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Break up annotation page by genome build so it can load in parallel
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annotation/templates/annotation/annotation_build_detail.html
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,203 @@ | ||
| {% load static %} | ||
| {% load js_tags %} | ||
| {% load ui_menu_bars %} | ||
| {% load ui_utils %} | ||
| {% load humanize %} | ||
| {% load tz %} | ||
| {% load settings_tags %} | ||
|
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| {% settings_value 'PYTHON_COMMAND' as python_command %} | ||
|
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||
| <div id="build-{{ build_name }}-details" class="card mt-4"> | ||
| <div class="card-header">{{ build_name }}</div> | ||
| <div class="card-body"> | ||
| {% labelled label="Latest" %}<a class="hover-link" href="{% url 'annotation_versions' %}">{{ details.latest }}</a>{% endlabelled %} | ||
| {% labelled label="Sync with current VEP" %} | ||
| {% if details.sync_with_current_vep %} | ||
| {{ details.sync_with_current_vep }} | ||
| {% endif %} | ||
| {% if details.out_of_sync_with_current_vep %} | ||
| <code> | ||
| {{ details.out_of_sync_with_current_vep }} | ||
| </code> | ||
| {% endif %} | ||
| {% install-instructions "Sync with current VEP" installed=details.sync_with_current_vep %} | ||
| <code>{{ python_command }} manage.py create_new_variant_annotation_version --genome_build={{ build_name }}</code> | ||
| {% endinstall-instructions %} | ||
| {% endlabelled %} | ||
| {% labelled label="Genome Fasta" %} | ||
| {% if details.reference_fasta %} | ||
| {{ details.reference_fasta }} | ||
| {% else %} | ||
| <div class="not-installed">Not found</div> | ||
| {% endif %} | ||
| {% install-instructions "Reference Fasta" installed=details.reference_fasta %} | ||
| <div class="mono">{{ details.reference_fasta_error }}</div> | ||
| You need to download the annotations, or change <code>settings.GENOME_BUILD_REFERENCE_FASTA</code> | ||
| {% endinstall-instructions %} | ||
| {% endlabelled %} | ||
| {% labelled label="Contigs" %} | ||
| <div class="{{ build_name }}"> | ||
| <b>Contigs:</b> {{ details.contigs.num_contigs }} <a href="#{{ build_name }}-contigs" data-toggle="collapse" class="toggle-link">Toggle</a> | ||
| <div id="{{ build_name }}-contigs" class='contig-details collapse'>{{ details.contigs.contigs }}</div> | ||
| </div> | ||
| {% endlabelled %} | ||
| {% labelled label="Gene/Transcript Information" %} | ||
| {% if details.genes_and_transcripts %} | ||
| <div> | ||
| <b>Lastest cdot</b> {{ details.genes_and_transcripts.latest_cdot }} | ||
| </div> | ||
| <div> | ||
| <b>Annotation:</b> {{ details.annotation_consortium }} | ||
| <b>Genes:</b> {{ details.genes_and_transcripts.genes | intcomma }} | ||
| <b>Transcripts:</b> {{ details.genes_and_transcripts.transcripts | intcomma }} | ||
| <a href="#{{ build_name }}-import-sources" data-toggle="collapse" class="toggle-link">Toggle import sources</a> | ||
| </div> | ||
| <div id="{{ build_name }}-import-sources" class='gene-transcript-instructions collapse'> | ||
| <b>Import Sources</b> | ||
| {% for import_source, import_stats in details.genes_and_transcripts.import_sources.items %} | ||
| <div> | ||
| {{ import_source }}: <b>{{ import_stats.transcripts }}</b> transcripts ({{ import_stats.created|localtime }}) | ||
| </div> | ||
| {% endfor %} | ||
| </div> | ||
| {% endif %} | ||
|
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||
| {% for cons_name, other_consortia_data in details.other_consortia.items %} | ||
| <div> | ||
| <b>Annotation:</b> {{ cons_name }} | ||
| <b>Genes:</b> {{ other_consortia_data.genes | intcomma }} | ||
| <b>Transcripts:</b> {{ other_consortia_data.transcripts | intcomma }} | ||
| <a href="#{{ build_name }}-other-import-sources" data-toggle="collapse" class="toggle-link">Toggle import sources</a> | ||
| </div> | ||
| <div id="{{ build_name }}-other-import-sources" class='gene-transcript-instructions collapse'> | ||
| <b>Import Sources</b> | ||
| {% for file_name, import_stats in other_consortia_data.import_sources.items %} | ||
| <div> | ||
| {{ file_name }}: <b>{{ import_stats.transcripts }}</b> transcripts ({{ import_stats.created|localtime }}) | ||
| </div> | ||
| {% endfor %} | ||
| </div> | ||
| {% endfor %} | ||
|
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||
| {% install-instructions build_name installed=details.genes_and_transcripts.transcripts %} | ||
| <p> | ||
| You can install both Ensembl and RefSeq transcripts (for HGVS) but you NEED the ones used by your variant annotation pipeline which is: '<b>{{ details.annotation_consortium }}</b>' | ||
| </p> | ||
|
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||
| <p> | ||
| Download data from <a href="https://github.com/SACGF/cdot/wiki/Download-JSON.gz-files">cdot</a>. See <a href="https://github.com/SACGF/variantgrid/wiki/Gene-and-Transcript-version-data">Gene and Transcript version data</a> for details and how to generate this from scratch | ||
| </p> | ||
|
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||
| <code> | ||
| export gene_annotation_dir=${VARIANTGRID_SETUP_DATA}/gene_annotation | ||
| mkdir -p ${gene_annotation_dir} | ||
| cd ${gene_annotation_dir} | ||
| </code> | ||
| {% if build_name == 'GRCh37' %} | ||
| <h5>Ensembl GRCh37</h5> | ||
|
|
||
| <code> | ||
| wget https://cdot.cc/download/{{ cdot_version }}/cdot-{{ cdot_version }}.ensembl.grch37.json.gz | ||
| {{ python_command }} manage.py import_gene_annotation --annotation-consortium=Ensembl --genome-build=GRCh37 --json-file ${gene_annotation_dir}/cdot-{{ cdot_version }}.ensembl.grch37.json.gz | ||
| </code> | ||
| {% elif build_name == 'GRCh38' %} | ||
| <h5>Ensembl GRCh38</h5> | ||
| <code> | ||
| wget https://cdot.cc/download/{{ cdot_version }}/cdot-{{ cdot_version }}.ensembl.grch38.json.gz | ||
| {{ python_command }} manage.py import_gene_annotation --annotation-consortium=Ensembl --genome-build=GRCh38 --json-file ${gene_annotation_dir}/cdot-{{ cdot_version }}.ensembl.grch38.json.gz | ||
| </code> | ||
| {% endif %} | ||
|
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||
| {% if build_name == 'GRCh37' %} | ||
| <h5>RefSeq GRCh37</h5> | ||
| <code> | ||
| wget https://cdot.cc/download/{{ cdot_version }}/cdot-{{ cdot_version }}.refseq.grch37.json.gz | ||
| {{ python_command }} manage.py import_gene_annotation --annotation-consortium=RefSeq --genome-build=GRCh37 --json-file ${gene_annotation_dir}/cdot-{{ cdot_version }}.refseq.grch37.json.gz | ||
| </code> | ||
| {% elif build_name == 'GRCh38' %} | ||
| <h5>RefSeq GRCh38</h5> | ||
| <code> | ||
| wget https://cdot.cc/download/{{ cdot_version }}/cdot-{{ cdot_version }}.refseq.grch38.json.gz | ||
| {{ python_command }} manage.py import_gene_annotation --annotation-consortium=RefSeq --genome-build=GRCh38 --json-file ${gene_annotation_dir}/cdot-{{ cdot_version }}.refseq.grch38.json.gz | ||
| </code> | ||
| {% endif %} | ||
| {% endinstall-instructions %} | ||
| {% endlabelled %} | ||
|
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| {% labelled label="Gene Annotation Release" %} | ||
| {% if details.gene_annotation_release %} | ||
| <span title="{{ details.gene_annotation_release.gene_annotation_import }}">{{ details.gene_annotation_release.name }}</span> | ||
| {% else %} | ||
| <div class="no-value">Not Installed</div> | ||
| {% endif %} | ||
| {% install-instructions "Gene Annotation Release" installed=details.gene_annotation_release %} | ||
| You need a Gene Annotation Release that matches the exact symbol/gene/transcript versions used by VEP. | ||
| <a href="https://github.com/SACGF/variantgrid/wiki/Gene-and-Transcript-Version-Data#gene-annotation-release---install">See Wiki for details</a> | ||
|
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||
| {% with vav=details.latest.variant_annotation_version %} | ||
| {% if vav.cdot_gene_release_filename %} | ||
| <code> | ||
| wget http://cdot.cc/download/{{ vav.get_annotation_consortium_display }}/{{ build_name }}/{{ vav.cdot_gene_release_filename }} | ||
| {{ python_command }} manage.py import_gene_annotation --annotation-consortium={{ vav.get_annotation_consortium_display }} --genome-build={{ build_name }} --json-file {{ vav.cdot_gene_release_filename }} --release={{ vav.suggested_gene_annotation_release_name }} | ||
| </code> | ||
| If it doesn't auto-link, go to <a href="{% url 'admin:annotation_variantannotationversion_change' vav.pk %}">Admin</a> then set the gene annotation release. | ||
| {% endif %} | ||
| {% endwith %} | ||
|
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||
| {% endinstall-instructions %} | ||
| {% endlabelled %} | ||
|
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| {% settings_value 'ANNOTATION_GENE_ANNOTATION_VERSION_ENABLED' as ANNOTATION_GENE_ANNOTATION_VERSION_ENABLED %} | ||
| {% if ANNOTATION_GENE_ANNOTATION_VERSION_ENABLED %} | ||
| {% labelled label="Gene Annotation" %} | ||
| {% if details.gene_level_annotation %} | ||
| {{ details.gene_level_annotation }} | ||
| {% else %} | ||
| <div class="no-value">Not Installed</div> | ||
| {% endif %} | ||
| {% install-instructions "Gene Annotation" installed=details.gene_level_annotation %} | ||
| <code>{{ python_command }} manage.py gene_annotation --gene-annotation-release={{ details.latest.variant_annotation_version.gene_annotation_release_id|default_if_none:'(Gene Annotation Release ID)' }}</code> | ||
| {% endinstall-instructions %} | ||
| {% endlabelled %} | ||
| {% endif %} | ||
|
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| {% labelled label="ClinVar" %} | ||
| {% if details.clinvar %} | ||
| {{ details.clinvar }} | ||
| {% else %} | ||
| <div class="no-value">Not installed</div> | ||
| {% endif %} | ||
| {% install-instructions "Clinvar" installed=details.clinvar %} | ||
| Download VCF (with date in file name) from <a href="https://www.ncbi.nlm.nih.gov/clinvar/">NCBI ClinVar</a> site, then run: | ||
|
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| <code>{{ python_command }} manage.py clinvar_import ${VARIANTGRID_SETUP_DATA}/clinvar_20180401.vcf.gz</code> | ||
| {% endinstall-instructions %} | ||
|
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||
| {% endlabelled %} | ||
| {% if somalier_enabled %} | ||
| {% labelled label="Somalier" %} | ||
| {% if details.somalier %} | ||
| {{ details.somalier }} | ||
| {% else %} | ||
| Not installed | ||
| {% endif %} | ||
| {% install-instructions "Somalier" installed=details.somalier %} | ||
| Upload the Somalier sites VCF for {{ build_name }}. | ||
| {% endinstall-instructions %} | ||
| {% endlabelled %} | ||
| {% endif %} | ||
| </div> | ||
| </div> | ||
|
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||
| <div> | ||
| Details.ok = {{ details.ok }} | ||
| </div> | ||
|
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| {% if not details.ok %} | ||
| <script> | ||
| $(document).ready(function() { | ||
| $("#installation-instructions").show(); | ||
| }); | ||
| </script> | ||
| {% endif %} |
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