Skip to content

Commit

Permalink
v0.1.0a
Browse files Browse the repository at this point in the history
  • Loading branch information
John Major committed Apr 30, 2023
1 parent ea14416 commit 8c01583
Show file tree
Hide file tree
Showing 525 changed files with 573,194 additions and 0 deletions.
5 changes: 5 additions & 0 deletions .gitignore
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

4 changes: 4 additions & 0 deletions .test_data/data/0.01x_3_wgs_HG002.samplesheet.csv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,instrument,lib_prep,bwa_kmer,subsample_pct
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,NOVASEQ,PCR-FREE,19,0.95
RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_2,RIH0_ANA0-HG002_DBC1_2,DBC2,RIH0,ANA0-HG002,2,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,NOVASEQ,PCR-FREE,19,0.95
RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_1,RIH0_ANA0-HG002_DBC1_1,DBC1,RIH0,ANA0-HG002,1,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,NOVASEQ,PCR-FREE,19,0.95
2 changes: 2 additions & 0 deletions .test_data/data/0.01xwgs_HG002.samplesheet.csv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,instrument,lib_prep,bwa_kmer,subsample_pct
RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,NOVASEQ,PCR-FREE,19,0.95
10 changes: 10 additions & 0 deletions .test_data/data/HG002_analysis_manifest.csv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,instrument,lib_prep,bwa_kmer,subsample_pct
RIH0_ANA0-HG002-NOVA-20_DBC0_0,RIH0_ANA0-HG002-NOVA-20_DBC0_1,RIH0_ANA0-HG002-NOVA-20_DBC0_1,DBC0,RIH0,ANA0-HG002-NOVA-20,1,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NOVA/HG002-novaseq-pcr-free-35x_S1_L001_R1_001.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NOVA/HG002-novaseq-pcr-free-35x_S1_L001_R2_001.fastq.gz,male,na,/fsx/data/genomic_data/organism_refrences/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood\,merge,HG002,NOVASEQ,PCR-FREE,20,0.9
RIH0_ANA0-HG002-NOVA-19_DBC0_0,RIH0_ANA0-HG002-NOVA-19_DBC0_2,RIH0_ANA0-HG002-NOVA-19_DBC0_2,DBC0,RIH0,ANA0-HG002-NOVA-19,2,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NOVA/HG002-novaseq-pcr-free-35x_S1_L001_R1_001.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NOVA/HG002-novaseq-pcr-free-35x_S1_L001_R2_001.fastq.gz,male,na,/fsx/data/genomic_data/organism_refrences/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood\,merge,HG002,NOVASEQ,PCR-FREE,19,0.9
RIH0_ANA0-HG002-BGI_DBC0_0,RIH0_ANA0-HG002-BGI_DBC0_1,RIH0_ANA0-HG002-BGI_DBC0_1,DBC0,RIH0,ANA0-HG002-BGI,1,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/BGISEQ500/BGISEQ500_PCRfree_NA24385_CL100076190_L01_read_1.fq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/BGISEQ500/BGISEQ500_PCRfree_NA24385_CL100076190_L01_read_2.fq.gz,male,na,/fsx/data/genomic_data/organism_refrences/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,BGISEQ-500,PCR-FREE,19,0.4403
RIH0_ANA0-HG002-BGI_DBC0_2,RIH0_ANA0-HG002-BGI_DBC0_2,RIH0_ANA0-HG002-BGI_DBC0_2,DBC0,RIH0,ANA0-HG002-BGI,2,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/BGISEQ500/BGISEQ500_PCRfree_NA24385_CL100076190_L02_read_1.fq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/BGISEQ500/BGISEQ500_PCRfree_NA24385_CL100076190_L02_read_2.fq.gz,male,na,/fsx/data/genomic_data/organism_refrences/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,BGISEQ-500,PCR-FREE,19,0.4403
RIH0_ANA0-HG002-HSQ25_DBC0_0,RIH0_ANA0-HG002-HSQ25_DBC0_34,RIH0_ANA0-HG002-HSQ25_DBC0_34,DBC0,RIH0,ANA0-HG002-HSQ25,34,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/NIST_Illumina_2x150bps_hiseq2500/reads/D1_S1_L001_R1_001.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/NIST_Illumina_2x150bps_hiseq2500/reads/D1_S1_L001_R2_001.fastq.gz,male,na,/fsx/data/genomic_data/organism_refrences/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HISEQ-2500,PCR-FREE,19,0.99
RIH0_ANA0-HG002-HSQ25_DBC0_0,RIH0_ANA0-HG002-HSQ25_DBC0_33,RIH0_ANA0-HG002-HSQ25_DBC0_33,DBC0,RIH0,ANA0-HG002-HSQ25,33,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/NIST_Illumina_2x150bps_hiseq2500/reads/D1_S1_L001_R1_002.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/NIST_Illumina_2x150bps_hiseq2500/reads/D1_S1_L001_R2_002.fastq.gz,male,na,/fsx/data/genomic_data/organism_refrences/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HISEQ-2500,PCR-FREE,19,0.99
RIH0_ANA0-HG002-HSQ25_DBC0_0,RIH0_ANA0-HG002-HSQ25_DBC0_32,RIH0_ANA0-HG002-HSQ25_DBC0_32,DBC0,RIH0,ANA0-HG002-HSQ25,32,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/NIST_Illumina_2x150bps_hiseq2500/reads/D1_S1_L001_R1_003.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/NIST_Illumina_2x150bps_hiseq2500/reads/D1_S1_L001_R2_003.fastq.gz,male,na,/fsx/data/genomic_data/organism_refrences/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HISEQ-2500,PCR-FREE,19,0.99
IH0_ANA0-HG002-HSQ25_DBC0_0,RIH0_ANA0-HG002-HSQ25_DBC0_31,RIH0_ANA0-HG002-HSQ25_DBC0_31,DBC0,RIH0,ANA0-HG002-HSQ25,31,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/NIST_Illumina_2x150bps_hiseq2500/reads/D1_S1_L001_R1_004.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/NIST_Illumina_2x150bps_hiseq2500/reads/D1_S1_L001_R2_004.fastq.gz,male,na,/fsx/data/genomic_data/organism_refrences/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HISEQ-2500,PCR-FREE,19,0.99
RIH0_ANA0-HG002-HSQ25_DBC0_0,RIH0_ANA0-HG002-HSQ25_DBC0_30,RIH0_ANA0-HG002-HSQ25_DBC0_30,DBC0,RIH0,ANA0-HG002-HSQ25,30,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/NIST_Illumina_2x150bps_hiseq2500/reads/D1_S1_L001_R1_005.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/HG002/NIST_Illumina_2x150bps_hiseq2500/reads/D1_S1_L001_R2_005.fastq.gz,male,na,/fsx/data/genomic_data/organism_refrences/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HISEQ-2500,PCR-FREE,19,0.99
Binary file added .test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz
View file
Binary file not shown.
Binary file added .test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz
View file
Binary file not shown.
10 changes: 10 additions & 0 deletions .test_data/data/all_giab_analysis_manifest.csv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,instrument,lib_prep,bwa_kmer
RIH0_ANA0-HG001-19_DBC0_0,RIH0_ANA0-HG001-19_DBC0_0,RIH0_ANA0-HG001-19_DBC0_0,DBC0,RIH0,ANA0-HG001-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG001.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG001.novaseq.pcr-free.30x.R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,HG001,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG002-19_DBC0_0,RIH0_ANA0-HG002-19_DBC0_0,RIH0_ANA0-HG002-19_DBC0_0,DBC0,RIH0,ANA0-HG002-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG002.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG002.novaseq.pcr-free.30x.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG003-19_DBC0_0,RIH0_ANA0-HG003-19_DBC0_0,RIH0_ANA0-HG003-19_DBC0_0,DBC0,RIH0,ANA0-HG003-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG003.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG003.novaseq.pcr-free.30x.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,HG003,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG004-19_DBC0_0,RIH0_ANA0-HG004-19_DBC0_0,RIH0_ANA0-HG004-19_DBC0_0,DBC0,RIH0,ANA0-HG004-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG004.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG004.novaseq.pcr-free.30x.R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,HG004,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG005-19_DBC0_0,RIH0_ANA0-HG005-19_DBC0_0,RIH0_ANA0-HG005-19_DBC0_0,DBC0,RIH0,ANA0-HG005-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG005.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG005.novaseq.pcr-free.30x.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,HG005,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG007-19_DBC0_0,RIH0_ANA0-HG007-19_DBC0_0,RIH0_ANA0-HG007-19_DBC0_0,DBC0,RIH0,ANA0-HG007-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG007.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG007.novaseq.pcr-free.30x.R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,HG007,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG006-19_DBC0_0,RIH0_ANA0-HG006-19_DBC0_0,RIH0_ANA0-HG006-19_DBC0_0,DBC0,RIH0,ANA0-HG006-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG006.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG006.novaseq.pcr-free.30x.R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,HG006,NOVASEQ,PCR-FREE,19


10 changes: 10 additions & 0 deletions .test_data/data/giab_30x_b37_analysis_manifest.csv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,external_sample_id,instrument,lib_prep,bwa_kmer
RIH0_ANA0-HG001-19_DBC0_0,RIH0_ANA0-HG001-19_DBC0_0,RIH0_ANA0-HG001-19_DBC0_0,DBC0,RIH0,ANA0-HG001-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG001.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG001.novaseq.pcr-free.30x.R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,HG001,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG002-19_DBC0_0,RIH0_ANA0-HG002-19_DBC0_0,RIH0_ANA0-HG002-19_DBC0_0,DBC0,RIH0,ANA0-HG002-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG002.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG002.novaseq.pcr-free.30x.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG003-19_DBC0_0,RIH0_ANA0-HG003-19_DBC0_0,RIH0_ANA0-HG003-19_DBC0_0,DBC0,RIH0,ANA0-HG003-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG003.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG003.novaseq.pcr-free.30x.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,HG003,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG004-19_DBC0_0,RIH0_ANA0-HG004-19_DBC0_0,RIH0_ANA0-HG004-19_DBC0_0,DBC0,RIH0,ANA0-HG004-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG004.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG004.novaseq.pcr-free.30x.R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,HG004,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG005-19_DBC0_0,RIH0_ANA0-HG005-19_DBC0_0,RIH0_ANA0-HG005-19_DBC0_0,DBC0,RIH0,ANA0-HG005-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG005.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG005.novaseq.pcr-free.30x.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,HG005,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG006-19_DBC0_0,RIH0_ANA0-HG006-19_DBC0_0,RIH0_ANA0-HG006-19_DBC0_0,DBC0,RIH0,ANA0-HG006-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG006.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG006.novaseq.pcr-free.30x.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,HG006,NOVASEQ,PCR-FREE,19
RIH0_ANA0-HG007-19_DBC0_0,RIH0_ANA0-HG007-19_DBC0_0,RIH0_ANA0-HG007-19_DBC0_0,DBC0,RIH0,ANA0-HG007-19,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG007.novaseq.pcr-free.30x.R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/google-brain/novaseq/pcr_free/30x/30x/HG007.novaseq.pcr-free.30x.R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,HG007,NOVASEQ,PCR-FREE,19


50 changes: 50 additions & 0 deletions DayDockerfile
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,50 @@
FROM condaforge/mambaforge:latest
LABEL io.github.snakemake.containerized="true"
LABEL io.github.snakemake.conda_env_hash="4f57563e7b653fd7ad7fcc0c65e1ce7cfb6e9b3c41c6395de03cf63291da4b01"
ENTRYPOINT ["/usr/bin/tini", "--"]

ARG DEBIAN_FRONTEND=noninteractive


RUN apt-get update && apt-get install -y wget
RUN apt-get install -y tzdata
RUN apt install -y software-properties-common
RUN add-apt-repository -y ppa:apptainer/ppa
RUN apt update
RUN apt install -y apptainer


# Step 1: Stage DAY conda environment

# Conda environment:
# source: ./DAY.yaml
# prefix: DAY
#--
#channels:
# - conda-forge
# - bioconda
# - anaconda
# - defaults
#dependencies:
# - snakemake==7.25.0
# - pandas==1.5.3
# - python
# - ipython
# - perl
# - yappi
# - snakedeploy
# - snakefmt
# - networkx
# - yamllint
# - pip
# - drmaa
# - docopt
# - colr
# - chromedriver-binary-auto
# - rgbw-colorspace-converter

RUN mkdir -p /conda-envs/daylily_v0.1.0
COPY config/day/DAY.yaml /conda-envs/daylily_v0.1.0/environment.yaml

RUN mamba env create -n DAY --file /conda-envs/daylily_v0.1.0/environment.yaml && \
mamba clean --all -y
Loading

0 comments on commit 8c01583

Please sign in to comment.