User:Lindenb/Notebook/UMR915/2012/04/02
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Dailyvariant_effect_predictor.plFix for proxyreplace unless(getstore($url, $target_file) == 200) by my $status = system("/usr/bin/curl --proxy 'http://proxy:3128' -o '$target_file' -L '$url'"); (...) my $status2 = system("/usr/bin/curl --proxy 'http://proxy:3128' -o '$target_file' -L --create-dirs '$BIOPERL_URL,'");
in the directory 'Bio': Align AlignIO Annotation Assembly Biblio bioperl-1.2.3 Cluster ClusterIO Coordinate Das DB EnsEMBL Event Expression Factory Graphics Index LiveSeq Location Map MapIO Matrix Ontology OntologyIO Phenotype Root Search SearchIO Seq SeqFeature SeqIO Structure Symbol Taxonomy tmp Tools Tree TreeIO Variation
Runperl variant_effect_predictor.pl --regulatory --sift=b --polyphen=b --regulatory --input_file 20120327.rs.vcf.gz --format vcf -o 20120402.vcf --vcf
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DJANGO
install ubuntu:
sudo apt-get install python-django
start a project
$ django-admin startproject gene2pubmed
$ find gene2pubmed/ gene2pubmed/ gene2pubmed/urls.py gene2pubmed/__init__.py gene2pubmed/manage.py gene2pubmed/settings.py