Redirect reference data references inside bwa-mem

ICGC-TCGA-PanCancer · Nov 18, 2016 · 688b2c3 · 688b2c3
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diff --git a/README.md b/README.md
@@ -90,20 +90,20 @@ and run it using the Dockstore command line.
 
 Some synthetic sample data.
 
-* https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/synthetic_bam_for_GNOS_upload/hg19.chr22.5x.normal2.bam
-* https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/synthetic_bam_for_GNOS_upload/hg19.chr22.5x.normal.bam
+* https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/synthetic_bam_for_GNOS_upload/hg19.chr22.5x.normal.bam
+* https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/synthetic_bam_for_GNOS_upload/hg19.chr22.5x.normal2.bam
 
 ## Reference Data
 
 We use a specific reference based on GRCh37.
 
-* http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz
-* http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.fai
-* http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.amb
-* http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.ann
-* http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.bwt
-* http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.pac
-* http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.sa
+* https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz
+* https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.fai
+* https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.amb
+* https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.ann
+* https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.bwt
+* https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.pac
+* https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.sa
 
 ## Authors
 

diff --git a/workflow/scripts/download_data.pl b/workflow/scripts/download_data.pl
@@ -8,13 +8,13 @@
 
 check_tools();
 
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz");
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.fai");
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.amb");
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.ann");
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.bwt");
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.pac");
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.sa");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.fai");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.amb");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.ann");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.bwt");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.pac");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.sa");
 # download("$link_dir/testData", "https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/synthetic_bam_for_GNOS_upload/sample_bam_sequence_synthetic_chr22_normal.tar.gz");
 # system("tar zxf $link_dir/testData/sample_bam_sequence_synthetic_chr22_normal.tar.gz -C $link_dir/testData/");
 

diff --git a/workflow/scripts/gnos_download_data.pl b/workflow/scripts/gnos_download_data.pl
@@ -8,14 +8,14 @@
 
 check_tools();
 
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz");
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.fai");
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.amb");
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.ann");
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.bwt");
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.pac");
-download("$link_dir/reference/bwa-0.6.2", "http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.sa");
-download("$link_dir/testData", "https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/synthetic_bam_for_GNOS_upload/sample_bam_sequence_synthetic_chr22_normal.tar.gz");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.fai");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.amb");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.ann");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.bwt");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.pac");
+download("$link_dir/reference/bwa-0.6.2", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.sa");
+download("$link_dir/testData", "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/synthetic_bam_for_GNOS_upload/sample_bam_sequence_synthetic_chr22_normal.tar.gz");
 system("tar zxf $link_dir/testData/sample_bam_sequence_synthetic_chr22_normal.tar.gz -C links/testData/");
 
 sub download {