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Gw dev #36

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merged 4 commits into from
Jul 26, 2024
Merged

Gw dev #36

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f648fe7
Added demo files (#31)
kcleal Jul 25, 2024
6352677
Added a tutorial. Fixed some issues with shift commands and tiled-bed…
kcleal Jul 25, 2024
3712774
Merge master (#33)
kcleal Jul 25, 2024
c140e7c
Merge branch 'master' into gw_dev
kcleal Jul 26, 2024
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5 changes: 3 additions & 2 deletions .gw.ini
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Expand Up @@ -30,6 +30,7 @@ log2_cov=false
expand_tracks=true
scale_bar=true
link=none
scale_bar=true
split_view_size=10000
threads=4
pad=500
Expand All @@ -40,7 +41,7 @@ font_size=14
sv_arcs=true
mods=false
mods_qual_threshold=50
session_file=/Users/sbi8kc2/CLionProjects/gw/.gw_session.ini
session_file=

[view_thresholds]
soft_clip=20000
Expand Down Expand Up @@ -72,7 +73,7 @@ parse_label=filter
labels=PASS,FAIL

[shift_keymap]
ampersand= 7
ampersand=7
bar=\
colon=;
curly_open=[
Expand Down
Binary file added docs/assets/data/demo1.bam
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106 changes: 106 additions & 0 deletions docs/assets/data/demo1.repeats.bed
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chr8 37023918 37024043 AluSz 880 +
chr8 37024043 37024067 AT_rich 24 +
chr8 37024913 37025154 MIR 504 -
chr8 37025202 37025265 MIR 225 -
chr8 37025299 37025475 L1ME4a 680 +
chr8 37025475 37025940 LOR1a 2460 -
chr8 37025940 37027033 L1ME4a 680 +
chr8 37027711 37027741 (CAAAAA)n 221 +
chr8 37027759 37027832 A-rich 211 +
chr8 37027832 37028118 AluSz 1926 +
chr8 37028118 37028205 A-rich 211 +
chr8 37028842 37029004 AluJb 1752 +
chr8 37029004 37029814 LTR1 4292 -
chr8 37029814 37029947 AluJb 1752 +
chr8 37030145 37030177 AT_rich 25 +
chr8 37030211 37030262 (TATAA)n 204 +
chr8 37030354 37030405 L2a 216 +
chr8 37030607 37030837 L1ME4a 483 +
chr8 37031008 37031355 L1ME4a 626 +
chr8 37031355 37031435 MADE1 531 -
chr8 37031435 37031453 L1ME4a 626 +
chr8 37031568 37031877 AluSx 2257 -
chr8 37032444 37032632 MIR 374 +
chr8 37032912 37033041 MLT1J2 505 -
chr8 37033041 37033440 MSTA 2345 -
chr8 37033440 37033590 MLT1J2 505 -
chr8 37033721 37034000 AluSg 2118 -
chr8 37034028 37034119 LTR81C 291 +
chr8 37034126 37034305 MIRb 256 -
chr8 37034824 37034946 MER103C 269 +
chr8 37037329 37037416 CT-rich 189 +
chr8 37037438 37037491 (TC)n 381 +
chr8 37040342 37040645 AluSg 2335 -
chr8 37040661 37040806 MIRb 460 -
chr8 37041195 37041357 GA-rich 218 +
chr8 37041425 37041471 (CA)n 216 +
chr8 37043199 37043531 MER61A 1858 +
chr8 37043534 37043751 MER58A 1200 +
chr8 37043753 37043786 (TGAA)n 192 +
chr8 37043881 37044166 Plat_L3 292 +
chr8 37044502 37044645 MIR 244 -
chr8 37044957 37045261 MLT1J2 540 -
chr8 37045738 37045891 L2c 225 -
chr8 37047131 37047432 AluJr4 1787 +
chr8 37047439 37047530 G-rich 252 +
chr8 37047681 37047772 MIRb 296 +
chr8 37047868 37048141 L3 767 +
chr8 37049256 37049308 MLT1B 265 +
chr8 37049308 37049428 L1PA4 1070 -
chr8 37049428 37050028 L1PA4 5285 +
chr8 37050031 37050175 MLT1B 1307 +
chr8 37050175 37050519 THE1B 1929 +
chr8 37050519 37050692 MLT1B 1307 +
chr8 37050885 37051853 LTR5_Hs 9034 -
chr8 37052583 37052916 HAL1 1377 +
chr8 37052916 37053106 MER5A 1044 +
chr8 37053106 37053261 HAL1 1377 +
chr8 37053261 37053882 MER73 3566 -
chr8 37053882 37054317 HAL1 1377 +
chr8 37054429 37054506 MER5A 333 -
chr8 37055247 37055268 AT_rich 21 +
chr8 37055271 37055576 AluSx3 2308 -
chr8 37055634 37056363 L1ME3D 1866 +
chr8 37056441 37057408 L1MEe 880 +
chr8 37057408 37057689 LTR41B 941 -
chr8 37057900 37058047 L1PA17 2316 +
chr8 37058047 37058092 (CAA)n 339 +
chr8 37058092 37058346 L1PA17 2316 +
chr8 37058391 37059004 ERVL-E-int 3377 -
chr8 37059004 37059333 MER2 1912 +
chr8 37059333 37059368 (TA)n 207 +
chr8 37059368 37059875 ERVL-E-int 3377 -
chr8 37059880 37060012 LTR41 399 -
chr8 37060211 37060399 LTR41 564 -
chr8 37060465 37060575 L1MEe 307 +
chr8 37060570 37060718 HAL1 514 +
chr8 37060844 37060975 HAL1 247 -
chr8 37061202 37061324 HAL1 444 -
chr8 37061516 37061638 AluSc 850 +
chr8 37061732 37062152 LTR16A1 1355 +
chr8 37062488 37062543 MIRc 224 -
chr8 37062543 37062848 AluSx1 2206 -
chr8 37062848 37062897 MIRc 224 -
chr8 37062968 37063066 MLT1H2 383 +
chr8 37063350 37063408 MIR 220 -
chr8 37063511 37063539 AT_rich 21 +
chr8 37067111 37068446 L1MB8 4523 +
chr8 37068446 37068475 (CAAA)n 221 +
chr8 37068475 37068989 L1MB8 4523 +
chr8 37069068 37069158 L1MB8 270 +
chr8 37069197 37069900 L1MB8 4186 +
chr8 37069900 37070049 AluJr 937 +
chr8 37070049 37071691 L1MB8 4186 +
chr8 37072743 37072850 MIR3 403 -
chr8 37073262 37073507 MER63A 417 -
chr8 37073576 37073718 MER103C 450 -
chr8 37073852 37074210 Tigger3a 2023 -
chr8 37074304 37074471 L2b 253 -
chr8 37074868 37074908 L2c 183 -
chr8 37075715 37075834 MIRb 291 +
chr8 37076525 37076821 Tigger15a 501 +
chr8 37076856 37077067 Tigger15a 653 +
chr8 37077598 37077762 MER5B 392 -
chr8 37077911 37078046 FLAM_C 896 +
chr8 37078182 37078315 FLAM_C 742 +
chr8 37079014 37079423 L4 532 -
187 changes: 187 additions & 0 deletions docs/assets/data/demo1.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##source=DYSGU
##FILTER=<ID=lowProb,Description="Probability below threshold set with --thresholds">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation">
##INFO=<ID=CHR2_POS,Number=1,Type=Integer,Description="Chromosome position for END coordinate in case of a translocation">
##INFO=<ID=GRP,Number=1,Type=Integer,Description="Group id for complex SVs">
##INFO=<ID=NGRP,Number=1,Type=Integer,Description="Number of SVs in group">
##INFO=<ID=RT,Number=1,Type=String,Description="Type of input reads, 1=paired-end, 2=pacbio, 3=nanopore">
##INFO=<ID=CT,Number=1,Type=String,Description="Paired-end signature induced connection type">
##INFO=<ID=CIPOS95,Number=1,Type=Integer,Description="Confidence interval size (95%) around POS for imprecise variants">
##INFO=<ID=CIEND95,Number=1,Type=Integer,Description="Confidence interval size (95%) around END for imprecise variants">
##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
##INFO=<ID=KIND,Number=1,Type=String,Description="Kind of join with respect to input regions">
##INFO=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
##INFO=<ID=WR,Number=1,Type=Integer,Description="Number of reads that have SV within-read">
##INFO=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
##INFO=<ID=SR,Number=1,Type=Integer,Description="Number of supplementary reads supporting the variant across all samples">
##INFO=<ID=SC,Number=1,Type=Integer,Description="Number of soft-clip reads supporting the variant across all samples">
##INFO=<ID=BND,Number=1,Type=Integer,Description="Number of break-end alignments supporting the variant">
##INFO=<ID=CONTIGA,Number=1,Type=String,Description="Contig from CHROM POS">
##INFO=<ID=CONTIGB,Number=1,Type=String,Description="Contig from CHR2 END">
##INFO=<ID=GC,Number=1,Type=Float,Description="GC% of assembled contigs">
##INFO=<ID=REP,Number=1,Type=Float,Description="Repeat score for contigs aligned bases">
##INFO=<ID=REPSC,Number=1,Type=Float,Description="Repeat score for contigs soft-clipped bases">
##INFO=<ID=LPREC,Number=1,Type=Integer,Description="SV length precise=1, inferred=0">
##INFO=<ID=NEXP,Number=1,Type=Integer,Description="Number of expanded repeat bases at break">
##INFO=<ID=STRIDE,Number=1,Type=Integer,Description="Repeat expansion stride or period">
##INFO=<ID=EXPSEQ,Number=1,Type=String,Description="Expansion sequence">
##INFO=<ID=RPOLY,Number=1,Type=Integer,Description="Number of reference polymer bases">
##INFO=<ID=OL,Number=1,Type=Integer,Description="Query overlap in bp">
##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">
##INFO=<ID=LEFT_SVINSSEQ,Number=.,Type=String,Description="Known left side of insertion for an insertion of unknown length">
##INFO=<ID=RIGHT_SVINSSEQ,Number=.,Type=String,Description="Known right side of insertion for an insertion of unknown length">
##INFO=<ID=MeanPROB,Number=1,Type=Float,Description="Mean probability of event being true across samples">
##INFO=<ID=MaxPROB,Number=1,Type=Float,Description="Max probability of event being true across samples">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=TRA,Description="Translocation">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality phred scaled">
##FORMAT=<ID=NMP,Number=1,Type=Float,Description="Mean edit distance for primary alignments supporting the variant">
##FORMAT=<ID=NMS,Number=1,Type=Float,Description="Mean edit distance for supplementary alignments supporting the variant">
##FORMAT=<ID=NMB,Number=1,Type=Float,Description="Mean basic, edit distance. Gaps >= 30 bp are ignored">
##FORMAT=<ID=MAPQP,Number=1,Type=Float,Description="Mean MAPQ for primary reads supporting the variant">
##FORMAT=<ID=MAPQS,Number=1,Type=Float,Description="Mean MAPQ for supplementary reads supporting the variant">
##FORMAT=<ID=NP,Number=1,Type=Integer,Description="Number of alignments in normal-pair orientation supporting the variant">
##FORMAT=<ID=MAS,Number=1,Type=Integer,Description="Maximum alignment score of supplementary reads supporting the variant">
##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
##FORMAT=<ID=WR,Number=1,Type=Integer,Description="Number of reads that have SV within-read">
##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired reads supporting the variant">
##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of supplementary alignments supporting the variant">
##FORMAT=<ID=SC,Number=1,Type=Integer,Description="Number of soft-clipped alignments supporting the variant">
##FORMAT=<ID=BND,Number=1,Type=Integer,Description="Number of break-end alignments supporting the variant">
##FORMAT=<ID=SQC,Number=1,Type=Float,Description="Soft-clip quality value correlation between reads">
##FORMAT=<ID=SCW,Number=1,Type=Float,Description="Soft-clip quality weight value">
##FORMAT=<ID=SQR,Number=1,Type=Float,Description="Soft-clip base-quality ratio wrt to aligned bases">
##FORMAT=<ID=BE,Number=1,Type=Integer,Description="Block edge metric">
##FORMAT=<ID=COV,Number=1,Type=Float,Description="Mean read coverage +/- 10kb around break site at A or B">
##FORMAT=<ID=MCOV,Number=1,Type=Float,Description="Maximum read coverage +/- 10kb around break site at A or B">
##FORMAT=<ID=LNK,Number=1,Type=Integer,Description="Contig A and contig B overlap">
##FORMAT=<ID=NEIGH,Number=1,Type=Integer,Description="Number of other break points within 1 bp of break site">
##FORMAT=<ID=NEIGH10,Number=1,Type=Integer,Description="Number of other break points within 10 kp of break site">
##FORMAT=<ID=RB,Number=1,Type=Integer,Description="Number of reference bases in contigs">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Number of reads on plus strand">
##FORMAT=<ID=MS,Number=1,Type=Integer,Description="Number of reads on minus strand">
##FORMAT=<ID=SBT,Number=1,Type=Float,Description="Strand-bias, one-sided binomial test p-value">
##FORMAT=<ID=NG,Number=1,Type=Float,Description="Mean number of small gaps < 30 bp">
##FORMAT=<ID=NSA,Number=1,Type=Float,Description="Mean number of SA tags per read">
##FORMAT=<ID=NXA,Number=1,Type=Float,Description="Mean number of XA tags per read">
##FORMAT=<ID=NMU,Number=1,Type=Float,Description="Mean number of mates unmapped per read">
##FORMAT=<ID=NDC,Number=1,Type=Integer,Description="Number of double-clips, alignments with left and right clips">
##FORMAT=<ID=RMS,Number=1,Type=Integer,Description="Remapping score">
##FORMAT=<ID=RED,Number=1,Type=Integer,Description="Remapping edit distance">
##FORMAT=<ID=BCC,Number=1,Type=Integer,Description="Bad soft-clip count within +/- 500 bp">
##FORMAT=<ID=FCC,Number=1,Type=Float,Description="Fold-coverage change for SVs">
##FORMAT=<ID=STL,Number=1,Type=Integer,Description="N reads with small TLEN below 0.05% of distribution">
##FORMAT=<ID=RAS,Number=1,Type=Integer,Description="Reverse soft-clip to alignment score">
##FORMAT=<ID=FAS,Number=1,Type=Integer,Description="Forward soft-clip to alignment score">
##FORMAT=<ID=ICN,Number=1,Type=Float,Description="Inner copy number">
##FORMAT=<ID=OCN,Number=1,Type=Float,Description="Outer copy number">
##FORMAT=<ID=CMP,Number=1,Type=Float,Description="Compression ratio of contigs">
##FORMAT=<ID=RR,Number=1,Type=Float,Description="Repeat score for reference">
##FORMAT=<ID=JIT,Number=1,Type=Float,Description="SV length jitter">
##FORMAT=<ID=PROB,Number=1,Type=Float,Description="Probability of event being true">
##contig=<ID=chrM,length=16571>
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4,length=191154276>
##contig=<ID=chr5,length=180915260>
##contig=<ID=chr6,length=171115067>
##contig=<ID=chr7,length=159138663>
##contig=<ID=chr8,length=146364022>
##contig=<ID=chr9,length=141213431>
##contig=<ID=chr10,length=135534747>
##contig=<ID=chr11,length=135006516>
##contig=<ID=chr12,length=133851895>
##contig=<ID=chr13,length=115169878>
##contig=<ID=chr14,length=107349540>
##contig=<ID=chr15,length=102531392>
##contig=<ID=chr16,length=90354753>
##contig=<ID=chr17,length=81195210>
##contig=<ID=chr18,length=78077248>
##contig=<ID=chr19,length=59128983>
##contig=<ID=chr20,length=63025520>
##contig=<ID=chr21,length=48129895>
##contig=<ID=chr22,length=51304566>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
##contig=<ID=chr1_gl000191_random,length=106433>
##contig=<ID=chr1_gl000192_random,length=547496>
##contig=<ID=chr4_ctg9_hap1,length=590426>
##contig=<ID=chr4_gl000193_random,length=189789>
##contig=<ID=chr4_gl000194_random,length=191469>
##contig=<ID=chr6_apd_hap1,length=4622290>
##contig=<ID=chr6_cox_hap2,length=4795371>
##contig=<ID=chr6_dbb_hap3,length=4610396>
##contig=<ID=chr6_mann_hap4,length=4683263>
##contig=<ID=chr6_mcf_hap5,length=4833398>
##contig=<ID=chr6_qbl_hap6,length=4611984>
##contig=<ID=chr6_ssto_hap7,length=4928567>
##contig=<ID=chr7_gl000195_random,length=182896>
##contig=<ID=chr8_gl000196_random,length=38914>
##contig=<ID=chr8_gl000197_random,length=37175>
##contig=<ID=chr9_gl000198_random,length=90085>
##contig=<ID=chr9_gl000199_random,length=169874>
##contig=<ID=chr9_gl000200_random,length=187035>
##contig=<ID=chr9_gl000201_random,length=36148>
##contig=<ID=chr11_gl000202_random,length=40103>
##contig=<ID=chr17_ctg5_hap1,length=1680828>
##contig=<ID=chr17_gl000203_random,length=37498>
##contig=<ID=chr17_gl000204_random,length=81310>
##contig=<ID=chr17_gl000205_random,length=174588>
##contig=<ID=chr17_gl000206_random,length=41001>
##contig=<ID=chr18_gl000207_random,length=4262>
##contig=<ID=chr19_gl000208_random,length=92689>
##contig=<ID=chr19_gl000209_random,length=159169>
##contig=<ID=chr21_gl000210_random,length=27682>
##contig=<ID=chrUn_gl000211,length=166566>
##contig=<ID=chrUn_gl000212,length=186858>
##contig=<ID=chrUn_gl000213,length=164239>
##contig=<ID=chrUn_gl000214,length=137718>
##contig=<ID=chrUn_gl000215,length=172545>
##contig=<ID=chrUn_gl000216,length=172294>
##contig=<ID=chrUn_gl000217,length=172149>
##contig=<ID=chrUn_gl000218,length=161147>
##contig=<ID=chrUn_gl000219,length=179198>
##contig=<ID=chrUn_gl000220,length=161802>
##contig=<ID=chrUn_gl000221,length=155397>
##contig=<ID=chrUn_gl000222,length=186861>
##contig=<ID=chrUn_gl000223,length=180455>
##contig=<ID=chrUn_gl000224,length=179693>
##contig=<ID=chrUn_gl000225,length=211173>
##contig=<ID=chrUn_gl000226,length=15008>
##contig=<ID=chrUn_gl000227,length=128374>
##contig=<ID=chrUn_gl000228,length=129120>
##contig=<ID=chrUn_gl000229,length=19913>
##contig=<ID=chrUn_gl000230,length=43691>
##contig=<ID=chrUn_gl000231,length=27386>
##contig=<ID=chrUn_gl000232,length=40652>
##contig=<ID=chrUn_gl000233,length=45941>
##contig=<ID=chrUn_gl000234,length=40531>
##contig=<ID=chrUn_gl000235,length=34474>
##contig=<ID=chrUn_gl000236,length=41934>
##contig=<ID=chrUn_gl000237,length=45867>
##contig=<ID=chrUn_gl000238,length=39939>
##contig=<ID=chrUn_gl000239,length=33824>
##contig=<ID=chrUn_gl000240,length=41933>
##contig=<ID=chrUn_gl000241,length=42152>
##contig=<ID=chrUn_gl000242,length=43523>
##contig=<ID=chrUn_gl000243,length=43341>
##contig=<ID=chrUn_gl000244,length=39929>
##contig=<ID=chrUn_gl000245,length=36651>
##contig=<ID=chrUn_gl000246,length=38154>
##contig=<ID=chrUn_gl000247,length=36422>
##contig=<ID=chrUn_gl000248,length=39786>
##contig=<ID=chrUn_gl000249,length=38502>
##FILTER=<ID=normal,Description="SV has read support in a normal vcf or alignment file">
##FILTER=<ID=lowSupport,Description="Not enough supporting evidence / too many nuisance reads">
##command="/home/kez/.pixi/envs/dysgu/bin/dysgu filter --min-prob 0.25 DB53.dysgu.vcf"
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DB53_bwamem
chr8 37050886 86128 T <DEL> . PASS SVMETHOD=DYSGUv1.3.16;SVTYPE=DEL;END=37051854;CHR2=chr8;GRP=86128;NGRP=1;CT=3to5;CIPOS95=0;CIEND95=0;SVLEN=968;CONTIGA=AACCACCTGTCTGTGATATTATTTTATGGCAGCCCTAGCAAACTATCTCAATGTGTTAAAGCAGTATTCTATGTGAGGCTGGGAGAGATGGCAGAGAGATTAATTATTATTTTTGTCCATTCTGTGACCCAGAGTTTTTAGTATTTTCACATTATTAAAGCATTGTTCATTCTATCAGTTTCAACCGTGAACTGACTTAATTCAAATTAAATTACTGCATTTACAGATAATTGATTTTcatggaaatgtccagtgttcatcagcacgaaactttctaaccgttctttggtttacctagttcta;CONTIGB=atcagtttcaaccgtgaactgacttaattcaaattaaattactgcatttacagataattGATTTTCATGGAAATGTCCAGTGTTCATCAGCACGAAACTTTCTAACCGTTCTTTGGTTTACCTAGTTCTAGGCATGATAGATAATTCTAGATACCGAATATTATTCTTTCAAGTAATGAAATAGTCAACAAAGTGACAAAAATCAGTTTAGTGGCTACTTATCCATGGTCAAAGTCCTTATAAAGcCCTTTCAACTTTTTAAATGGGAGATACCTGCACACAAAGAATAACTAACATGCCACACTT;KIND=extra-regional;GC=33.83;NEXP=0;STRIDE=0;EXPSEQ;RPOLY=10;OL=0;SU=16;WR=0;PE=16;SR=0;SC=12;BND=0;LPREC=1;RT=pe GT:GQ:MAPQP:SU:WR:PE:SR:SC:BND:COV:NEIGH10:PS:MS:RMS:RED:BCC:FCC:ICN:OCN:PROB 1/1:40:60:16:0:16:0:12:0:18.51:1:16:16:0:0:25:0:0:0.708:0.895
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11 changes: 10 additions & 1 deletion docs/docs/install/MacOS.md
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Expand Up @@ -16,7 +16,16 @@ installers below, or head over to the GitHub [Releases page](https://github.com/
[GW Apple arm64 mac dmg installer](https://github.com/kcleal/gw/releases/download/v1.0.0/gw_macos_m1.dmg)


GW can be copied to your bin directory to make it available as a command-line tool:
To install the desktop app, open one of the dmg files above then drop GW into your Applications folder, then perform the
following:

- In the Finder on your Mac, locate the app you want to open.
Don’t use Launchpad to locate the app.
- Control-click the GW app icon, then choose Open from the shortcut menu.
- Click Open.


GW can also be copied to your bin directory if needs be to make it available as a command-line tool:
```shell
cp /Applications/gw.app/Contents/MacOS/gw /usr/local/bin
```
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