Merge pull request #465 from iobio/tony_dev_458_bed38

#458 Serve GRCh37 and GRCh38 bed from AWS S3 bucket rather than from …
iobio · Jan 6, 2022 · bf8bc00 · bf8bc00
2 parents 2aeb414 + 4bc6cd0
commit bf8bc00
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diff --git a/src/components/pages/LandingPage.vue b/src/components/pages/LandingPage.vue
@@ -262,7 +262,7 @@
               <!-- <v-card> -->
                 <v-card-text>
                   <p style="text-align: justify">
-                    Users can enter files (.VCF, .BAM) and sample information using a configuration file.  <a href="https://iobio.s3.amazonaws.com/examples/clin_iobio_data_input_config_GRCh38.csv" target="_blank" style="font-weight: 500;padding-left:10px">Example configuration file</a>
+                    Users can enter files (.VCF, .BAM) and sample information using a configuration file.  <a href="https://iobio.s3.amazonaws.com/clin.iobio/example_file_config_GRCh38.csv" target="_blank" style="font-weight: 500;padding-left:10px">Example configuration file</a>
                   </p>
                   <div class="mb-3" v-if="validationErrors.length">
                     <ValidationErrors
@@ -294,7 +294,7 @@
                     Users can enter a list of genes or variants into clin.iobio. 
                     These are the genes and/or variants that will be reviewed in the clinical workflow steps of the app.
                     <br>
-                    Variants can be imported from a .CSV file.  <a href="https://iobio.s3.amazonaws.com/examples/clin_iobio_variants_to_import_GRCh38.csv" target="_blank" style="font-weight: 500;padding-left:10px">Example variant file</a>.
+                    Variants can be imported from a .CSV file.  <a href="https://iobio.s3.amazonaws.com/clin.iobio/example_imported_variants_GRCh38.csv" target="_blank" style="font-weight: 500;padding-left:10px">Example variant file</a>.
                   </p>
 
                   <div class="row"

diff --git a/src/components/partials/BedData.vue b/src/components/partials/BedData.vue
@@ -85,9 +85,9 @@
         showUrlField: false,
         bed_url_exome: '', 
         bed_url_genome: '',
-        bedFileUrl: 'https://raw.githubusercontent.com/chmille4/bam.iobio.io/vue/client/data/20130108.exome.targets.bed',
-        bedFile37: 'https://raw.githubusercontent.com/chmille4/bam.iobio.io/vue/client/data/20130108.exome.targets.bed',
-        bedFile38: 'https://raw.githubusercontent.com/adityaekawade/bam.iobio.io/vue/client/data/20130108.exome.targets.grch38.bed',
+        bedFileUrl: 'https://iobio.s3.amazonaws.com/clin.iobio/20130108.exome.targets.bed',
+        bedFile37: 'https://iobio.s3.amazonaws.com/clin.iobio/20130108.exome.targets.bed',
+        bedFile38: 'https://iobio.s3.amazonaws.com/clin.iobio/20130108.exome.targets.grch38.bed',
         urlRules: [
           v => /https?:\/\/(www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0-9()@:%_\+.~#?&//=]*)/.test(v) || 'URL must be valid',
         ],

diff --git a/src/data/example_file_config_GRCh38.csv b/src/data/example_file_config_GRCh38.csv
@@ -1,6 +1,6 @@
 #PROJECT_NAME: demo project GRCh38
 #PROJECT_DESCRIPTION: Exome sequencing project for three samples. 
-#BED_URL: https://raw.githubusercontent.com/adityaekawade/bam.iobio.io/vue/client/data/20130108.exome.targets.bed
+#BED_URL: https://iobio.s3.amazonaws.com/clin.iobio/20130108.exome.targets.grch38.bed
 #BUILD: GRCh38
 ID,SAMPLE_ID,PATERNAL_ID,MATERNAL_ID,SEX,AFFECTED_STATUS,RELATION,VCF_URL,TBI_URL,BAM_URL,BAI_URL
 1,NA12878,NA12891,NA12892,1,2,proband,https://iobio.s3.amazonaws.com/samples/vcf/2021_platinum/2021_platinum_exomes_GRCh38.vcf.gz,,https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12878.cram,