diff --git a/README.md b/README.md
index 2907e24..f0ca649 100644
--- a/README.md
+++ b/README.md
@@ -33,3 +33,8 @@ TODO:
 - [ ] automate the above build steps
 - [ ] fix the breadcrumbs so they just update search params instead of triggering page refresh
 
+This is a `vite` site. Clone the repository and then start a development server with:
+
+```
+npm run dev
+```
\ No newline at end of file
diff --git a/public/bulker/cdid.yaml b/public/bulker/cdid.yaml
deleted file mode 100644
index dd0b4cb..0000000
--- a/public/bulker/cdid.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-description: "Two druids that describe the manifest"
-type: object
-properties:
-  imports:
-    type: string
-  commands:
-    type: string
-recursive:
-  - imports
-  - commands
-required:
-  - commands
\ No newline at end of file
diff --git a/public/bulker/cmdlist.yaml b/public/bulker/cmdlist.yaml
deleted file mode 100644
index 5fcb200..0000000
--- a/public/bulker/cmdlist.yaml
+++ /dev/null
@@ -1,16 +0,0 @@
-description: "A list of commands and the containers that run them."
-type: array
-items:
-  type: object
-  properties:
-    command:
-      type: string
-    docker_args:
-      type: string
-    docker_image:
-      type: string
-    docker_command:
-      type: string
-  required:
-    - command
-    - docker_image
\ No newline at end of file
diff --git a/public/bulker/importlist.yaml b/public/bulker/importlist.yaml
deleted file mode 100644
index 630f2c1..0000000
--- a/public/bulker/importlist.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-description: "A priority list of bulker manifests that are imported."
-type: array
-items:
-  type: string
diff --git a/public/bulker/manifest.yaml b/public/bulker/manifest.yaml
deleted file mode 100644
index 93122b2..0000000
--- a/public/bulker/manifest.yaml
+++ /dev/null
@@ -1,31 +0,0 @@
-description: "Schema for bulker manifest"
-properties:
-  manifest:
-    type: object
-    properties:
-      name:
-        type: string
-      version:
-        type: string
-      imports:
-        type: array
-        items:
-          type: string
-      commands:
-        type: array
-        items:
-          type: object
-          properties:
-            command:
-              type: string
-            docker_args:
-              type: string
-            docker_image:
-              type: string
-            docker_command:
-              type: string
-          required:
-            - command
-            - docker_image
-    required:
-      - commands
diff --git a/public/bulker/schemas.json b/public/bulker/schemas.json
deleted file mode 100644
index ff7dcd1..0000000
--- a/public/bulker/schemas.json
+++ /dev/null
@@ -1,26 +0,0 @@
-{
-    "cdid": {
-        "namespace": "bulker",
-        "schema": "cdid",
-        "url": "bulker/cdid.yaml",
-        "description": "Two druids that describe the manifest"
-    },
-    "cmdlist": {
-        "namespace": "bulker",
-        "schema": "cmdlist",
-        "url": "bulker/cmdlist.yaml",
-        "description": "A list of commands and the containers that run them."
-    },
-    "manifest": {
-        "namespace": "bulker",
-        "schema": "manifest",
-        "url": "bulker/manifest.yaml",
-        "description": "Schema for bulker manifest"
-    },
-    "importlist": {
-        "namespace": "bulker",
-        "schema": "importlist",
-        "url": "bulker/importlist.yaml",
-        "description": "A priority list of bulker manifests that are imported."
-    }
-}
\ No newline at end of file
diff --git a/public/list.json b/public/list.json
deleted file mode 100644
index 5266998..0000000
--- a/public/list.json
+++ /dev/null
@@ -1,147 +0,0 @@
-{
-    "schemas/bulker/cdid": {
-        "project": "bulker",
-        "url": "bulker/cdid.yaml",
-        "description": "Two druids that describe the manifest"
-    },
-    "schemas/bulker/cmdlist": {
-        "project": "bulker",
-        "url": "bulker/cmdlist.yaml",
-        "description": "A list of commands and the containers that run them."
-    },
-    "schemas/bulker/manifest": {
-        "project": "bulker",
-        "url": "bulker/manifest.yaml",
-        "description": "Schema for bulker manifest"
-    },
-    "schemas/bulker/importlist": {
-        "project": "bulker",
-        "url": "bulker/importlist.yaml",
-        "description": "A priority list of bulker manifests that are imported."
-    },
-    "schemas/refget/SeqColArraySetInherent": {
-        "project": "refget",
-        "url": "refget/SeqColArraySetInherent.yaml",
-        "description": "SeqColArraySet"
-    },
-    "schemas/refget/sequence": {
-        "project": "refget",
-        "url": "refget/sequence.yaml",
-        "description": "Schema for a single raw sequence"
-    },
-    "schemas/refget/annotated_collection_digest": {
-        "project": "refget",
-        "url": "refget/annotated_collection_digest.yaml",
-        "description": "Schema for an Annotated Collection Digest; this is analogous to a single fasta file with metadata."
-    },
-    "schemas/refget/ArrayedNestedSequenceCollection": {
-        "project": "refget",
-        "url": "refget/ArrayedNestedSequenceCollection.yaml",
-        "description": "A collection of sequences"
-    },
-    "schemas/refget/ASDList": {
-        "project": "refget",
-        "url": "refget/ASDList.yaml",
-        "description": "Schema for List of ASDs"
-    },
-    "schemas/refget/annotated_sequence_digest": {
-        "project": "refget",
-        "url": "refget/annotated_sequence_digest.yaml",
-        "description": "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata"
-    },
-    "schemas/refget/ACDList": {
-        "project": "refget",
-        "url": "refget/ACDList.yaml",
-        "description": "Schema for a list of ACDs; analogous to a collection of fasta files"
-    },
-    "schemas/refget/ArrayedSequenceCollection": {
-        "project": "refget",
-        "url": "refget/ArrayedSequenceCollection.yaml",
-        "description": "A collection of sequences"
-    },
-    "schemas/refget/RawSeqCol": {
-        "project": "refget",
-        "url": "refget/RawSeqCol.yaml",
-        "description": "Schema for List of ASDs"
-    },
-    "schemas/refget/TASeqCol": {
-        "project": "refget",
-        "url": "refget/TASeqCol.yaml",
-        "description": "TAseqcol"
-    },
-    "schemas/refget/CustomAnnotatedArrayedSequenceCollection": {
-        "project": "refget",
-        "url": "refget/CustomAnnotatedArrayedSequenceCollection.yaml",
-        "description": "A collection of sequences"
-    },
-    "schemas/refget/SeqColArraySet": {
-        "project": "refget",
-        "url": "refget/SeqColArraySet.yaml",
-        "description": "SeqColArraySet"
-    },
-    "schemas/refget/AnnotatedArrayedSequenceCollection": {
-        "project": "refget",
-        "url": "refget/AnnotatedArrayedSequenceCollection.yaml",
-        "description": "A collection of sequences"
-    },
-    "schemas/refget/AnnotatedSequenceList": {
-        "project": "refget",
-        "url": "refget/AnnotatedSequenceList.yaml",
-        "description": "Schema for List of ASDs"
-    },
-    "schemas/refgenie/refgenie_build": {
-        "project": "refgenie",
-        "url": "refgenie/refgenie_build.yaml",
-        "description": "databio_genomes PEP schema"
-    },
-    "schemas/pep/2.1.0": {
-        "project": "pep",
-        "url": "pep/2.1.0.yaml",
-        "description": "Schema for a minimal PEP"
-    },
-    "schemas/pep/2.0.0": {
-        "project": "pep",
-        "url": "pep/2.0.0.yaml",
-        "description": "Schema for a minimal PEP"
-    },
-    "schemas/pipelines/pipeline_interface": {
-        "project": "pipelines",
-        "url": "pipelines/pipeline_interface.yaml",
-        "description": "pipeline interface schema"
-    },
-    "schemas/pipelines/geofetch_sra_convert": {
-        "project": "pipelines",
-        "url": "pipelines/geofetch_sra_convert.yaml",
-        "description": "A PEP for converting SRA files into fastq or bam format."
-    },
-    "schemas/pipelines/bedmaker": {
-        "project": "pipelines",
-        "url": "pipelines/bedmaker.yaml",
-        "description": "bedmaker PEP schema"
-    },
-    "schemas/pipelines/bedbuncher": {
-        "project": "pipelines",
-        "url": "pipelines/bedbuncher.yaml",
-        "description": "bedbuncher PEP schema"
-    },
-    "schemas/pipelines/pepatac": {
-        "project": "pipelines",
-        "url": "pipelines/pepatac.yaml",
-        "description": "A PEP for ATAC-seq samples for the PEPATAC pipeline."
-    },
-    "schemas/pipelines/ProseqPEP": {
-        "project": "pipelines",
-        "url": "pipelines/ProseqPEP.yaml",
-        "description": "A PEP for nascent RNA samples for the PEPPRO pipeline."
-    },
-    "schemas/pipelines/bedstat": {
-        "project": "pipelines",
-        "url": "pipelines/bedstat.yaml",
-        "description": "bedstat PEP schema"
-    },
-    "schemas/pipelines/bedboss": {
-        "project": "pipelines",
-        "url": "pipelines/bedboss.yaml",
-        "description": "bedboss run-all pep schema"
-    }
-}
\ No newline at end of file
diff --git a/public/namespaces.json b/public/namespaces.json
deleted file mode 100644
index e29f22f..0000000
--- a/public/namespaces.json
+++ /dev/null
@@ -1,7 +0,0 @@
-[
-    "bulker",
-    "refget",
-    "refgenie",
-    "pep",
-    "pipelines"
-]
\ No newline at end of file
diff --git a/public/pep/2.0.0.yaml b/public/pep/2.0.0.yaml
deleted file mode 100644
index 56f2034..0000000
--- a/public/pep/2.0.0.yaml
+++ /dev/null
@@ -1,69 +0,0 @@
-description: "Schema for a minimal PEP"
-version: "2.0.0"
-properties:
-  config:
-    properties:
-      name: 
-        type: string
-        pattern: "^\\S*$"
-        description: "Project name with no whitespace"
-      pep_version:
-        description: "Version of the PEP Schema this PEP follows"
-        type: string
-      sample_table:
-        type: string
-        description: "Path to the sample annotation table with one row per sample"
-      subsample_table:
-        type: string
-        description: "Path to the subsample annotation table with one row per subsample and sample_name attribute matching an entry in the sample table"
-      sample_modifiers:
-        type: object
-        properties:
-          append:
-            type: object
-          duplicate:
-            type: object
-          imply:
-            type: array
-            items:
-              type: object
-              properties:
-                if:
-                  type: object
-                then:
-                  type: object
-          derive:
-            type: object
-            properties:
-              attributes:
-                type: array
-                items:
-                  type: string
-              sources:
-                type: object
-        project_modifiers:
-          type: object
-          properties:
-            amend:
-              description: "Object overwriting original project attributes"
-              type: object
-            import:
-              description: "List of external PEP project config files to import"
-              type: array
-              items:
-                type: string
-    required:
-      - pep_version
-  samples:
-    type: array
-    items:
-      type: object
-      properties:
-        sample_name: 
-          type: string
-          pattern: "^\\S*$"
-          description: "Unique name of the sample with no whitespace"
-      required:
-        - sample_name
-required:
-  - samples
diff --git a/public/pep/2.1.0.yaml b/public/pep/2.1.0.yaml
deleted file mode 100644
index e3982aa..0000000
--- a/public/pep/2.1.0.yaml
+++ /dev/null
@@ -1,77 +0,0 @@
-description: "Schema for a minimal PEP"
-version: "2.1.0"
-properties:
-  config:
-    properties:
-      name: 
-        type: string
-        pattern: "^\\S*$"
-        description: "Project name with no whitespace"
-      pep_version:
-        description: "Version of the PEP Schema this PEP follows"
-        type: string
-      sample_table:
-        type: string
-        description: "Path to the sample annotation table"
-      subsample_table:
-        type: string
-        description: "Path to the subsample annotation table with one row per subsample and sample_name attribute matching an entry in the sample table"
-      sample_table_index: 
-        type: string
-        pattern: "^\\S*$"
-        description: "Name of the column in sample table to use as an index. It's 'sample_name' by default"
-      subsample_table_index: 
-        type: array
-        items:
-          type: string
-          pattern: "^\\S*$"
-        description: "Names of the columns in subsample table to use as an index. It's ['sample_name', 'subsample_name'] by default"
-      sample_modifiers:
-        type: object
-        properties:
-          append:
-            type: object
-          duplicate:
-            type: object
-          imply:
-            type: array
-            items:
-              type: object
-              properties:
-                if:
-                  type: object
-                then:
-                  type: object
-          derive:
-            type: object
-            properties:
-              attributes:
-                type: array
-                items:
-                  type: string
-              sources:
-                type: object
-        project_modifiers:
-          type: object
-          properties:
-            amend:
-              description: "Object overwriting original project attributes"
-              type: object
-            import:
-              description: "List of external PEP project config files to import"
-              type: array
-              items:
-                type: string
-    required:
-      - pep_version
-  samples:
-    type: array
-    items:
-      type: object
-      properties:
-        sample_name: 
-          type: string
-          pattern: "^\\S*$"
-          description: "Unique name of the sample with no whitespace"
-required:
-  - samples
diff --git a/public/pep/schemas.json b/public/pep/schemas.json
deleted file mode 100644
index eef3d24..0000000
--- a/public/pep/schemas.json
+++ /dev/null
@@ -1,14 +0,0 @@
-{
-    "2.1.0": {
-        "namespace": "pep",
-        "schema": "2.1.0",
-        "url": "pep/2.1.0.yaml",
-        "description": "Schema for a minimal PEP"
-    },
-    "2.0.0": {
-        "namespace": "pep",
-        "schema": "2.0.0",
-        "url": "pep/2.0.0.yaml",
-        "description": "Schema for a minimal PEP"
-    }
-}
\ No newline at end of file
diff --git a/public/pipelines/ProseqPEP.yaml b/public/pipelines/ProseqPEP.yaml
deleted file mode 100644
index ab1f130..0000000
--- a/public/pipelines/ProseqPEP.yaml
+++ /dev/null
@@ -1,50 +0,0 @@
-description: A PEP for nascent RNA samples for the PEPPRO pipeline.
-imports:
-  - http://schema.databio.org/pep/2.0.0.yaml
-properties:
-  samples:
-    type: array
-    items:
-      type: object
-      properties:
-        sample_name: 
-          type: string
-          description: "Name of the sample"
-        organism: 
-          type: string
-          description: "Organism"
-        protocol: 
-          type: string
-          description: "Specifies whether the sample is pro-seq or gro-seq"
-          enum: ["PRO", "pro", "PRO-SEQ", "PRO-seq", "proseq", "PROSEQ", "GRO", "gro", "groseq", "GROSEQ", "GRO-SEQ", "GRO-seq"]
-        genome:
-          type: string
-          description: "Refgenie genome registry identifier"
-        read_type:
-          type: string
-          description: "Is this single or paired-end data?"
-          enum: ["SINGLE", "PAIRED"]
-        read1:
-          anyOf:
-            - type: string
-              description: "Fastq file for read 1"
-            - type: array
-              items:
-                type: string
-        read2:
-          anyOf:
-            - type: string
-              description: "Fastq file for read 2 (for paired-end experiments)"
-            - type: array
-              items:
-                type: string
-        umi_len:
-          type: string
-          description: "Length of the Unique Molecular Identifier, if any"
-      required:
-        - sample_name
-        - protocol
-        - read1
-        - genome
-required:
-  - samples
diff --git a/public/pipelines/bedboss.yaml b/public/pipelines/bedboss.yaml
deleted file mode 100644
index e6ffa0c..0000000
--- a/public/pipelines/bedboss.yaml
+++ /dev/null
@@ -1,47 +0,0 @@
-description: bedboss run-all pep schema
-
-properties:
-  samples:
-    type: array
-    items:
-      type: object
-      properties:
-        sample_name: 
-          type: string
-          description: "Name of the sample"
-        input_file:
-          type: string
-          description: "Absolute path to the input file"
-        input_type:
-          type: string
-          description: "file format"
-          enum: [ "bigWig", "bigBed", "bed", "wig", "bedGraph" ]
-        genome:
-          type: string
-          description: "organism genome code"
-        format_type:
-          type: string
-          description: "whether the regions are narrow (transcription factor implies narrow, histone mark implies broad peaks)"
-          enum: [ "narrowPeak", "broadPeak" ]
-        description:
-          type: string
-          description: "freeform description of the sample"
-        open_signal_matrix:
-          type: string
-          description: "A full path to the openSignalMatrix required for the tissue"
-        chrom_sizes:
-          type: string
-          description: "A full path to the chrom.sizes required for the bedtobigbed conversion"
-        treatment:
-          type: string
-          description: "freeform description of the sample treatment"
-        cell_type:
-          type: string
-          description: "cell type code"
-      required:
-        - sample_name
-        - input_file
-        - input_type
-        - genome
-required:
-  - samples
diff --git a/public/pipelines/bedbuncher.yaml b/public/pipelines/bedbuncher.yaml
deleted file mode 100644
index cd42998..0000000
--- a/public/pipelines/bedbuncher.yaml
+++ /dev/null
@@ -1,25 +0,0 @@
-description: bedbuncher PEP schema
-imports: 
-  - http://schema.databio.org/pep/2.0.0.yaml
-
-properties:
-  samples:
-    type: array
-    items:
-      type: object
-      properties:
-        JSONquery_path: 
-          type: string
-          description: "path to the JSON file with the Elasticsearch query"
-        bedset_name:
-          type: string
-          pattern: "^\\S*$"
-          description: "name of the bedset that will be created"
-        bbconfig_path:
-          type: string
-          description: "path to bedbase config file"
-      required:
-        - JSONquery_path
-        - bedset_name
-required:
-  - samples
\ No newline at end of file
diff --git a/public/pipelines/bedmaker.yaml b/public/pipelines/bedmaker.yaml
deleted file mode 100644
index 93806d0..0000000
--- a/public/pipelines/bedmaker.yaml
+++ /dev/null
@@ -1,59 +0,0 @@
-description: bedmaker PEP schema
-
-properties:
-  samples:
-    type: array
-    items:
-      type: object
-      properties:
-        sample_name: 
-          type: string
-          description: "name of the sample, which is the name of the output BED file"
-        input_file_path: 
-          type: string
-          description: "absolute path the file to convert"
-        output_bed_path: 
-          type: string
-          description: "absolute path the file to the output BED file (derived attribute)"
-        output_bigbed_path: 
-          type: string
-          description: "absolute path the file to the output bigBed file (derived attribute)"
-        genome:
-          type: string
-          description: "organism genome code"
-        narrowpeak:
-          type: boolean
-          description: "whether the regions are narrow (transcription factor implies narrow, histone mark implies broad peaks)"
-        format:
-          type: string
-          description: "file format"
-          enum: ["bigWig", "bigBed", "bed", "wig", "bedGraph"]
-        cell_type:
-          type: string
-          description: "cell type code"
-        antibody:
-          type: string
-          description: "antibody used if ChIP-seq experiment"
-        description:
-          type: string
-          description: "freeform description of the sample"
-        exp_protocol:
-          type: string
-          description: "type of the experiment the file was generated in"
-        data_source:
-          type: string
-          description: "source of the sample, preferably a GSE* code"
-        treatment:
-          type: string
-          description: "freeform description of the sample treatment"
-      required_files:
-        - input_file_path
-      required:
-        - input_file_path
-        - output_bed_path
-        - output_bigbed_path
-        - genome
-        - narrowpeak
-        - sample_name
-required:
-  - samples
diff --git a/public/pipelines/bedstat.yaml b/public/pipelines/bedstat.yaml
deleted file mode 100644
index 8810191..0000000
--- a/public/pipelines/bedstat.yaml
+++ /dev/null
@@ -1,41 +0,0 @@
-description: bedstat PEP schema
-imports: 
-  - http://schema.databio.org/pep/2.0.0.yaml
-
-properties:
-  samples:
-    type: array
-    items:
-      type: object
-      properties:
-        output_file_path: 
-          type: string
-          description: "absolute path to the output BED files (.bed or .bed.gz)"
-        genome:
-          type: string
-          description: "organism reference genome"
-        cell_type:
-          type: string
-          description: "cell type used to perform the experimental protocol"
-        antibody:
-          type: string
-          description: "TF or Histone mark antibody used if ChIP-seq experiment"
-        description:
-          type: string
-          description: "freeform description of the sample"
-        exp_protocol:
-          type: string
-          description: "experimental protocol used to generate the genomic regions"
-        data_source:
-          type: string
-          description: "source of the sample, preferably a GSE* code"
-        treatment:
-          type: string
-          description: "freeform description of the sample treatment"
-      required_files:
-        - output_file_path
-      required:
-        - output_file_path
-        - genome
-required:
-  - samples
diff --git a/public/pipelines/geofetch_sra_convert.yaml b/public/pipelines/geofetch_sra_convert.yaml
deleted file mode 100644
index dd057d7..0000000
--- a/public/pipelines/geofetch_sra_convert.yaml
+++ /dev/null
@@ -1,27 +0,0 @@
-description: A PEP for converting SRA files into fastq or bam format.
-imports:
-  - http://schema.databio.org/pep/2.0.0.yaml
-properties:
-  samples:
-    type: array
-    items:
-      type: object
-      properties:
-        sample_name: 
-          type: string
-          description: "Name of the sample"
-        protocol: 
-          type: string
-          description: "Can be anything"
-        SRR_files:
-          type: string
-          description: "SRR files"
-      required_files:
-        - SRR_files
-      files:
-        - SRR_files
-      required:
-        - sample_name
-        - SRR_files
-required:
-  - samples
diff --git a/public/pipelines/pepatac.yaml b/public/pipelines/pepatac.yaml
deleted file mode 100644
index 5b204c5..0000000
--- a/public/pipelines/pepatac.yaml
+++ /dev/null
@@ -1,51 +0,0 @@
-description: A PEP for ATAC-seq samples for the PEPATAC pipeline.
-imports:
-  - http://schema.databio.org/pep/2.0.0.yaml
-properties:
-  samples:
-    type: array
-    items:
-      type: object
-      properties:
-        sample_name: 
-          type: string
-          description: "Name of the sample"
-        organism: 
-          type: string
-          description: "Organism"
-        protocol: 
-          type: string
-          description: "Must be an ATAC-seq or DNAse-seq sample"
-        genome:
-          type: string
-          description: "Refgenie genome registry identifier"
-        read_type:
-          type: string
-          description: "Is this single or paired-end data?"
-          enum: ["SINGLE", "PAIRED"]
-        read1:
-          anyOf:
-            - type: string
-              description: "Fastq file for read 1"
-            - type: array
-              items:
-                type: string
-        read2:
-          anyOf:
-            - type: string
-              description: "Fastq file for read 2 (for paired-end experiments)"
-            - type: array
-              items:
-                type: string
-      required_files:
-        - read1
-      files:
-        - read1
-        - read2
-      required:
-        - sample_name
-        - protocol
-        - read1
-        - genome
-required:
-  - samples
diff --git a/public/pipelines/pipeline_interface.yaml b/public/pipelines/pipeline_interface.yaml
deleted file mode 100644
index d428e3d..0000000
--- a/public/pipelines/pipeline_interface.yaml
+++ /dev/null
@@ -1,47 +0,0 @@
-description: pipeline interface schema
-
-properties:
-  pipeline_name:
-    type: string
-    pattern: "^\\S*$"
-    description: "name of the pipeline with no whitespaces"
-  pipeline_type:
-    type: string
-    enum: ["project", "sample"]
-    description: "type of the pipeline, either 'project' or 'sample'"
-  command_template:
-    type: string
-    description: "Jinja2-like template to construct the command to run"
-  path:
-    type: string
-    description: "path to the pipeline program. Relative to pipeline interface file or absolute."
-  compute:
-    type: object
-    description: "Section that defines compute environment settings"
-    properties:
-      dynamic_variables_command_template:
-        type: string
-        description: "Jinja2-like template to construct the command that returns a JSON object used to populate compute environment settings"
-      size_dependent_variables:
-        type: string
-        description: "Path to the TSV-formatted file with compute environment settings"
-      bulker_crate:
-        type: string
-        description: "Bulker registry path idendifying the crate to use"
-      docker_image:
-        type: string
-        description: "Docker image identifier"
-      singularity_image:
-        type: string
-        description: "Singularity image identifier"
-if:
-  properties:
-    pipeline_type:
-      const: "project"
-then:
-  properties:
-    linked_pipeline_interfaces:
-      type: array
-      items:
-        type: string
-required: [pipeline_name, pipeline_type, command_template]
\ No newline at end of file
diff --git a/public/pipelines/schemas.json b/public/pipelines/schemas.json
deleted file mode 100644
index 895c315..0000000
--- a/public/pipelines/schemas.json
+++ /dev/null
@@ -1,50 +0,0 @@
-{
-    "pipeline_interface": {
-        "namespace": "pipelines",
-        "schema": "pipeline_interface",
-        "url": "pipelines/pipeline_interface.yaml",
-        "description": "pipeline interface schema"
-    },
-    "geofetch_sra_convert": {
-        "namespace": "pipelines",
-        "schema": "geofetch_sra_convert",
-        "url": "pipelines/geofetch_sra_convert.yaml",
-        "description": "A PEP for converting SRA files into fastq or bam format."
-    },
-    "bedmaker": {
-        "namespace": "pipelines",
-        "schema": "bedmaker",
-        "url": "pipelines/bedmaker.yaml",
-        "description": "bedmaker PEP schema"
-    },
-    "bedbuncher": {
-        "namespace": "pipelines",
-        "schema": "bedbuncher",
-        "url": "pipelines/bedbuncher.yaml",
-        "description": "bedbuncher PEP schema"
-    },
-    "pepatac": {
-        "namespace": "pipelines",
-        "schema": "pepatac",
-        "url": "pipelines/pepatac.yaml",
-        "description": "A PEP for ATAC-seq samples for the PEPATAC pipeline."
-    },
-    "ProseqPEP": {
-        "namespace": "pipelines",
-        "schema": "ProseqPEP",
-        "url": "pipelines/ProseqPEP.yaml",
-        "description": "A PEP for nascent RNA samples for the PEPPRO pipeline."
-    },
-    "bedstat": {
-        "namespace": "pipelines",
-        "schema": "bedstat",
-        "url": "pipelines/bedstat.yaml",
-        "description": "bedstat PEP schema"
-    },
-    "bedboss": {
-        "namespace": "pipelines",
-        "schema": "bedboss",
-        "url": "pipelines/bedboss.yaml",
-        "description": "bedboss run-all pep schema"
-    }
-}
\ No newline at end of file
diff --git a/public/refgenie/refgenie_build.yaml b/public/refgenie/refgenie_build.yaml
deleted file mode 100644
index bbd293c..0000000
--- a/public/refgenie/refgenie_build.yaml
+++ /dev/null
@@ -1,42 +0,0 @@
-description: databio_genomes PEP schema
-
-properties:
-  samples:
-    type: array
-    items:
-      type: object
-      properties:
-        sample_name: 
-          type: string
-          description: "name of the sample, which is the name of the output BED file"
-        genome:
-          type: string
-          description: "namespace for the assets to be build"
-          pattern: ^[^/:]*$
-        asset:
-          type: string
-          description: "name of the asset to be build"
-          pattern: ^[^/:]*$
-        tag:
-          type: string
-          description: "tag of the asset to be build"
-          pattern: ^[^/:]*$
-        input_value:
-          type: string
-          description: "value of refgenie build function input"
-        local_input:
-          type: string
-          description: "absolute path for the input file"
-        input_type:
-          type: string
-          pattern: "^assets*|^params*|^files*"
-          description: "type of the refgenie build function input"
-      files:
-        - local_input
-      required:
-        - sample_name
-        - asset
-        - genome
-        - local_input
-required:
-  - samples
\ No newline at end of file
diff --git a/public/refgenie/schemas.json b/public/refgenie/schemas.json
deleted file mode 100644
index bb36f76..0000000
--- a/public/refgenie/schemas.json
+++ /dev/null
@@ -1,8 +0,0 @@
-{
-    "refgenie_build": {
-        "namespace": "refgenie",
-        "schema": "refgenie_build",
-        "url": "refgenie/refgenie_build.yaml",
-        "description": "databio_genomes PEP schema"
-    }
-}
\ No newline at end of file
diff --git a/public/refget/ACDList.yaml b/public/refget/ACDList.yaml
deleted file mode 100644
index 6ba1309..0000000
--- a/public/refget/ACDList.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-description: "Schema for a list of ACDs; analogous to a collection of fasta files"
-type: array
-items:
-  type: object
-  properties:
-    name:
-      type: string
-    collection_digest:
-      type: string
-  required:
-    - collection_digest
-  recursive:
-    - collection_digest
diff --git a/public/refget/ASDList.yaml b/public/refget/ASDList.yaml
deleted file mode 100644
index 8f2f299..0000000
--- a/public/refget/ASDList.yaml
+++ /dev/null
@@ -1,25 +0,0 @@
-description: "Schema for List of ASDs"
-type: array
-items: 
-  type: object
-  properties:
-    name:
-      type: string
-    length:
-      type: "integer"
-    topology:
-      type: string
-      enum: ["circular", "linear"]
-      default: "linear"
-    sequence_digest:
-      type: string
-      description: "The sequence digest"
-  required:
-    - length
-    - name
-    - topology
-  recursive:
-    - sequence_digest
-  not:
-    required:
-      - sequence
diff --git a/public/refget/AnnotatedArrayedSequenceCollection.yaml b/public/refget/AnnotatedArrayedSequenceCollection.yaml
deleted file mode 100644
index a64dcd5..0000000
--- a/public/refget/AnnotatedArrayedSequenceCollection.yaml
+++ /dev/null
@@ -1,48 +0,0 @@
-description: "A collection of sequences"
-type: object
-henge_class: "ArrayedNestedSequenceCollection"
-properties:
-  seqcol:
-    type: object
-    henge_class: "SeqCol"
-    properties:
-      names:
-        type: array
-        henge_class: "Names"
-        items:
-          type: string
-      lengths:
-        type: array
-        henge_class: "Lengths"
-        items:
-          type: integer
-      sequences:
-        type: array
-        henge_class: "Sequences"
-        items:
-          type: string
-          henge_class: "Sequence"
-          description: "Actual sequence content"
-  annotation:
-    type: object
-    henge_class: "SeqColAnno"
-    properties:
-      topologies:
-        type: array
-        henge_class: "Topologies"
-        items:
-          type: string
-          enum: ["circular", "linear"]
-          default: "linear"
-      masks:
-        type: array
-        henge_class: "Masks"
-        items:
-          type: string
-      importances:
-        type: array
-        henge_class: "Importances"
-        items:
-          type: boolean
-required:
-  - lengths
diff --git a/public/refget/AnnotatedSequenceList.yaml b/public/refget/AnnotatedSequenceList.yaml
deleted file mode 100644
index 320fdf9..0000000
--- a/public/refget/AnnotatedSequenceList.yaml
+++ /dev/null
@@ -1,33 +0,0 @@
-description: "Schema for List of ASDs"
-henge_class: "AnnotatedSequenceList"
-recursive: true
-type: array
-items: 
-  description: "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata"
-  type: object
-  henge_class: ASD
-  properties:
-    name:
-      type: string
-    length:
-      type: "integer"
-    topology:
-      type: string
-      enum: ["circular", "linear"]
-      default: "linear"
-    sequence:
-      description: "Schema for a single raw sequence"
-      henge_class: sequence
-      type: object
-      properties:
-        sequence:
-          type: string
-          description: "Actual sequence content"
-      required:
-        - sequence
-  required:
-    - length
-    - name
-    - topology
-  recursive:
-    - sequence
diff --git a/public/refget/ArrayedNestedSequenceCollection.yaml b/public/refget/ArrayedNestedSequenceCollection.yaml
deleted file mode 100644
index ad0b060..0000000
--- a/public/refget/ArrayedNestedSequenceCollection.yaml
+++ /dev/null
@@ -1,44 +0,0 @@
-description: "A collection of sequences"
-type: object
-henge_class: "ArrayedNestedSequenceCollection"
-properties:
-  seqcol:
-    type: object
-    henge_class: "SeqCol"
-    properties:
-      names:
-        type: array
-        henge_class: "Names"
-        items:
-          type: string
-      lengths:
-        type: array
-        henge_class: "Lengths"
-        items:
-          type: integer
-      sequences:
-        type: array
-        henge_class: "Sequences"
-        items:
-          type: string
-          henge_class: "Sequence"
-          description: "Actual sequence content"
-  topologies:
-    type: array
-    henge_class: "Topologies"
-    items:
-      type: string
-      enum: ["circular", "linear"]
-      default: "linear"
-  masks:
-    type: array
-    henge_class: "Masks"
-    items:
-      type: string
-  importances:
-    type: array
-    henge_class: "Importances"
-    items:
-      type: boolean
-required:
-  - lengths
diff --git a/public/refget/ArrayedSequenceCollection.yaml b/public/refget/ArrayedSequenceCollection.yaml
deleted file mode 100644
index 196813f..0000000
--- a/public/refget/ArrayedSequenceCollection.yaml
+++ /dev/null
@@ -1,40 +0,0 @@
-description: "A collection of sequences"
-type: object
-henge_class: "ArrayedSequenceCollection"
-properties:
-  names:
-    type: array
-    henge_class: "Names"
-    items:
-      type: string
-  lengths:
-    type: array
-    henge_class: "Lengths"
-    items:
-      type: integer
-  sequences:
-    type: array
-    henge_class: "Sequences"
-    items:
-      type: string
-      henge_class: "Sequence"
-      description: "Actual sequence content"
-  topologies:
-    type: array
-    henge_class: "Topologies"
-    items:
-      type: string
-      enum: ["circular", "linear"]
-      default: "linear"
-  masks:
-    type: array
-    henge_class: "Masks"
-    items:
-      type: string
-  importances:
-    type: array
-    henge_class: "Importances"
-    items:
-      type: boolean
-required:
-  - lengths
diff --git a/public/refget/CustomAnnotatedArrayedSequenceCollection.yaml b/public/refget/CustomAnnotatedArrayedSequenceCollection.yaml
deleted file mode 100644
index decf5d8..0000000
--- a/public/refget/CustomAnnotatedArrayedSequenceCollection.yaml
+++ /dev/null
@@ -1,38 +0,0 @@
-description: "A collection of sequences"
-type: object
-henge_class: "AnnotatedArrayedSequenceCollection"
-properties:
-  seqcol:
-    type: object
-    henge_class: "SeqCol"
-    properties:
-      names:
-        type: array
-        henge_class: "Names"
-        items:
-          type: string
-      lengths:
-        type: array
-        henge_class: "Lengths"
-        items:
-          type: integer
-      sequences:
-        type: array
-        henge_class: "Sequences"
-        items:
-          type: string
-          henge_class: "Sequence"
-          description: "Actual sequence content"
-  annotation:
-    type: array
-    henge_class: "SeqColAnnos"
-    items:
-      type: object
-      henge_class: "SeqColAnno"
-      properties:
-        property_name:
-          type: string
-        property_value:
-          type: array
-required:
-  - lengths
diff --git a/public/refget/RawSeqCol.yaml b/public/refget/RawSeqCol.yaml
deleted file mode 100644
index 1881280..0000000
--- a/public/refget/RawSeqCol.yaml
+++ /dev/null
@@ -1,19 +0,0 @@
-description: "Schema for List of ASDs"
-type: array
-henge_class: "RawSeqCol"
-items: 
-  description: "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata"
-  type: object
-  henge_class: ASD
-  properties:
-    name:
-      type: string
-    length:
-      type: "integer"
-    sequence:
-      description: "Actual sequence content for a single raw sequence"
-      henge_class: sequence
-      type: string
-  required:
-    - length
-    - name
diff --git a/public/refget/SeqColArraySet.yaml b/public/refget/SeqColArraySet.yaml
deleted file mode 100644
index d37158f..0000000
--- a/public/refget/SeqColArraySet.yaml
+++ /dev/null
@@ -1,27 +0,0 @@
-description: "SeqColArraySet"
-type: object
-henge_class: "SeqColArraySet"
-properties:
-  topologies:
-    type: array
-    henge_class: "array"
-    items:
-      type: string
-      enum: ["circular", "linear"]
-      default: "linear"  
-  names:
-    type: array
-    henge_class: "array"
-    items:
-      type: string    
-  lengths:
-    type: array
-    henge_class: "array"
-    items:
-      type: string    
-  sequences:
-    type: array
-    henge_class: "seqarray"
-    items:
-      type: string
-      henge_class: sequence
diff --git a/public/refget/SeqColArraySetInherent.yaml b/public/refget/SeqColArraySetInherent.yaml
deleted file mode 100644
index 743cc28..0000000
--- a/public/refget/SeqColArraySetInherent.yaml
+++ /dev/null
@@ -1,36 +0,0 @@
-description: "SeqColArraySet"
-type: object
-henge_class: "SeqColArraySet"
-properties:
-  topologies:
-    type: array
-    henge_class: "strarray"
-    items:
-      type: string
-      enum: ["circular", "linear"]
-      default: "linear"  
-  names:
-    type: array
-    henge_class: "strarray"
-    items:
-      type: string    
-  lengths:
-    type: array
-    henge_class: "intarray"
-    items:
-      type: integer
-  sequences:
-    type: array
-    henge_class: "seqarray"
-    items:
-      type: string
-      henge_class: sequence
-  sorted_name_length_pairs:
-    type: array
-    henge_class: "strarray"
-    items:
-      type: string
-inherent:
-  - names
-  - lengths
-  - sequences
diff --git a/public/refget/TASeqCol.yaml b/public/refget/TASeqCol.yaml
deleted file mode 100644
index 19a4eb7..0000000
--- a/public/refget/TASeqCol.yaml
+++ /dev/null
@@ -1,31 +0,0 @@
-description: "TAseqcol"
-type: object
-henge_class: "TASeqCol"
-properties:
-  topology:
-    type: array
-    henge_class: "TopologyVec"
-    items:
-      type: string
-      enum: ["circular", "linear"]
-      default: "linear"  
-  rawseqcol:
-    description: "Schema for List of ASDs"
-    type: array
-    henge_class: "RawSeqCol"
-    items: 
-      description: "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata"
-      type: object
-      henge_class: ASD
-      properties:
-        name:
-          type: string
-        length:
-          type: "integer"
-        sequence:
-          type: string
-          henge_class: sequence
-          description: "Actual sequence content"
-      required:
-        - length
-        - name
diff --git a/public/refget/annotated_collection_digest.yaml b/public/refget/annotated_collection_digest.yaml
deleted file mode 100644
index b351c2c..0000000
--- a/public/refget/annotated_collection_digest.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-description: "Schema for an Annotated Collection Digest; this is analogous to a single fasta file with metadata."
-type: object
-properties:
-  name:
-    type: string
-  collection_digest:
-    type: string
-required:
-  - collection_digest
-recursive:
-  - collection_digest
\ No newline at end of file
diff --git a/public/refget/annotated_sequence_digest.yaml b/public/refget/annotated_sequence_digest.yaml
deleted file mode 100644
index a9062a8..0000000
--- a/public/refget/annotated_sequence_digest.yaml
+++ /dev/null
@@ -1,23 +0,0 @@
-description: "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata"
-type: object
-properties:
-  name:
-    type: string
-  length:
-    type: "integer"
-  topology:
-    type: string
-    enum: ["circular", "linear"]
-    default: "linear"
-  sequence_digest:
-    type: string
-    description: "The sequence digest"
-required:
-  - length
-  - name
-  - topology
-recursive:
-  - sequence_digest
-not:
-  required:
-    - sequence  
diff --git a/public/refget/schemas.json b/public/refget/schemas.json
deleted file mode 100644
index d22f569..0000000
--- a/public/refget/schemas.json
+++ /dev/null
@@ -1,86 +0,0 @@
-{
-    "SeqColArraySetInherent": {
-        "namespace": "refget",
-        "schema": "SeqColArraySetInherent",
-        "url": "refget/SeqColArraySetInherent.yaml",
-        "description": "SeqColArraySet"
-    },
-    "sequence": {
-        "namespace": "refget",
-        "schema": "sequence",
-        "url": "refget/sequence.yaml",
-        "description": "Schema for a single raw sequence"
-    },
-    "annotated_collection_digest": {
-        "namespace": "refget",
-        "schema": "annotated_collection_digest",
-        "url": "refget/annotated_collection_digest.yaml",
-        "description": "Schema for an Annotated Collection Digest; this is analogous to a single fasta file with metadata."
-    },
-    "ArrayedNestedSequenceCollection": {
-        "namespace": "refget",
-        "schema": "ArrayedNestedSequenceCollection",
-        "url": "refget/ArrayedNestedSequenceCollection.yaml",
-        "description": "A collection of sequences"
-    },
-    "ASDList": {
-        "namespace": "refget",
-        "schema": "ASDList",
-        "url": "refget/ASDList.yaml",
-        "description": "Schema for List of ASDs"
-    },
-    "annotated_sequence_digest": {
-        "namespace": "refget",
-        "schema": "annotated_sequence_digest",
-        "url": "refget/annotated_sequence_digest.yaml",
-        "description": "Schema for an Annotated Sequence Digest; a digested Sequence plus metadata"
-    },
-    "ACDList": {
-        "namespace": "refget",
-        "schema": "ACDList",
-        "url": "refget/ACDList.yaml",
-        "description": "Schema for a list of ACDs; analogous to a collection of fasta files"
-    },
-    "ArrayedSequenceCollection": {
-        "namespace": "refget",
-        "schema": "ArrayedSequenceCollection",
-        "url": "refget/ArrayedSequenceCollection.yaml",
-        "description": "A collection of sequences"
-    },
-    "RawSeqCol": {
-        "namespace": "refget",
-        "schema": "RawSeqCol",
-        "url": "refget/RawSeqCol.yaml",
-        "description": "Schema for List of ASDs"
-    },
-    "TASeqCol": {
-        "namespace": "refget",
-        "schema": "TASeqCol",
-        "url": "refget/TASeqCol.yaml",
-        "description": "TAseqcol"
-    },
-    "CustomAnnotatedArrayedSequenceCollection": {
-        "namespace": "refget",
-        "schema": "CustomAnnotatedArrayedSequenceCollection",
-        "url": "refget/CustomAnnotatedArrayedSequenceCollection.yaml",
-        "description": "A collection of sequences"
-    },
-    "SeqColArraySet": {
-        "namespace": "refget",
-        "schema": "SeqColArraySet",
-        "url": "refget/SeqColArraySet.yaml",
-        "description": "SeqColArraySet"
-    },
-    "AnnotatedArrayedSequenceCollection": {
-        "namespace": "refget",
-        "schema": "AnnotatedArrayedSequenceCollection",
-        "url": "refget/AnnotatedArrayedSequenceCollection.yaml",
-        "description": "A collection of sequences"
-    },
-    "AnnotatedSequenceList": {
-        "namespace": "refget",
-        "schema": "AnnotatedSequenceList",
-        "url": "refget/AnnotatedSequenceList.yaml",
-        "description": "Schema for List of ASDs"
-    }
-}
\ No newline at end of file
diff --git a/public/refget/sequence.yaml b/public/refget/sequence.yaml
deleted file mode 100644
index fe33ead..0000000
--- a/public/refget/sequence.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-description: "Schema for a single raw sequence"
-type: object
-properties:
-  sequence:
-    type: string
-    description: "Actual sequence content"
-required:
-  - sequence
\ No newline at end of file