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| CACHEDIR=$(shell pwd)/tmp | |
| default-target: | |
| @echo 'There is no default target here.' | |
| @echo 'You probably want either "make daily" or "make install".' | |
| daily: update_editors_summary dump_database data_local bionotate_history | |
| install: php-openid-2.2.2 textile-2.0.0 public_html/js/wz_tooltip.js public_html/js/tip_balloon.js DataTables-1.8.1.zip public_html/DataTables-1.8.1 public_html/jquery-ui | |
| php-openid-2.2.2: | |
| [ -d php-openid/.git ] || git clone http://github.com/openid/php-openid.git | |
| cd php-openid && git fetch --tags http://github.com/openid/php-openid.git | |
| cd php-openid && git checkout 2.2.2 | |
| cd php-openid && patch -p1 <../patch-yadis-noprotocol | |
| ln -s php-openid php-openid-2.2.2 | |
| textile-2.0.0: | |
| wget -c http://textile.thresholdstate.com/file_download/2/textile-2.0.0.tar.gz | |
| [ `md5sum textile-2.0.0.tar.gz | head -c 32` = c4f2454b16227236e01fc1c761366fe3 ] | |
| tar xzf textile-2.0.0.tar.gz | |
| patch -p0 <textile-2.0.0-php-5.2.4.patch | |
| DataTables-1.8.1.zip: | |
| wget -c http://www.datatables.net/releases/DataTables-1.8.1.zip | |
| public_html/DataTables-1.8.1: DataTables-1.8.1.zip | |
| cd public_html && unzip ../DataTables-1.8.1.zip | |
| touch $@ | |
| public_html/jquery-ui: jquery-ui-1.8.14.custom.zip | |
| mkdir -p public_html/jquery-ui && cd public_html/jquery-ui && unzip ../../jquery-ui-1.8.14.custom.zip | |
| public_html/js/wz_tooltip.js: | |
| ######## Walter Zorn's tooltip library seems to be homeless, so we | |
| ######## have a copy in our repo for now | |
| # wget -c http://www.walterzorn.com/scripts/wz_tooltip.zip | |
| # [ `md5sum wz_tooltip.zip | head -c 32` = 6b78dce5ab64ed21d278646f541fbc7a ] | |
| ######## | |
| mkdir -p wz_tooltip | |
| (cd wz_tooltip && unzip ../wz_tooltip.zip) | |
| cp -p wz_tooltip/wz_tooltip.js public_html/js/ | |
| public_html/js/tip_balloon.js: | |
| ######## As above | |
| # wget -c http://www.walterzorn.com/scripts/tip_balloon.zip | |
| ######## | |
| mkdir -p wz_tooltip | |
| (cd wz_tooltip && unzip ../tip_balloon.zip) | |
| mkdir -p public_html/js/tip_balloon | |
| cp -p wz_tooltip/tip_balloon/* public_html/js/tip_balloon/ | |
| perl -p -e 's:".*?":"/js/tip_balloon/": if m:^config\.\s*BalloonImgPath:' < wz_tooltip/tip_balloon.js > public_html/js/tip_balloon.js | |
| update_editors_summary: | |
| ./update_editors_summary.php | |
| import_omim: $(CACHEDIR)/OmimVarLocusIdSNP.bcp $(CACHEDIR)/morbidmap | |
| ./import_omim.php $(CACHEDIR)/OmimVarLocusIdSNP.bcp $(CACHEDIR)/morbidmap | |
| OmimVarLocusIdSNP.bcp: | |
| cd $(CACHEDIR) && wget ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data/OmimVarLocusIdSNP.bcp.gz | |
| gunzip $(CACHEDIR)/OmimVarLocusIdSNP.bcp.gz | |
| morbidmap: | |
| cd $(CACHEDIR) && wget ftp://ftp.ncbi.nih.gov/repository/OMIM/morbidmap | |
| GETEVIDENCEHOST?=evidence.personalgenomes.org | |
| TRAITOMATICHOST?=snp.oxf.freelogy.org | |
| PID:=$(shell echo $$PPID) | |
| dump_database: | |
| ./dump_database.php public_html/get-evidence.sql.gz | |
| data_local: latest_flat_tmp_local latest_flat latest_flat.gz vis_data | |
| data_http: latest_flat_tmp_http latest_flat latest_flat.gz vis_data | |
| latest_flat_tmp_local: | |
| mkdir -p $(CACHEDIR) | |
| (cd public_html && php ./download.php latest flat) > $(CACHEDIR)/latest-flat.tsv.tmp | |
| (cd public_html && php ./download.php latest json) | gzip -c > $(CACHEDIR)/getev-latest.json.gz.tmp | |
| latest_flat_tmp_http: | |
| mkdir -p $(CACHEDIR) | |
| wget -O$(CACHEDIR)/latest-flat.tsv.tmp http://$(GETEVIDENCEHOST)/latest-flat.tsv | |
| wget -O$(CACHEDIR)/getev-latest.json.gz.tmp http://$(GETEVIDENCEHOST)/getev-latest.json.gz | |
| latest_flat: | |
| mv $(CACHEDIR)/latest-flat.tsv.tmp public_html/latest-flat.tsv | |
| mv $(CACHEDIR)/getev-latest.json.gz.tmp public_html/getev-latest.json.gz | |
| latest_flat.gz: latest_flat | |
| gzip -9n <public_html/latest-flat.tsv >public_html/latest-flat.tsv.gz | |
| latest_locator: public_html/getev-latest.json.gz | |
| whput --in-manifest public_html/getev-latest.json.gz >public_html/getev-latest.locator.tmp | |
| mv public_html/getev-latest.locator.tmp public_html/getev-latest.locator | |
| vis_data: | |
| cd get_evidence_vis && ./ProcessTableForVis.pl ../public_html/latest-flat.tsv nsSNP-freq.gff >../public_html/latest_vis_data.tsv.tmp | |
| cd public_html && mv latest_vis_data.tsv.tmp latest_vis_data.tsv | |
| bionotate_history: | |
| ./export_bionotate.php > $(CACHEDIR)/bionotate-history.csv.tmp | |
| gzip < $(CACHEDIR)/bionotate-history.csv.tmp > public_html/bionotate-history.csv.gz | |
| DATADIR:=$(shell . server/script/config-local.sh 2>/dev/null && echo $$DATA) | |
| analysis_data_tarball.%.locator: $(DATADIR)/b130_SNPChrPosOnRef_36_3_sorted.bcp $(DATADIR)/b132_SNPChrPosOnRef_37_1_sorted.bcp \ | |
| $(DATADIR)/knownGene_hg18_sorted.txt $(DATADIR)/knownGene_hg19_sorted.txt \ | |
| $(DATADIR)/hg18.2bit $(DATADIR)/hg19.2bit \ | |
| $(DATADIR)/genetests-data.txt \ | |
| server/genome_stats.txt | |
| wc -c $^ | tail -n1 | |
| tar --transform 's/^.*\///' -cf - $^ | gzip -1n | WAREHOUSE=$* whput --progress --in-manifest --use-filename=analysis_data.tar.gz --name=/get-evidence/analysis_data-$(date +%Y%M%d-%H%m) - | tee $@.tmp | |
| mv $@.tmp $@ |