
- perl-db-file
- samtools >=1.3
- bowtie2 >=2.1
- gmap >=2017.11.15
test:
commands:
- "GMAP-fusion --help 2>&1 | grep Required"
# The following scripts all need to be tested from their install location.
- "$PREFIX/share/{{ name }}-{{ version }}-{{ build }}/util/compare_fusion_align_to_best_nonfusion_align.pl 2>&1 | grep usage"
- "$PREFIX/share/{{ name }}-{{ version }}-{{ build }}/util/estimate_fusion_read_support.pl 2>&1 | grep usage"
- "$PREFIX/share/{{ name }}-{{ version }}-{{ build }}/util/filter_gmap_chims_via_dist_from_exon_bounds.pl 2>&1 | grep usage"
- "$PREFIX/share/{{ name }}-{{ version }}-{{ build }}/util/gmap_genome_gff3_to_chim_summary.pl 2>&1 | grep Required"
- "$PREFIX/share/{{ name }}-{{ version }}-{{ build }}/util/prep_evidence_for_IGV.pl 2>&1 | grep usage"
- "$PREFIX/share/{{ name }}-{{ version }}-{{ build }}/util/retrieve_fusion_transcript_candidates.pl 2>&1 | grep usage"
- "$PREFIX/share/{{ name }}-{{ version }}-{{ build }}/util/revise_chim_candidate_list_via_split_align_reassessment.pl 2>&1 | grep usage"
- "$PREFIX/share/{{ name }}-{{ version }}-{{ build }}/util/screen_fusion_genome_breakpoint_for_confounding_kmers.pl 2>&1 | grep usage"
- "$PREFIX/share/{{ name }}-{{ version }}-{{ build }}/util/screen_fusion_trans_genes_for_kmer_confounders.pl 2>&1 | grep usage"
- "$PREFIX/share/{{ name }}-{{ version }}-{{ build }}/util/split_fusion_gmap_parts.pl 2>&1 | grep usage"
- "$PREFIX/share/{{ name }}-{{ version }}-{{ build }}/util/write_GMAP_Fusion_annot_report.pl 2>&1 | grep usage"
about:
home: "https://github.com/GMAP-fusion/GMAP-fusion"
license: BSD-3-Clause
license_file: LICENSE
summary: "GMAP-fusion is a utility for identifying candidate fusion transcripts based on transcript sequences reconstructed via RNA-Seq de novo transcriptome assembly."
You can’t perform that action at this time.